| Homstrad Family code | No of members | Average size | Family name |
| zf-CCHH | 15 | 29 | zinc finger -- CCHH-type |
| zf-CCHC | 2 | 17 | zinc finger -- CCHC-type |
| xia | 6 | 388 | xylose isomerase |
| vprotease | 2 | 150 | Alphavirus core protein |
| utg | 2 | 73 | Uteroglobin |
| ung | 3 | 224 | uracil-DNA glycosylase |
| uce | 13 | 149 | ubiquitin conjugating enzyme |
| trfl | 7 | 526 | transferrin |
| toxin | 20 | 63 | snake toxin |
| tms | 5 | 285 | thymidylate synthase |
| tln | 4 | 308 | zinc metalloproteinase, thermolysin-like |
| tim | 10 | 249 | triose phosphate isomerase |
| thiored | 6 | 95 | thioredoxin |
| thionin | 3 | 46 | thionin |
| tgfb | 8 | 97 | Transforming growth factor-beta (TGF-beta) |
| tbpc | 4 | 183 | TATA-box binding protein, C-terminal domain |
| taf | 2 | 69 | TBP-associated factors |
| svmp | 3 | 199 | snake venom metalloproteinase |
| sugbp | 4 | 293 | periplasmic binding protein -- sugar |
| subt | 11 | 294 | subtilase |
| stpp | 2 | 306 | serine/threonine protein phosphatase |
| sti | 5 | 173 | soybean trypsin inhibitor (Kunitz) |
| squash | 4 | 30 | serine proteinase inhibitor -- squash-type |
| spidertoxin | 2 | 48 | spider toxin |
| sodfe | 8 | 198 | Fe/Mn superoxide dismutase |
| sodcu | 7 | 152 | Cu/Zn superoxide dismutase |
| slectin | 5 | 133 | S-lectin |
| sh3 | 20 | 63 | Src homology 3 domains |
| sh2 | 11 | 105 | Src homology 2 domains |
| serpin | 8 | 376 | serine proteinase inhibitor -- serpin-type |
| sermam | 27 | 232 | serine proteinase - eukaryotic |
| serbact | 5 | 188 | serine proteinase -- bacterial |
| seatoxin | 5 | 47 | sea anemone toxin |
| sdr | 13 | 259 | short-chain dehydrogenases/reductases |
| scorptoxin | 8 | 64 | long-chain scorpion toxin |
| S_100 | 6 | 87 | S-100/ICaBP type calcium binding protein |
| rvp | 6 | 106 | retroviral proteinase |
| rvintegrase | 2 | 146 | retroviral integrase |
| rub | 5 | 51 | rubredoxin |
| rnr | 3 | 303 | ribonucleotide-diphosphate reductase |
| rnh | 3 | 140 | ribonuclease H |
| rnasemam | 6 | 121 | pancreatic ribonuclease |
| rnase | 3 | 104 | Microbial ribonucleases |
| ricin | 7 | 254 | Ribosome inactivating protein |
| rhv | 6 | 780 | picornavirus coat proteins |
| rep | 4 | 72 | DNA-binding repressor |
| ptpase | 3 | 284 | protein-tyrosine phosphatase |
| prt | 3 | 173 | phosphoribosyltransferase |
| protg | 4 | 65 | immunoglobulin-binding domain |
| profilin | 5 | 128 | profilin |
| prc | 2 | 841 | photosynthetic reaction center |
| ppase | 4 | 200 | inorganic pyrophospatase |
| pp | 3 | 36 | pancreatic hormone |
| pot | 4 | 65 | serine proteinase inhibitor -- potato I-type |
| porin | 4 | 315 | porin |
| pnp | 3 | 271 | purine nucleoside phosphorylase |
| planttoxin | 3 | 46 | plant toxin |
| plantltp | 5 | 88 | plant lipid-transfer proteins |
| piplc | 2 | 285 | phosphatidylinositol-specific phospholipase C - bacterial |
| phs | 3 | 825 | oligosaccharide phosphorylase |
| phoslip | 18 | 121 | phospholipase A2 |
| phosfruc | 2 | 319 | phosphofructokinase |
| phero | 3 | 39 | ciliate pheromone |
| phc | 12 | 166 | phycocyanin |
| pgk | 4 | 405 | phosphoglycerate kinase |
| peroxidase | 5 | 334 | peroxidase |
| pentraxin | 2 | 205 | pentraxin (pentaxin) |
| pdc | 4 | 539 | thiamine pyrophosphate enzymes |
| pcd | 2 | 216 | protocatechuate-3,4-dioxygenase, alpha and beta chains |
| parv | 7 | 107 | calcium-binding protein -- parvalbumin-like |
| p450 | 12 | 408 | cytochrome p450 |
| oat | 4 | 431 | aminotransferase class-III |
| ngf | 4 | 109 | nerve growth factor |
| neurotox | 3 | 34 | short-chain scorpion toxin |
| ndk | 4 | 149 | nucleotide diphosphate kinase |
| mycin | 4 | 111 | antibacterial protein |
| mthinb | 3 | 30 | metallothionein -- beta-domain |
| mthina | 3 | 31 | metallothionein -- alpha-domain |
| msb | 8 | 126 | C-type lectin |
| mofe | 6 | 489 | nitrogenase molybdenum-iron protein, alpha and beta chains |
| mmp | 6 | 164 | matrix metalloproteinase |
| mle | 3 | 362 | muconate lactonizing enzyme-like |
| mdd | 3 | 385 | acyl-CoA dehydrogenase |
| mcp2 | 2 | 142 | methyl-accepting chemotaxis protein II |
| ltn | 12 | 234 | legume lectin |
| ltb | 3 | 101 | heat-labile enterotoxin/cholera toxin, B subunit |
| lta | 3 | 187 | heat-labile enterotoxin/cholera toxin, A subunit |
| lipase | 5 | 446 | pancreatic lipase |
| lh2 | 2 | 52 | light-harvesting complex II |
| ldh | 14 | 319 | lactate/malate dehydrogenase |
| lamb | 3 | 418 | maltoporin (LamB protein) |
| kunitz | 10 | 57 | serine proteinase inhibitor -- Kunitz-type |
| kringle | 9 | 82 | kringle domain |
| kinase | 15 | 320 | Serine/Threonine protein kinases, catalytic domain |
| kex | 3 | 437 | serine carboxypeptidase |
| kazal | 6 | 56 | serine proteinase inhibitor -- Kazal-type |
| intb | 6 | 137 | interleukin 1-beta-like growth factor |
| int | 5 | 192 | integrin I-domain |
| ins | 6 | 55 | insulin |
| il8 | 11 | 68 | interleukin 8-like protein |
| il10 | 2 | 148 | interleukin-10 (IL-10) |
| igvar-l | 26 | 112 | immunoglobulin domain -- V set - immunoglobulin light chain |
| igvar-h | 21 | 123 | immunoglobulin domain -- V set - immunoglobulin heavy chain |
| igV | 9 | 108 | immunoglobulin domain -- V set - variable non immunoglobulin |
| igps | 3 | 219 | tryptophan biosynthesis enzyme |
| igI | 9 | 98 | immunoglobulin domain -- I set |
| igcon | 12 | 98 | immunoglobulin domain -- I set |
| igC2 | 2 | 75 | immunoglobulin domain -- C2 set |
| igC1 | 5 | 97 | immunoglobulin domain -- C1 set - constant non immunoglobulin |
| icd | 5 | 367 | isocitrate and isopropylmalate dehydrogenase |
| hsp90 | 2 | 210 | heat shock protein 90, N-terminal domain |
| hr | 5 | 74 | hormone receptor (DNA-binding domain) |
| hpr | 5 | 87 | histidine-containing phosphocarrier protein |
| hom | 8 | 63 | DNA-binding homeodomain |
| hla | 5 | 178 | histocompatibility antigen-binding domain |
| hip | 5 | 74 | high potential iron-sulfur protein |
| hemopexin | 4 | 199 | hemopexin-like |
| hemocyan | 2 | 617 | haemocyanin |
| hemery | 2 | 116 | hemerythrin |
| gtp | 8 | 174 | GTP-binding protein |
| grs | 11 | 452 | pyridine nucleotide-disulphide oxidoreductases class-I |
| gpr | 3 | 154 | glucose permease |
| gpdh | 8 | 338 | glyceraldehyde 3-phosphate dehydrogenase |
| gluts | 14 | 215 | glutathione S-transferase |
| glob | 41 | 146 | globin |
| glnasn | 4 | 326 | glutaminase-asparagainase |
| ghf34 | 3 | 389 | glycosyl hydrolase family 34 (neuraminidase) |
| ghf22 | 12 | 126 | glycosyl hydrolase family 22 (lysozyme) |
| gdh | 2 | 347 | formate/glycerate dehydrogenases |
| flavbb | 2 | 356 | FMN-linked oxidoreductases |
| flav | 6 | 161 | flavodoxin |
| fkbp | 4 | 113 | FKBP-type peptidyl-prolyl cis-trans isomerase |
| fer4 | 14 | 72 | ferredoxin (4Fe-4S) |
| fer2 | 13 | 98 | ferredoxin (2Fe-2S) |
| egf | 12 | 47 | epidermal growth factor-like domain |
| ech | 3 | 266 | enoyl-CoA hydratase |
| e3 | 2 | 40 | E3-binding domain |
| dutpase | 3 | 124 | deoxyuridine 5'-triphosphate nucleotidohydrolase |
| dpo1 | 4 | 595 | DNA polymerase I |
| dpb | 2 | 512 | Bacterial extracellular solute-binding proteins, family 5 |
| dhfr | 4 | 172 | dihydrofolate reductase |
| cytprime | 4 | 127 | cytochrome c' |
| cyto | 3 | 153 | cytokine -- granulocyte colony stimulating factor |
| cytb | 6 | 86 | cytochrome b5 |
| cyt5 | 6 | 81 | cytochrome-c5 |
| cyt3 | 6 | 110 | cytochrome-c3 |
| cystatin | 3 | 101 | cystatin |
| cys | 13 | 223 | Papain family cysteine proteinase |
| cyclo | 6 | 171 | cyclophilin (peptidylprolyl isomerase) |
| csp | 3 | 67 | cold-shock DNA-binding domain |
| cryst | 7 | 174 | beta/gamma crystallins |
| cpa | 4 | 311 | zinc carboxypeptidases |
| cox | 4 | 541 | GMC oxidoreductase |
| cks | 3 | 81 | cyclin-dependent kinases regulatory subunit |
| cdh | 3 | 104 | cadherin |
| ccH | 4 | 59 | complement control protein module (SUSHI) (SCR) |
| cbp | 8 | 159 | calcium-binding protein -- calmodulin-like |
| cat3 | 4 | 232 | CoA-dependent acetyltransferase |
| cat | 3 | 566 | catalase |
| cah | 5 | 249 | Eukaryotic-type carbonic anhydrase |
| bv | 7 | 175 | plant virus coat protein |
| bowman | 5 | 50 | serine proteinase inhibitor -- Bowman-Birk-type |
| blmb | 6 | 241 | Metallo-beta-lactamase superfamily |
| blm | 8 | 261 | beta-lactamase |
| az | 29 | 113 | azurin/plastocyanin |
| avi | 2 | 121 | avidin |
| asprs | 3 | 470 | tRNA synthetases class II (D and K) |
| aspg | 2 | 142 | glycosyl-asparaginase |
| asp | 13 | 332 | aspartic proteinase |
| apbact | 3 | 279 | bacterial exopeptidases |
| annexin | 6 | 317 | annexin |
| aminobp | 2 | 345 | periplasmic binding protein - branched-chain amino acid |
| aldosered | 7 | 310 | aldo/keto reductase |
| aldose | 3 | 355 | fructose-1,6-bisphosphate aldolase |
| adk | 9 | 207 | nucleotide kinase |
| adh | 5 | 373 | alcohol dehydrogenase |
| ADF | 3 | 147 | actin-depolymerizing proteins |
| acyo | 2 | 98 | acylphosphatase |
| actin | 4 | 377 | actin/heat-shock cognate |
| ace | 6 | 533 | alpha beta-hydrolase |
| aat | 10 | 403 | aminotransferases class-I |
| aadh | 8 | 415 | amino acid dehydrogenase |
| aabp | 3 | 232 | bacterial extracellular solute-binding proteins, family 3 |
| Zn_dep_PLPC | 2 | 246 | Zinc dependent phospholipase C |
| zf-TAZ | 2 | 91 | TAZ zinc finger |
| YgbB | 3 | 153 | YgbB family |
| Yers_vir_YopE | 3 | 116 | Yersinia virulence determinant (YopE) |
| XPG_NI | 2 | 213 | XPG N-terminal domain and I-region |
| XPG_NC | 2 | 327 | XPG |
| XPG_C | 2 | 114 | XPG C-terminal domain |
| WW | 4 | 39 | WW domain |
| WHEP-TRS | 2 | 56 | WHEP-TRS domain |
| WH1 | 2 | 107 | WH1 domain |
| WD40 | 2 | 344 | WD domain, G-beta repeat |
| VPR | 2 | 48 | VPR/VPX protein |
| voltage_CLC | 2 | 440 | Voltage gated chloride channel |
| VHS | 2 | 149 | VHS domain |
| VAT-Nn | 2 | 93 | VAT-N domain, N-terminal region |
| VAT-Nc | 2 | 88 | VAT-N domain, C-terminal region |
| VAT-N | 2 | 181 | VAT-N domain |
| UvrD-helicase | 2 | 629 | UvrD/REP helicase |
| Usp | 2 | 141 | Universal stress protein family |
| URO-D | 2 | 350 | Uroporphyrinogen decarboxylase (URO-D) |
| Uricase | 2 | 147 | Uricase |
| UreE | 2 | 138 | UreE urease accessory protein |
| urease_gamma | 2 | 100 | Urease, gamma subunit |
| Urease_beta | 2 | 111 | Urease beta subunit |
| urease | 2 | 567 | Urease, alpha subunit |
| UPP_synthetase | 2 | 213 | Putative undecaprenyl diphosphate synthase |
| UPF0076 | 3 | 125 | YjgF family |
| UPF0044 | 2 | 97 | Uncharacterised protein family UPF0044 |
| UPF0033 | 2 | 89 | Uncharacterized protein family UPF0033 |
| UCR_TM | 3 | 69 | Ubiquinol cytochrome reductase transmembrane region |
| UcrQ | 3 | 84 | UcrQ family |
| UCR_14kD | 2 | 115 | Ubiquinol-cytochrome C reductase complex 14kD subunit |
| UCH | 2 | 210 | Ubiquitin carboxyl-terminal hydrolase, family 1 |
| UBX | 2 | 85 | UBX domain |
| UBQ | 3 | 74 | Ubiquitin homologues |
| tyrosinase | 2 | 279 | Common central domain of tyrosinase |
| TyrKc | 7 | 276 | Tyrosine kinase, catalytic domain |
| Tymo_coat | 2 | 171 | Tymovirus coat protein |
| tubulin | 2 | 433 | Tubulin |
| Trypan_glycop | 2 | 360 | Trypanosome variant surface glycoprotein |
| tryp_alpha_amyl | 3 | 114 | Cereal trypsin/alpha-amylase inhibitor family |
| trp_syntA | 2 | 253 | Tryptophan synthase alpha chain |
| TrpBP | 2 | 68 | Tryptophan RNA-binding attenuator protein |
| tRNA-synt_2d | 2 | 223 | tRNA synthetases class II (F) |
| tRNA-synt_2b | 5 | 307 | tRNA synthetases class II (G, H, P and S) |
| tRNA-synt_1_edit | 2 | 191 | tRNA synthetases class I (I, L, M and V), editing domain |
| tRNA-synt_1d_N | 2 | 114 | tRNA synthetases class I (R), N-terminal domain |
| tRNA-synt_1d_M | 2 | 358 | tRNA synthetases class I (R), catalytic domain |
| tRNA-synt_1d_C | 2 | 124 | tRNA synthetases class I (R), C-terminal domain |
| tRNA-synt_1d | 2 | 597 | tRNA synthetases class I (R) |
| tRNA-synt_1c | 2 | 326 | tRNA synthetases class I (E and Q) |
| tRNA-synt_1b | 2 | 321 | tRNA synthetases class I (W and Y) |
| tRNA-synt_1 | 3 | 618 | tRNA synthetases class I (I, L, M and V), catalytic and anticodon-binding domains |
| tRNA_bind | 3 | 109 | Putative tRNA binding domain |
| TrkA-N | 2 | 133 | TrkA-N domain |
| TRANSTHYRETIN | 3 | 116 | Transthyretin (prealbumin) |
| trans_reg_C | 2 | 101 | Transcriptional regulatory protein, C-terminal |
| Transpeptidase | 2 | 341 | Penicillin binding protein transpeptidase domain |
| transket_pyr | 3 | 193 | Transketolase, pyridine binding domain |
| transketolase_PC | 3 | 332 | Transketolase, pyridine binding and C-terminal domains |
| transketolase_C | 3 | 139 | Transketolase, C-terminal domain |
| transketolase | 2 | 369 | Transketolase, thiamine diphosphate binding domain |
| Transglut_core | 2 | 319 | Transglutaminase-like superfamily core domain |
| Transglutamin_NC | 2 | 686 | Transglutaminase-like superfamily |
| Transglutamin_N | 2 | 142 | Transglutaminase-like superfamily N terminal domain |
| Transglutamin_C | 2 | 106 | Transglutaminase family |
| transcript_fac2 | 2 | 198 | Transcription factor TFIIB repeat |
| Transaldolase | 2 | 319 | Transaldolase |
| TPR | 6 | 153 | TPR Domain |
| TPK_catalytic | 2 | 195 | Thiamin pyrophosphokinase, catalytic domain |
| TPK_B1_binding | 2 | 90 | Thiamin pyrophosphokinase, vitamin B1 binding domain |
| TPK | 2 | 285 | Thiamin pyrophosphokinase |
| toxin_2 | 21 | 35 | Scorpion short toxin |
| Toprim | 3 | 110 | Toprim domain |
| Topoisomerase_I_core | 2 | 231 | Eukaryotic DNA topoisomerase I, catalytic core |
| Topoisomerase_I | 2 | 218 | Eukaryotic DNA topoisomerase I |
| Topoisom_bac | 2 | 258 | DNA topoisomerase |
| TonB_dep_Rec | 2 | 683 | TonB-dependent receptor proteins |
| TNFR_c6 | 2 | 125 | TNFR/NGFR cysteine-rich region |
| TNF | 5 | 149 | TNF(Tumor Necrosis Factor) family |
| TMV_coat | 4 | 157 | Tobacco mosaic virus coat |
| TmpK | 2 | 207 | thymidylate kinase |
| TIR | 2 | 150 | TIR domain |
| TIMP | 2 | 181 | Tissue inhibitor of metalloproteinase family |
| TIL | 4 | 66 | Serine protease inhibitors |
| TIG | 6 | 84 | IPT/TIG domain |
| thymid_phosphorylase | 2 | 436 | Thymidine and pyrimidine-nucleoside phosphorylases |
| Thr_dehydrat_C | 2 | 81 | C-terminal domain of Threonine dehydratase |
| thiolase | 2 | 400 | Thiolase/Beta-ketoacyl synthases |
| Thioesterase | 2 | 244 | Thioesterase domain |
| THF_DHG_CYH | 2 | 286 | Tetrahydrofolate dehydrogenase/cyclohydrolase |
| THAUMATIN | 3 | 207 | Thaumatin |
| TGT | 2 | 353 | Queuine tRNA-ribosyltransferase |
| TFIIS | 2 | 53 | Transcription factor S-II (TFIIS) |
| tetR | 2 | 66 | Bacterial regulatory proteins, tetR family, N-terminal domain |
| Terpene_synth_NC | 2 | 519 | Terpene synthase family |
| Terpene_synth_N | 2 | 200 | Terpene synthase, N-terminal domain |
| Terpene_synth_C | 2 | 319 | Terpene synthase family, C-terminal, metal binding domain |
| tcl1_mtcp1 | 2 | 108 | T-cell prolymphocytic leukemia oncogenes |
| T-box | 2 | 184 | T-box |
| TBCA | 2 | 100 | Tubulin binding cofactor A |
| Tautomerase | 2 | 60 | Tautomerase enzyme |
| Syntaxin | 2 | 157 | Syntaxin |
| Sulfotransfer | 5 | 281 | Sulfotransferase protein |
| Sulfatase | 2 | 477 | Sulfatase |
| SUI1 | 2 | 85 | eIF1-like |
| Sua5_yciO_yrdC | 2 | 196 | yrdC domain |
| S_T_dehydratase | 2 | 363 | Pyridoxal-phosphate dependent enzymes |
| STAT | 2 | 551 | STAT protein, domains 2-4 |
| STAS | 2 | 113 | STAS domain |
| START | 2 | 205 | START domain |
| Stap_Strp_toxin | 6 | 220 | Staphylococcal/Streptococcal toxin |
| Staphylokinase | 2 | 129 | Staphylokinase/Streptokinase family |
| SSB | 2 | 101 | Single-strand binding proteins |
| SRP54M | 2 | 103 | Signal peptide-binding domain |
| SRP54 | 2 | 291 | SRP54-type protein |
| SRP19 | 2 | 109 | SRP19 protein |
| SRF-TF | 3 | 80 | SRF-type transcription factor (DNA-binding and dimerisation domain) |
| SpoU_methylase_N | 2 | 88 | SpoU rRNA Methylase family, N-terminal domain |
| SpoU_methylase_C | 2 | 158 | SpoU rRNA Methylase family, C-terminal domain |
| SpoU_methylase | 2 | 246 | SpoU rRNA Methylase family |
| Spermine_synth | 2 | 278 | Spermine/spermidine synthase |
| SPEC | 2 | 102 | Spectrin repeats |
| SNAP-25 | 2 | 70 | SNAP-25 family |
| Sm | 4 | 76 | Sm protein |
| SLT_beta | 2 | 68 | Shiga-like toxin beta subunit |
| SLT | 2 | 176 | Transglycosylase SLT domain |
| Skp1 | 2 | 102 | Skp1 family |
| SKI | 2 | 158 | Shikimate kinase |
| SIS | 2 | 183 | SIS domain |
| SIR2 | 2 | 284 | Sir2 family |
| sigma54 | 2 | 82 | Sigma-54 transcription factors |
| sialidase_N | 2 | 194 | Vibrio cholerae sialidase, N-terminal and insertion domains |
| SHMT | 2 | 443 | Serine hydroxymethyltransferase |
| SET | 2 | 259 | SET domain |
| Seedstore_7s | 2 | 353 | 7S seed storage protein |
| Sec7 | 2 | 197 | Sec7 domain |
| Sec23_NC | 2 | 733 | Sec23/Sec24 |
| Sec1 | 2 | 541 | Sec1 family |
| SCP2 | 2 | 119 | SCP-2 sterol transfer family |
| SCP | 2 | 172 | SCP-like extracellular protein |
| SBP_bacterial_1 | 3 | 329 | Bacterial extracellular solute-binding protein, family 1 |
| SAP | 3 | 43 | SAP domain |
| SAM_PNT | 2 | 93 | Sterile alpha motif (SAM)/Pointed domain |
| SAM_decarbox | 2 | 309 | Adenosylmethionine decarboxylase |
| SAM | 2 | 73 | Sterile alpha motif. |
| SAICAR_synt | 2 | 253 | SAICAR synthetase |
| S-AdoMet_synt_NC | 2 | 372 | S-adenosylmethionine synthetase |
| S-AdoMet_syntD3 | 2 | 148 | S-adenosylmethionine synthetase, C-terminal domain |
| S-AdoMet_syntD2 | 2 | 123 | S-adenosylmethionine synthetase, central domain |
| S-AdoMet_synt | 2 | 100 | S-adenosylmethionine synthetase, N-terminal domain |
| S4 | 3 | 47 | S4 domain |
| S1 | 2 | 73 | Ribosomal protein S1-like RNA-binding domain |
| rvt | 2 | 241 | Reverse transcriptase (RNA-dependent DNA polymerase) |
| RuvA | 2 | 186 | Bacterial DNA recombination protein, RuvA |
| RuBisCO_small | 7 | 124 | Ribulose bisphosphate carboxylase, small chain |
| RuBisCO_large_NC | 7 | 453 | Ribulose bisphosphate carboxylase large chain |
| RuBisCO_large_N | 6 | 132 | Ribulose bisphosphate carboxylase large chain, N-terminal domain |
| RuBisCO_large | 7 | 320 | Ribulose bisphosphate carboxylase large chain, catalytic domain |
| RrnaAD | 2 | 240 | Ribosomal RNA adenine dimethylases |
| rrm | 20 | 86 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) |
| RRF | 4 | 184 | Ribosome recycling factor |
| Rotamase | 2 | 107 | PPIC-type PPIASE domain |
| Rop | 2 | 60 | Rop protein |
| RNase_U2 | 2 | 146 | Ribonuclease U2 |
| RNase_HII | 3 | 210 | Ribonuclease HII |
| RNA_pol_N | 2 | 60 | RNA polymerases N / 8 kDa subunit |
| RNA_pol_K | 2 | 105 | RNA polymerases K / 14 to 18 kDa subunit |
| RNA_pol_H | 2 | 74 | RNA polymerases H / 23 kDa subunit |
| RNA_pol_A_CTD | 2 | 75 | Bacterial RNA polymerase, alpha chain C-terminal domain |
| RNA_pol_A_bac | 2 | 225 | Bacterial RNA polymerase, alpha chain |
| RNA_dep_RNA_pol | 2 | 404 | RNA dependent RNA polymerase |
| RING | 3 | 58 | Ring finger |
| Ricin_B_lectin | 2 | 264 | Similarity to lectin domain of ricin beta-chain, 3 copies. |
| Ribosomal_S8 | 2 | 133 | Ribosomal protein S8 |
| Ribosomal_S7 | 2 | 136 | Ribosomal protein S7 |
| Ribosomal_S5_N | 2 | 71 | Ribosomal protein S5, N-terminal domain |
| Ribosomal_S5_C | 2 | 76 | Ribosomal protein S5, C-terminal domain |
| Ribosomal_S5 | 2 | 147 | Ribosomal protein S5 |
| Ribosomal_S30AE | 2 | 109 | Sigma 54 modulation protein / S30EA ribosomal protein |
| Ribosomal_S15 | 2 | 86 | Ribosomal protein S15 |
| Ribosomal_L7Ae | 3 | 116 | Ribosomal protein L7Ae/L30e/S12e/Gadd45 family |
| Ribosomal_L6_D | 4 | 84 | Ribosomal protein L6 domain |
| Ribosomal_L6 | 2 | 168 | Ribosomal protein L6 |
| Ribosomal_L5_NC | 2 | 159 | ribosomal L5P family |
| Ribosomal_L4 | 2 | 209 | Ribosomal protein L4/L1 family |
| Ribosomal_L30 | 2 | 107 | Ribosomal protein L30p/L7e |
| Ribosomal_L2_N | 2 | 69 | Ribosomal Proteins L2, N-terminal domain |
| Ribosomal_L2_C | 2 | 68 | Ribosomal Proteins L2, C-terminal domain |
| Ribosomal_L22 | 2 | 129 | Ribosomal protein L22p/L17e |
| Ribosomal_L2 | 2 | 137 | Ribosomal Proteins L2 |
| Ribosomal_L18p | 2 | 138 | Ribosomal L18p/L5e family |
| Ribosomal_L14 | 2 | 127 | Ribosomal protein L14p/L23e |
| Ribosomal_L12 | 2 | 69 | Ribosomal protein L7/L12 C-terminal domain |
| Ribosomal_L11 | 2 | 68 | Ribosomal protein L11 |
| Ribosomal_L1 | 3 | 216 | Ribosomal protein L1p/L10e family |
| ribonuclease_T2 | 2 | 206 | ribonuclease T2 |
| Ribonuclease_P | 2 | 115 | Ribonuclease P |
| ribokinase | 2 | 324 | Ribokinase-like |
| Rib_hydrolayse | 2 | 250 | ADP-ribosyl cyclase |
| RhoGEF | 2 | 206 | DBL homology domain |
| Rho_GDI | 2 | 160 | RHO protein GDP dissociation inhibitor |
| RhoGAP | 2 | 190 | GTPase-activator protein for Rho-like GTPases |
| Rhodanese | 6 | 150 | Rhodanese-like domain |
| RHD | 2 | 298 | Rel homology domain (RHD). |
| RGS | 4 | 134 | Regulator of G protein signaling domain |
| response_reg | 13 | 122 | Response regulator receiver domain |
| reductases | 7 | 266 | reductases |
| recombinase | 3 | 48 | Site-specific recombinases |
| Recep_L_domain | 2 | 160 | Receptor L domain |
| recA_N | 2 | 247 | recA bacterial DNA recombination protein, N terminal ATPase domain |
| recA_C | 2 | 60 | recA bacterial DNA recombination protein, C terminal domain |
| recA | 2 | 307 | recA bacterial DNA recombination protein |
| rasgap | 2 | 291 | GTPase activating protein |
| Ran_BP1 | 2 | 140 | RanBP1 domain |
| RA | 2 | 88 | Ras association (RalGDS/AF-6) domain |
| QRPTase | 2 | 286 | Quinolinate phosphoribosyl transferase |
| PyrI_NC | 2 | 152 | Aspartate carbamoyltransferase regulatory chain |
| Pyridox_oxidase | 2 | 200 | Pyridoxamine 5'-phosphate oxidase |
| PyrI | 2 | 100 | Aspartate carbamoyltransferase regulatory chain N-terminal domain |
| PX | 2 | 136 | PX domain |
| PTS_EIIA_2 | 2 | 147 | phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 |
| PTB | 3 | 147 | Phosphotyrosine-binding (PTB) domain, phosphotyrosine-interaction (PI) domain |
| PSI_PsaE | 3 | 69 | Photosystem I reaction centre subunit IV / PsaE |
| psaA_psaB | 2 | 739 | Photosystem I psaA/psaB protein |
| proteasome | 17 | 223 | Proteasome A-type and B-type |
| Propep_M14 | 4 | 92 | Carboxypeptidase activation peptide |
| Pro_CA | 4 | 226 | Prokaryotic/plant carbonic anhydrase |
| pro_aminopeptidase | 2 | 313 | prolyl aminopeptidase |
| PRK | 2 | 292 | Phosphoribulokinase / Uridine kinase family |
| Prismane | 2 | 548 | Prismane |
| prenyltrans | 2 | 384 | Prenyltransferase and squalene oxidase repeats |
| PPTA | 2 | 320 | Protein prenyltransferase alpha subunit repeat |
| PPDK_N_term | 2 | 386 | Pyruvate phosphate dikinase, PEP/pyruvate binding domain |
| pp-binding | 2 | 81 | Phosphopantetheine attachment site |
| pou | 2 | 71 | Pou domain - N-terminal to homeobox domain |
| PotD | 2 | 331 | PotD/PotF |
| PNTB | 2 | 176 | NAD(P) transhydrogenase beta subunit |
| PMSR | 2 | 199 | Peptide methionine sulfoxide reductase |
| Plectin | 2 | 213 | Plectin repeat |
| PKD | 2 | 94 | Repeats in polycystic kidney disease 1 (PKD1) and other proteins |
| PK | 4 | 490 | Pyruvate kinase |
| pilin | 3 | 135 | Pilin (bacterial filament) |
| pili_assembly | 2 | 205 | Gram-negative pili assembly chaperone |
| P-II | 2 | 103 | Nitrogen regulatory protein P-II |
| phycoerythr_ab | 2 | 70 | Phycoerythrin, alpha/beta chain |
| phosphotriesterase | 2 | 310 | Phosphotriesterase-like |
| PHBH | 2 | 419 | PHBH-like |
| Phage_lysozyme | 2 | 168 | Phage lysozyme |
| Phage_integrase | 4 | 183 | Phage integrase |
| Phage_G | 2 | 176 | Major spike protein (G protein) |
| Phage_F | 2 | 421 | Capsid protein (F protein) |
| PH | 13 | 122 | PH domain |
| PGM_PMM_NC | 2 | 566 | Phosphoglucomutase/phosphomannomutase |
| PGM_PMM_III | 2 | 118 | Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III |
| PGM_PMM_II | 2 | 115 | Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II |
| PGM_PMM_I | 2 | 197 | Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I |
| PGM_PMM | 2 | 135 | Phosphoglucomutase/phosphomannomutase, C-terminal domain |
| PGI | 2 | 498 | Phosphoglucose isomerase |
| PGAM | 3 | 215 | Phosphoglycerate mutase |
| Pertussis_S2S3_NC | 2 | 196 | Pertussis toxin, subunit 2 and 3 |
| Pertussis_S2S3_N | 2 | 86 | Pertussis toxin, subunit 2 and 3, N-terminal domain |
| Pertussis_S2S3 | 2 | 110 | Pertussis toxin, subunit 2 and 3, C-terminal domain |
| Peripla_BP_2 | 2 | 253 | Periplasmic binding protein |
| PEP-utilizers_NC | 2 | 885 | PEP-utilizing enzyme |
| PEP-utilizers_C | 2 | 367 | PEP-utilizing enzyme, TIM barrel domain |
| PEP-utilizers | 3 | 128 | PEP-utilizing enzyme, mobile domain |
| Peptidase_S9 | 2 | 268 | Prolyl oligopeptidase family |
| Peptidase_S24 | 2 | 102 | Peptidase family S24 |
| Peptidase_S21 | 3 | 210 | Assemblin (Peptidase family S21) |
| Peptidase_S15_N | 2 | 366 | X-Pro dipeptidyl-peptidase (S15 family), N-terminal domain |
| Peptidase_S15_C | 2 | 218 | X-Pro dipeptidyl-peptidase (S15 family), C-terminal domain |
| Peptidase_S15 | 2 | 584 | X-Pro dipeptidyl-peptidase (S15 family) |
| Peptidase_S11 | 2 | 252 | D-alanyl-D-alanine carboxypeptidase |
| Peptidase_M27 | 2 | 529 | Clostridial neurotoxin zinc protease |
| Peptidase_M24 | 4 | 267 | metallopeptidase family M24 |
| Peptidase_M17_N | 2 | 169 | Cytosol aminopeptidase family, N-terminal domain |
| Peptidase_M17 | 2 | 324 | Cytosol aminopeptidase family, catalytic domain |
| Peptidase_M16 | 2 | 432 | Insulinase (Peptidase family M16) |
| Peptidase_M10A | 2 | 469 | Peptidase family M10A |
| Peptidase_C2_D2 | 2 | 138 | Calpain family cysteine protease, catalytic domain, subdomain 2 |
| Peptidase_C2_D1 | 2 | 198 | Calpain family cysteine protease, catalytic domain, N-terminal subdomain |
| Peptidase_C2 | 2 | 337 | Calpain family cysteine protease, catalytic domain (domain II) |
| Peptidase_C15 | 2 | 215 | Pyroglutamyl peptidase |
| Peptidase_A6 | 2 | 326 | Insect virus proteins |
| Pept_C1-like | 2 | 452 | Peptidase C1-like family |
| Pep_deformylase | 2 | 170 | Polypeptide deformylase |
| PEPCK_ATP | 2 | 527 | Phosphoenolpyruvate carboxykinase |
| Penicil_amidase | 2 | 738 | Penicillin amidase |
| Pectinesterase | 2 | 330 | Pectinesterase |
| pec_lyase | 4 | 367 | Pectin/pectate lyase |
| PDZ | 6 | 93 | PDZ Domain |
| PDGF | 2 | 91 | Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) |
| PCNA | 2 | 253 | Proliferating cell nuclear antigen |
| PCMT | 2 | 214 | Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) |
| PBP_NC | 2 | 557 | Penicillin binding protein |
| PBP_GOBP | 2 | 122 | PBP/GOBP family |
| PBP_C2 | 2 | 58 | Penicillin binding protein, C-terminal domain 2 |
| PBP_C1 | 2 | 61 | Penicillin binding protein, C-terminal domain 1 |
| PBP | 2 | 169 | Phosphatidylethanolamine-binding protein |
| PBD | 2 | 70 | P21-Rho-binding domain |
| PAX | 2 | 128 | Paired box domain |
| PAS | 3 | 124 | PAS domain |
| Parvo_coat2 | 2 | 554 | Parvovirus coat protein VP2 |
| PARP_reg | 2 | 131 | Poly(ADP-ribose) polymerase, regulatory domain |
| PARP | 2 | 216 | Poly(ADP-ribose) polymerase, C-terminal catalytic domain |
| PARATHYROID | 2 | 34 | Parathyroid |
| PA_phosphatase | 3 | 304 | Purple acid phosphatase |
| PAP2 | 2 | 575 | vanadium-dependent haloperoxidase |
| PAN | 2 | 89 | PAN domain |
| PAH | 2 | 87 | Paired amphipathic helix repeat |
| PAF-AH | 2 | 212 | Platelet activating factor acetylhydrolase |
| PAC | 2 | 107 | PAC motif |
| PABP | 2 | 61 | Poly-adenylate binding protein, unique domain |
| P53 | 2 | 30 | P53 |
| P | 3 | 55 | P or trefoil or TFF domain |
| oxidored_q6 | 5 | 265 | NADH ubiquinone oxidoreductase, 20 Kd subunit |
| oxidored_FMN | 2 | 369 | FMN oxidoreductase |
| OTCace | 5 | 318 | Aspartate/ornithine carbamoyltransferase |
| Orn_DAP_Arg_deC | 3 | 152 | Pyridoxal-dependent decarboxylase, C-terminal sheet domain |
| Orn_Arg_deC_NC | 2 | 382 | Pyridoxal-dependent decarboxylase |
| Orn_Arg_deC_N | 2 | 229 | Pyridoxal-dependent decarboxylase, pyridoxal binding domain |
| Orbi_VP7 | 2 | 130 | Orbivirus inner capsid protein VP7 |
| OMPdecase | 2 | 252 | Orotidine 5'-phosphate decarboxylases |
| NusB | 2 | 135 | NusB family |
| NTP_transferase | 4 | 269 | Nucleotidyl transferase |
| NTP_transf_2_N2 | 2 | 482 | Nucleotidyltransferase, N-terminal domain and domain 2 |
| NTP_transf_2_2 | 3 | 145 | Nucleotidyltransferase, domain 2 |
| NTP_transf_2 | 2 | 345 | Nucleotidyltransferase, N-terminal domain |
| NO_synthase | 3 | 386 | Nitric oxide synthase, oxygenase domain |
| NMT | 2 | 407 | Myristoyl-CoA |
| Nitroreductase | 3 | 215 | Nitroreductase |
| Nitrophorin | 2 | 182 | Nitrophorin |
| nir | 2 | 544 | cytochrome cd1-nitrite reductase |
| NiFeSe_Hases | 3 | 535 | Nickel-dependent hydrogenases, large subunit |
| NHase_beta | 2 | 219 | Nitrile hydratase beta subunit |
| NHase_alpha | 2 | 196 | Nitrile hydratase, alpha chain |
| neur_chan_memb | 2 | 25 | Neurotransmitter-gated ion-channel transmembrane region |
| NADHdh_2 | 3 | 258 | NAD(P)H dehydrogenase (quinone) |
| N6_N4_Mtase | 2 | 276 | DNA methylase |
| MYSc | 2 | 748 | Myosin, Large ATPases |
| myb_DNA-binding | 5 | 53 | Myb-like DNA-binding domain |
| mutT | 2 | 147 | MutT-like domain |
| MutS_NC | 2 | 755 | MutS family |
| MutS_N | 2 | 113 | MutS family, N-terminal domain |
| MutS_D3 | 2 | 282 | MutS family, domain 3 |
| MutS_D2 | 2 | 146 | MutS family, domain 2 |
| MutS_C | 2 | 213 | mutS family, C-terminal domain |
| Mur_ligase_C | 3 | 127 | Mur ligase family, glutamate ligase domain |
| Mur_ligase | 2 | 238 | Mur ligase family |
| MurB_C | 2 | 125 | UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain |
| Mu_DNA_bind | 2 | 72 | Mu DNA-binding domain |
| MSP_domain | 2 | 124 | MSP (Major sperm protein) domain |
| molybdopterin | 4 | 759 | Prokaryotic molybdopterin oxidoreductases |
| ModE_C | 2 | 138 | Molybdenum-binding protein C-terminal domain |
| ModA | 2 | 231 | Molybdate-binding protein, ModA |
| MoCF_biosynth | 4 | 163 | Probable molybdopterin binding domain |
| MMOB | 3 | 93 | Monooxygenase (hydroxylase) regulatory protein |
| mmob | 2 | 383 | methane monooxygenase component A beta chain |
| mmoa | 2 | 511 | methane monooxygenase component A alpha chain |
| mmo | 2 | 164 | methane monooxygenase component A gamma chain |
| MM_CoA_mutase_N | 2 | 507 | Methylmalonyl-CoA mutase, N-terminal domain |
| MM_CoA_mutase | 4 | 149 | Cobalamin (vitamin B12)-binding domain |
| MIP | 2 | 239 | Major intrinsic protein |
| MIF4G | 2 | 208 | MIF4G domain |
| MIF | 3 | 115 | Macrophage migration inhibitory factor (MIF) |
| MHC_II_N | 13 | 83 | Class II histocompatibility antigen, N-terminal domain |
| MHC_II_C | 8 | 99 | Class II histocompatibility antigen, C-terminal domain |
| MHC_II_beta_NC | 4 | 192 | Class II histocompatibility antigen, beta chain |
| MHC_II_alpha_NC | 4 | 181 | Class II histocompatibility antigen, alpha chain |
| MGS | 2 | 143 | MGS-like domain |
| Methyltransf_2 | 2 | 342 | O-methyltransferase |
| Methyltransf_1 | 3 | 166 | 6-O-methylguanine DNA methyltransferase |
| merR | 2 | 112 | Bacterial regulatory proteins, merR family, N-terminal domain |
| Me-amine-deh_L | 2 | 123 | Methylamine dehydrogenase, L chain |
| mdm2 | 2 | 86 | MDM2 oncoprotein |
| MDH | 2 | 65 | Methanol dehydrogenase beta subunit |
| MCR_gamma | 3 | 247 | Methyl-coenzyme M reductase gamma subunit |
| MCR_beta_NC | 3 | 436 | Methyl-coenzyme M reductase beta subunit |
| MCR_beta_N | 3 | 184 | Methyl-coenzyme M reductase beta subunit, N-terminal domain |
| MCR_beta | 3 | 252 | Methyl-coenzyme M reductase beta subunit, C-terminal domain |
| MCR_alpha_NC | 3 | 550 | Methyl-coenzyme M reductase alpha subunit |
| MCR_alpha_N | 3 | 271 | Methyl-coenzyme M reductase alpha subunit, N-terminal domain |
| MCR_alpha | 3 | 279 | Methyl-coenzyme M reductase alpha subunit, C-terminal domain |
| MBD | 2 | 83 | Methyl-CpG binding domain |
| MATH | 2 | 151 | MATH domain |
| MAP1_LC3 | 2 | 116 | Microtubule associated protein 1A/1B, light chain 3 |
| malt_amylase_NC | 2 | 586 | maltogenic amylase |
| malic_N | 2 | 271 | Malic enzyme, N-terminal domain |
| malic_C | 2 | 297 | Malic enzyme, C-terminal domain |
| malic | 2 | 568 | Malic enzyme |
| Malate_synthase | 2 | 694 | Malate synthase |
| MAAL_N | 2 | 157 | Methylaspartate ammonia-lyase, N-terminal domain |
| MAAL_C | 2 | 241 | Methylaspartate ammonia-lyase, C-terminal domain |
| MAAL | 2 | 398 | Methylaspartate ammonia-lyase |
| LysR_substrate | 2 | 224 | Bacterial regulatory helix-turn-helix protein, lysR family |
| Lyase_8_NC | 2 | 697 | Polysaccharide lyase family 8 |
| Lyase_8_N | 2 | 339 | Polysaccharide lyase family 8, N terminal domain |
| Lyase_8_C | 2 | 89 | Polysaccharide lyase family 8, C-terminal beta-sandwich domain |
| Lyase_8 | 2 | 269 | Polysaccharide lyase family 8, super-sandwich domain |
| lyase_1 | 5 | 444 | Lyase |
| LuxS | 4 | 149 | LuxS protein |
| Lum_binding | 4 | 102 | Lumazine binding domain |
| LRR | 3 | 419 | ribonuclease inhibitor |
| LMWPc | 3 | 157 | Low molecular weight phosphatase |
| lipoxygenase | 2 | 837 | Lipoxygenase |
| Lipoprotein_6 | 2 | 163 | Lipoprotein family 6 |
| Lipoprotein_4 | 2 | 281 | Periplasmic solute binding protein family |
| Lipase_3 | 3 | 266 | fungal lipase |
| linker_histone | 2 | 74 | linker histone H1 and H5 family |
| LIM | 5 | 69 | Zinc-binding domain present in Lin-11, Isl-1, Mec-3. |
| ligase-CoA_NC | 2 | 389 | CoA-ligase |
| ligase-CoA | 3 | 152 | CoA-ligase C-terminal domain |
| LIF_OSM | 2 | 167 | LIF / OSM family |
| Levi_coat | 4 | 125 | Levivirus coat protein |
| leukocidin | 3 | 294 | Leukocidin (pore-forming toxin) |
| LEM | 2 | 55 | LEM domain |
| LDLa | 4 | 41 | Low-density lipoprotein receptor domain class A |
| LBP_BPI_CETP | 2 | 228 | LBP / BPI / CETP family |
| laminin_G | 4 | 181 | Laminin G domain |
| lacI | 3 | 57 | Bacterial regulatory proteins, lacI family |
| L15 | 2 | 130 | Ribosomal protein L15 |
| ku | 2 | 511 | KU domain |
| KSI | 2 | 124 | Delta-5-3-ketosteroid isomerase, steroid delta-isomerase, KSI |
| KISc | 4 | 335 | Kinesin motor, catalytic domain ATPase |
| KH | 2 | 80 | KH-domain |
| Kchannel | 2 | 101 | Tetramerization domain of potassium channels |
| KAS | 6 | 344 | Chalcone and stilbene synthases |
| Jacalin | 2 | 133 | Jacalin-like lectin domain |
| IU_nuc_hydro | 2 | 312 | |
| ISP | 2 | 127 | Rieske iron-sulfur protein (ISP), watersoluble domain |
| Isochorismatase | 2 | 220 | Isochorismatase family |
| isoamylase_NC | 2 | 653 | Isoamylase and glycosyltrehalose trehalohydrolase |
| isoamylase_N | 2 | 126 | Isoamylase N-terminal domain |
| IRF | 2 | 107 | Interferon regulatory factor transcription factor |
| Invasin | 3 | 97 | invasin |
| internalin | 2 | 184 | leucine rich repeats in splicesomal U2A' protein and internalin B |
| INTERFERON_A_B_D | 2 | 165 | Interferon alpha, beta and delta. |
| Integrase_Zn | 2 | 50 | Integrase Zinc binding domain |
| integrase | 2 | 54 | Integrase DNA binding domain |
| inositol_P | 3 | 342 | Inositol monophosphatase family |
| Inos-1-P_synth | 2 | 426 | Myo-inositol-1-phosphate synthase |
| Inh | 2 | 102 | Protease inhibitor Inh |
| IMS | 2 | 202 | impB/mucB/samB family |
| IMPDH | 2 | 316 | IMP dehydrogenase / GMP reductase |
| IFN-gamma | 2 | 123 | Interferon gamma |
| IF4E | 2 | 196 | Eukaryotic initiation factor 4E |
| IF3 | 2 | 89 | Translation initiation factor IF-3 |
| ICL | 2 | 470 | Isocitrate lyase family |
| Hydrolase | 2 | 232 | haloacid dehalogenase-like hydrolase |
| Huristasin | 3 | 51 | Huristasin-like |
| HTH_AraC_2 | 2 | 117 | Bacterial regulatory helix-turn-helix proteins, araC family, the two structural repeats |
| HTH_AraC | 4 | 58 | Bacterial regulatory helix-turn-helix proteins, araC family, single structural repeat |
| HSP20 | 2 | 132 | Hsp20/alpha crystallin family |
| HSF_DNA-bind | 2 | 94 | HSF-type DNA-binding domain |
| Hpr_kinase | 2 | 156 | Hpr Serine kinase |
| HPPK | 2 | 159 | 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK) |
| hormone_rec | 5 | 248 | Ligand-binding domain of nuclear hormone receptors |
| hormone5 | 2 | 88 | Neurohypophysial hormones, C-terminal domain |
| hormone | 2 | 170 | Somatotropin hormone family |
| HMG-CoA_red | 2 | 396 | Hydroxymethylglutaryl-coenzyme A reductase |
| HMG_box | 5 | 76 | HMG (high mobility group) box |
| HMA | 3 | 70 | Heavy-metal-associated domain |
| HLH | 5 | 71 | Helix-loop-helix DNA-binding domain |
| HIT | 2 | 120 | HIT family |
| histone | 4 | 82 | Nucleosome core histone H2A/H2B/H3/H4 |
| Histidine_kinase | 2 | 168 | Histidine kinase |
| His_biosynth | 2 | 245 | Histidine biosynthesis protein |
| Hint | 2 | 161 | Hint (Hedgehog/Intein) domain |
| HGTP_anticodon | 6 | 104 | Anticodon binding domain |
| hexokinase | 3 | 447 | Hexokinase |
| hexapep | 3 | 160 | Bacterial transferase hexapeptide repeats |
| Heme_oxygenase | 2 | 213 | Heme oxygenase |
| helicase_NC | 3 | 482 | Helicase |
| helicase_C | 5 | 163 | Helicase conserved C-terminal domain |
| HCV_NS3 | 2 | 194 | Viral proteases |
| HATPase_c | 6 | 206 | Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase |
| Ham1p_like | 2 | 194 | Ham1 family |
| Haloperoxidase | 9 | 286 | Haloperoxidase |
| GXGXG | 2 | 269 | Domain of unknown function DUF14 |
| GTP_cyclohydroI | 2 | 208 | GTP cyclohydrolase I |
| GSH_synth_ATP | 2 | 372 | Eukaryotic glutathione synthase, ATP binding domain |
| GSH_synthase_NC | 2 | 476 | Eukaryotic glutathione synthase |
| GSH_synthase | 2 | 104 | Eukaryotic glutathione synthase, insertion domain |
| GroEL | 2 | 248 | GroEL-like chaperones, ATPase domain |
| GP41 | 2 | 90 | Envelope Polyprotein GP41 |
| GP120 | 2 | 305 | Envelope glycoprotein GP120 |
| Gly_radical | 2 | 646 | Glycine radical |
| Glyco_transf_8 | 2 | 266 | Glycosyl transferase family 8 |
| Glyco_transf_6 | 2 | 275 | Glycosyltransferase family 6 |
| Glyco_transf_28 | 2 | 366 | Glycosyltransferase family 28 |
| Glyco_hydro_67 | 2 | 689 | Glycosyl hydrolase family 67 |
| Glyco_hydro_48 | 2 | 635 | Glycosyl hydrolase family 48 |
| Glyco_hydro_47 | 2 | 482 | Glycosyl hydrolase family 47 |
| Glyco_hydro_2_N | 2 | 205 | Glycosyl hydrolases family 2, sugar binding domain |
| Glyco_hydro_20b | 2 | 140 | Glycosyl hydrolase family 20, domain 2 |
| Glyco_hydro_20 | 2 | 399 | Glycosyl hydrolase family 20, catalytic domain |
| Glyco_hydro_2 | 3 | 107 | Glycosyl hydrolases family 2, immunoglobulin-like beta-sandwich domain |
| Glyco_hydro_19 | 2 | 242 | Chitinase class I |
| Glyco_hydro_18_D2 | 4 | 73 | Glycosyl hydrolases family 18, insertion domain |
| Glyco_hydro_18_D1 | 4 | 336 | Glycosyl hydrolases family 18, TIM barrel domain |
| Glyco_hydro_18 | 4 | 409 | Glycosyl hydrolases family 18, TIM barrel domain and insertion domain |
| Glu_synth_NTN | 2 | 421 | Glutamate synthase amidotransferase domain |
| Glu_syn_central | 2 | 773 | Glutamate synthase central domain |
| Glucosamine_iso | 2 | 273 | Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase |
| GLUCAGON | 2 | 29 | glucagon |
| gln-synt_NC | 2 | 472 | Glutamine synthetase |
| gln-synt_N | 2 | 101 | Glutamine synthetase, beta-Grasp domain |
| gln-synt | 2 | 371 | Glutamine synthetase, catalytic domain |
| GLA | 4 | 40 | Domain containing Gla (gamma-carboxyglutamate) residues |
| GHMP_kinases_N | 2 | 174 | GHMP kinases putative ATP-binding protein, N-terminal domain |
| GHMP_kinases_C | 2 | 165 | GHMP kinases putative ATP-binding protein, C-terminal domain |
| GHMP_kinases | 2 | 339 | GHMP kinases putative ATP-binding protein |
| ghf9 | 2 | 450 | glycosyl hydrolases family 9 |
| ghf7 | 4 | 399 | glycosyl hydrolase family 7 |
| ghf6 | 3 | 336 | glycosyl hydrolases family 6 |
| ghf5 | 6 | 327 | glycosyl hydrolase family 5 |
| ghf46 | 2 | 248 | glycosyl hydrolase family 46 (chitosanase) |
| ghf33 | 4 | 397 | glycosyl hydrolase family 33 (sialidases or neuraminidases) |
| ghf28 | 2 | 399 | glycosyl hydrolase family 28 |
| ghf2 | 2 | 298 | glycosyl hydrolase family 2 |
| ghf18 | 5 | 279 | glycosyl hydrolases family 18 |
| ghf17 | 2 | 306 | glycosyl hydrolases family 17 |
| ghf16 | 2 | 214 | glycosyl hydrolases family 16 |
| ghf15 | 2 | 482 | glycosyl hydrolases family 15 |
| ghf14 | 3 | 469 | glycosyl hydrolase family 14 (beta-amylase) |
| ghf11 | 5 | 185 | glycosyl hydrolase family 11 |
| ghf10 | 5 | 316 | glycosyl hydrolases family 10 |
| ghf1 | 8 | 445 | glycosyl hydrolase family 1 |
| GFP | 2 | 222 | Green/red fluorescent protein |
| GFO_IDH_MocA_NC | 2 | 336 | Oxidoreductase family |
| GFO_IDH_MocA_C | 2 | 140 | Oxidoreductase family, C-terminal alpha/beta domain |
| GFO_IDH_MocA | 2 | 144 | Oxidoreductase family, NAD-binding Rossmann fold |
| GerE | 2 | 67 | Bacterial regulatory proteins, luxR family |
| GEL | 5 | 118 | Gelsolin homology domain |
| GATase_2 | 3 | 395 | Glutamine amidotransferases class-II |
| GATase | 3 | 209 | Glutamine amidotransferase class-I |
| GATA | 3 | 59 | GATA zinc finger |
| galpha | 3 | 317 | heterotrimeric G proteins - alpha subunit |
| GAL4 | 3 | 39 | GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain |
| gag_p17 | 2 | 114 | gag gene protein p17 (matrix protein) |
| GAF | 3 | 156 | GAF domain |
| GAD | 2 | 126 | GAD domain |
| GA | 2 | 59 | GA module |
| G6PD_NC | 2 | 486 | glucose-6-phosphate 1-dehydrogenase |
| G6PD_C | 2 | 293 | glucose-6-phosphate 1-dehydrogenase, C-terminal domain |
| G6PD | 2 | 192 | glucose-6-phosphate 1-dehydrogenase, N-terminal domain |
| Fz | 2 | 123 | Fz domain |
| FYVE | 2 | 65 | FYVE zinc finger |
| fusion_gly | 2 | 51 | Fusion glycoprotein F0 |
| Furin-like | 2 | 148 | Furin-like cysteine rich region |
| FTR | 2 | 148 | FTR |
| Frataxin_Cyay | 2 | 112 | Frataxin-like domain |
| formyl_transf | 2 | 194 | Formyl transferase |
| Fork_head | 3 | 92 | Fork head domain |
| FolB | 2 | 120 | Dihydroneopterin aldolase |
| fn3 | 14 | 98 | fibronectin type III domain |
| FN2 | 2 | 52 | Fibronectin type 2 domain |
| FN1 | 3 | 47 | Fibronectin type 1 domain |
| Flavoprotein | 2 | 174 | Flavoprotein |
| Flavin_Reduct | 2 | 176 | Flavin reductase like domain |
| Fimbrial | 2 | 135 | Fimbrial proteins |
| Filamin | 3 | 104 | Filamin/ABP280 repeat |
| fibrinogen_C | 3 | 234 | Fibrinogen beta and gamma chains, C-terminal globular domain |
| FHA | 2 | 154 | FHA domain |
| Ferrochelatase | 2 | 334 | Ferrochelatase |
| ferritin | 4 | 166 | ferritin |
| fer4_NifH | 2 | 277 | nitrogenase iron protein |
| Fe_hyd_SSU | 2 | 60 | Iron hydrogenase small subunit |
| Fe_hyd_lg_C | 2 | 392 | Iron only hydrogenase large subunit, C-terminal region |
| Fe_dep_repr_M | 2 | 76 | Iron dependent repressor, metal binding and dimerization domain |
| Fe_dep_repress | 2 | 62 | Iron dependent repressor, N-terminal DNA binding domain |
| Fe_Asc_oxidored | 2 | 304 | Iron/Ascorbate oxidoreductase |
| Fe-ADH | 2 | 365 | Iron-containing alcohol dehydrogenase |
| fbpase | 4 | 321 | fructose-1,6-bisphosphatase |
| F_bP_aldolase | 2 | 315 | Fructose-bisphosphate aldolase class-II |
| Fapy_DNA_glyco | 4 | 262 | Formamidopyrimidine-DNA glycosylase |
| FAD-oxidase_NC | 4 | 527 | FAD linked oxidases |
| FAD-oxidase_C | 4 | 281 | FAD linked oxidases, C-terminal domain |
| FAD_binding_5 | 2 | 294 | FAD binding domain in molybdopterin dehydrogenase |
| FAD_binding_2 | 2 | 527 | Succinate dehydrogenase/fumarate reductase |
| FAD_binding | 2 | 271 | FAD_binding domain |
| fabp | 17 | 131 | Fatty acid binding protein-like |
| FAA_hydrolase | 2 | 250 | Fumarylacetoacetate (FAA) hydrolase family |
| FA58C | 2 | 146 | galactose-binding domain |
| F5_F8_type_C | 2 | 159 | F5/8 type C domain |
| Extradiol_dioxy | 3 | 290 | Extradiol ring-cleavage dioxygenase |
| Exonuclease | 2 | 182 | Exonuclease |
| ets | 4 | 93 | ETS domain |
| ETF_beta | 2 | 249 | Electron transfer flavoprotein beta subunit |
| ETF_alpha | 2 | 309 | Electron transfer flavoprotein alpha subunit |
| Esterase | 2 | 282 | Putative esterase |
| ERM | 2 | 94 | Ezrin/radixin/moesin family |
| EPSP_syntase | 2 | 422 | EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) |
| Epimerase | 4 | 332 | NAD dependent epimerase/dehydratase family |
| envelope | 2 | 69 | Viral envelope |
| ENTH | 3 | 225 | ENTH domain |
| enolase | 2 | 434 | enolase |
| endotoxin | 2 | 580 | delta endotoxin |
| Endonuclease_3 | 2 | 218 | Endonuclease III |
| END | 2 | 21 | Endothelin |
| Elicitin | 2 | 98 | Elicitin |
| eIF6 | 2 | 224 | eIF-6 family |
| eIF-5a | 2 | 132 | Eukaryotic initiation factor 5A hypusine (eIF-5A) |
| eIF-1a | 2 | 82 | Eukaryotic initiation factor 1A |
| Egg_lysin | 2 | 126 | Egg lysin (Sperm-lysin) |
| EGF_Lam | 3 | 54 | Laminin-type epidermal growth factor-like domain |
| EFTU_C | 3 | 97 | Elongation factor Tu (EF-Tu), C-terminal domain |
| EFTU_2 | 4 | 102 | Elongation factor Tu (EF-Tu), domain 2 |
| EF_TS | 3 | 141 | Elongation factor TS, dimerization domain |
| EFG_IV | 2 | 145 | Elongation factor G, domain IV |
| EFG_C | 2 | 97 | Elongation factor G C-terminus |
| EF1BD | 3 | 90 | EF-1 guanine nucleotide exchange domain |
| E2_N | 2 | 172 | E2 (early) protein, N terminal |
| E2_C | 3 | 79 | E2 (early) protein, C terminal |
| E1_dehydrog | 2 | 388 | Dehydrogenase E1 component |
| Dwarfin | 2 | 192 | Dwarfin |
| DUF50 | 2 | 119 | holliday junction resolvase |
| DUF28 | 2 | 237 | Domain of unknown function DUF28 |
| DUF170 | 3 | 72 | ThiS family |
| DUF153 | 2 | 114 | MTH1175-like domain (DUF153/COG1433) |
| DUF101 | 2 | 132 | Protein of unknown function DUF101 |
| dTDP_sugar_isom | 2 | 183 | dTDP-4-dehydrorhamnose 3,5-epimerase |
| dsrm | 3 | 82 | Double-stranded RNA binding motif |
| DSPc | 2 | 161 | Dual specificity phosphatase, catalytic domain |
| DSBA | 2 | 184 | DSBA oxidoreductase |
| DPS | 2 | 154 | Dps protein family |
| dNK | 2 | 212 | Deoxynucleoside kinase |
| DNA_topoisoIV | 2 | 473 | Type II DNA topoisomerase, domains 2-4 |
| DNA_PPF | 4 | 114 | DNA polymerase processivity factor |
| DNA_polymeraseX | 2 | 180 | DNA polymerase X family |
| DNA_pol_B_exo | 2 | 361 | DNA polymerase family B, exonuclease domain |
| DNA_pol_B | 2 | 450 | DNA polymerase family B, C-terminal region |
| DNA_pol3_beta | 3 | 122 | DNA polymerase III beta subunit |
| DNA_photolyase | 2 | 472 | DNA photolyase |
| DNA_mis_repair_NM | 2 | 325 | DNA mismatch repair protein, N-terminal domain and second domain |
| DNA_mis_repair_M | 2 | 120 | DNA mismatch repair protein, second domain |
| DNA_methylase | 2 | 325 | C-5 cytosine-specific DNA methylase |
| DNA_ligase_N | 2 | 312 | NAD-dependent DNA ligase adenylation domain |
| DNA_ligase_C | 2 | 90 | ATP dependent DNA ligase C-terminal domain |
| DNA_ligase | 2 | 207 | ATP dependent DNA ligase N-terminal domain |
| DnaJ | 2 | 76 | DnaJ molecular chaperone homology domain |
| DNA_gyraseB_N2 | 2 | 387 | DNA gyrase B, 2 N-terminal domains |
| DNA_gyraseB | 2 | 172 | DNA gyrase B, domain 2 |
| DMRL_synthase | 5 | 158 | 6,7-dimethyl-8-ribityllumazine synthase |
| DISIN | 3 | 62 | Homologues of snake disintegrins |
| DHquinase_II | 2 | 143 | Dehydroquinase class II |
| DHPS | 2 | 273 | Dihydropteroate synthase |
| DHOdehase | 4 | 323 | Dihydroorotate dehydrogenase |
| DHHA2 | 3 | 119 | DHHA2 domain |
| DHH | 3 | 185 | DHH family |
| DHDPS | 2 | 291 | Dihydrodipicolinate synthetase family |
| DHBP_synthase | 2 | 210 | 3,4-dihydroxy-2-butanone 4-phosphate synthase |
| Desulfoferrodox | 2 | 106 | Desulfoferrodoxin |
| DEP | 2 | 94 | Domain found in Dishevelled, Egl-10, and Pleckstrin |
| DeoC | 2 | 251 | Deoxyribose-phosphate aldolase |
| Dehydratase_SU | 2 | 137 | Dehydratase small subunit |
| Dehydratase_MU | 2 | 181 | Dehydratase medium subunit |
| Dehydratase_LU | 2 | 553 | Dehydratase large subunit |
| DegT_DnrJ_EryC1 | 2 | 363 | DegT/DnrJ/EryC1/StrS family |
| DEFSN | 2 | 34 | Defensin/corticostatin |
| DEATH | 7 | 107 | DEATH domain, found in proteins involved in cell death (apoptosis) |
| DEAD | 4 | 285 | subset of the extended AAA-ATPase domain family including DEAD/DEAH box helicases |
| dCMP_cyt_deam | 3 | 120 | Cytidine and deoxycytidylate deaminase zinc-binding region |
| DAP_epimerase | 2 | 136 | DAP_epimerase |
| DAO | 2 | 351 | FAD dependent oxidoreductase |
| Dala_Dala_ligas_N | 2 | 114 | D-alanine--D-alanine ligase, N terminal domain |
| Dala_Dala_ligas_C | 2 | 219 | D-alanine--D-alanine ligase, C terminal domain |
| Dala_Dala_ligas | 2 | 333 | D-alanine--D-alanine ligase |
| DAHP_synth_1 | 3 | 295 | DAHP synthetase I family |
| CytoC_RC | 2 | 321 | Photosynthetic reaction center cytochrome C subunit |
| Cytochrome_C1_N | 2 | 196 | Cytochrome C1 family, N-terminal domain |
| Cytochrome_C1_C | 2 | 46 | Cytochrome C1 family transmembrane region |
| Cytochrome_C1 | 2 | 243 | Cytochrome C1 family |
| cytochrome_b | 2 | 379 | Cytochrome b |
| cytochr_c552 | 2 | 472 | Cytochrome c552 |
| Cytidylyltransf | 2 | 141 | Cytidylyltransferase |
| Cytidylyl_trans | 2 | 228 | Cytidylyltransferase |
| Cys-protease-3C | 3 | 191 | 3C cysteine protease (picornain 3C) |
| Cys_Met_Meta_PP | 3 | 390 | Cystathionine synthase |
| Cys_knot | 2 | 108 | Cystine-knot domain |
| Cyclotide | 3 | 29 | Cyclotide family |
| Cyclodex_gly_tran | 6 | 684 | Cyclodextrin glycosyltransferase |
| cyclin | 3 | 252 | Cyclin |
| CYCc | 2 | 189 | Adenylyl- / guanylyl cyclase, catalytic domain |
| Cutinase | 2 | 202 | Cutinase |
| Cu-oxidase | 2 | 528 | Multicopper oxidase |
| Cu_nir | 3 | 334 | copper-containing nitrite reductase |
| Cucumo_coat | 2 | 165 | Cucumovirus coat protein |
| Cu_bind_like | 3 | 99 | Plastocyanin-like domain |
| CUB | 3 | 110 | Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. |
| Cu_amine_oxid | 4 | 637 | Copper amine oxidase |
| CPSase_L_chain | 4 | 115 | Carbamoyl-phosphate synthase L chain and Phosphoribosylglycinamide synthetase, N-terminal domain |
| CPS | 3 | 240 | Biotin carboxylase/Carbamoyl phosphate synthetase |
| cpn60_TCP1 | 4 | 160 | TCP-1/cpn60 chaperonin family, apical domain |
| cpn10 | 2 | 98 | Chaperonin 10 kD subunit |
| COX3 | 3 | 239 | Cytochrome c oxidase subunit III |
| COX2 | 3 | 212 | Cytochrome C oxidase subunit II |
| COX1 | 2 | 521 | Cytochrome C and Quinol oxidase polypeptide I |
| CopC | 2 | 101 | Copper resistance protein CopC |
| Colicin_Pyocin | 3 | 85 | Colicin immunity protein / pyocin immunity protein |
| Colicin | 3 | 194 | Colicin pore forming domain |
| Cohesin | 2 | 140 | Cohesin domain |
| CODH | 2 | 621 | Ni-containing carbon monoxide dehydrogenase |
| CoA_trans | 2 | 267 | Coenzyme A transferase |
| CoA_binding | 2 | 125 | CoA binding domain |
| cNMP | 2 | 123 | Cyclic nucleotide-monophosphate binding domain |
| CN_hydrolase | 2 | 286 | Carbon-nitrogen hydrolase |
| CMAS | 2 | 287 | Cyclopropane-fatty-acyl-phospholipid synthase |
| Clp_N | 2 | 136 | Clp amino terminal domain |
| citrate_synt | 3 | 394 | Citrate synthase |
| CIDE-N | 2 | 104 | CIDE-N domain |
| ChtBD | 5 | 42 | Chitin binding domain |
| chromo | 3 | 71 | chromo (CHRomatin Organization MOdifier domain) |
| Chorismate_mut | 2 | 218 | Chorismate mutase |
| chorismate_bind | 3 | 481 | chorismate binding enzyme |
| CH | 4 | 115 | Calponin homology domain |
| CDC48 | 2 | 184 | Cdc48-like, domains 1 and 2 |
| CCP_MauG_NC | 2 | 312 | Di-haem cytochrome c peroxidase |
| CCP_MauG_C | 2 | 155 | Di-haem cytochrome c peroxidase, C-terminal domain |
| CCP_MauG | 2 | 157 | Di-haem cytochrome c peroxidase, N-terminal domain |
| CcmE | 2 | 107 | CcmE |
| CC4 | 2 | 182 | two-domain cytochrome c |
| CBS | 4 | 53 | CBS domain |
| CBM_20 | 8 | 105 | Starch binding domain |
| cbm12 | 3 | 52 | carbohydrate binding module family 12 |
| CBD_6 | 2 | 152 | Cellulose binding domain |
| CBD_3 | 3 | 153 | carbohydrate binding module family 3 |
| CBD_2 | 2 | 98 | Cellulose binding domain family 2 |
| CAT_RBD | 2 | 55 | CAT RNA binding domain |
| CASc | 2 | 243 | Caspase, interleukin-1 beta converting enzyme (ICE) homologues |
| CARD | 2 | 96 | Caspase recruitment domain |
| capsid_n | 2 | 137 | viral capsid protein (n-terminal domain) |
| capsid_c | 2 | 73 | viral capsid protein (c-terminus) |
| CAP_GLY | 2 | 99 | CAP-Gly domain |
| C4 | 2 | 226 | C-terminal tandem repeated domains in type 4 procollagen |
| C2 | 3 | 129 | Protein kinase C conserved region 2 (CalB) |
| C1q | 2 | 127 | C1q domain |
| C1 | 3 | 56 | Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) |
| bromodomain | 4 | 120 | Bromodomain |
| BRCT | 2 | 92 | BRCA1 C Terminus (BRCT) domain |
| bontoxilysin | 2 | 438 | Clostridium neurotoxins |
| B_lectin | 3 | 108 | Bulb-type mannose-specific lectin |
| BIR | 4 | 110 | Inhibitor of Apoptosis domain |
| biopterin_H | 2 | 316 | Biopterin-dependent aromatic amino acid hydroxylase |
| Binary_toxA | 3 | 204 | Clostridial binary toxin A |
| Bet_v_I | 2 | 159 | Pathogenesis-related protein Bet v I family |
| Beta_elim_lyase | 2 | 445 | Beta-eliminating lyase |
| Bcl-2 | 3 | 166 | Apoptosis regulator proteins, Bcl-2 family |
| BChl_A | 2 | 353 | Bacteriochlorophyll A protein |
| Band_41_NME | 3 | 288 | FERM and ERM domains (Band 4.1 family) |
| Band_41_N | 3 | 83 | FERM domain (Band 4.1 family), region 1 |
| Band_41_M | 3 | 109 | FERM domain (Band 4.1 family), region 2 |
| BAG | 2 | 123 | BAG domain |
| Bacteriofer | 2 | 158 | Bacterioferritin |
| Bacterial_PQQ | 3 | 582 | PQQ enzyme |
| Bac_rhodopsin | 3 | 226 | Bacteriorhodopsin |
| bac_luciferase | 4 | 276 | Bacterial luciferase |
| bac_lipase | 2 | 317 | bacterial lipase |
| Bac_globin | 2 | 118 | Protozoan/cyanobacterial globin |
| Bac_DNA_binding | 4 | 90 | Bacterial DNA-binding protein |
| ATP-synt_g | 2 | 241 | ATP synthase, gamma subunit |
| ATP-synt_DE_N | 2 | 86 | ATP synthase, Delta/Epsilon chain, beta-sandwich domain |
| ATP-synt | 4 | 481 | ATP synthase |
| ATP-sulfurylase | 2 | 541 | ATP-sulfurylase |
| ATP-gua_Ptrans | 3 | 367 | ATP-guanido phosphotransferase |
| Astacin | 2 | 199 | Astacin (Peptidase family M12A) |
| Asp_Glu_race_D | 4 | 109 | Asp/Glu/Hydontoin racemase domain |
| Asp_Glu_race | 2 | 240 | Asp/Glu/Hydontoin racemase |
| Asn_synthase_NC | 2 | 493 | Asparagine synthase |
| Asn_synthase | 2 | 298 | Asparagine synthase, C-terminal domain |
| Arthro_defensin | 2 | 39 | Arthropod defensin |
| arrestin_NC | 2 | 364 | Arrestin (or S-antigen) |
| arrestin_C | 2 | 191 | Arrestin (or S-antigen), C-terminal domain |
| arrestin | 2 | 173 | Arrestin (or S-antigen), N-terminal domain |
| ARM | 3 | 431 | Armadillo/beta-catenin-like repeats |
| ARID | 2 | 117 | ARID/BRIGHT DNA binding domain |
| Arg_repressor_N | 2 | 76 | Arginine repressor (ArgR), N-terminal DNA-binding domain |
| Arg_repressor_C | 2 | 71 | arginine repressor, C-terminal domain |
| Arginosuc_synth | 2 | 412 | Arginosuccinate synthase |
| arginase | 2 | 303 | Arginase family |
| Arch_histone | 2 | 68 | Histone-like transcription factors (CBF/NF-Y) and archaeal histones |
| Apocytochrome_F | 2 | 250 | Apocytochrome F |
| AP_endonucleas1 | 2 | 271 | AP endonuclease family 1 |
| AP_endonuc_2 | 3 | 271 | AP endonuclease family 2 |
| APC10 | 2 | 170 | Anaphase-promoting complex, subunit 10 (APC10) |
| Antifreeze | 3 | 67 | Antifreeze protein |
| Anperoxidase | 2 | 540 | animal haem peroxidase |
| ANK | 3 | 127 | ankyrin repeats |
| ANATO | 2 | 69 | Anaphylatoxin homologous domain |
| AMP-binding | 2 | 514 | AMP-binding enzyme |
| aminotran_5 | 2 | 360 | Aminotransferases class-V |
| aminotran_4 | 2 | 286 | Aminotransferase class IV |
| Amino_oxidase_D2 | 2 | 112 | Flavin containing amine oxidase, domain 2 |
| Amino_oxidase_D1 | 2 | 358 | Flavin containing amine oxidase, domain 1 |
| Amino_oxidase | 2 | 470 | Flavin containing amine oxidase |
| Amidinotransferase | 2 | 354 | Amidinotransferase |
| Amidase_2 | 2 | 166 | N-acetylmuramoyl-L-alanine amidase |
| Amidase | 2 | 449 | Amidase |
| alpha-amylase_NC | 23 | 486 | Alpha amylase, catalytic and C-terminal domains |
| alpha-amylase_N | 2 | 121 | Alpha amylase, N-terminal ig-like domain |
| alpha-amylase | 23 | 401 | Alpha amylase, catalytic domain |
| Alpha_adaptinC2 | 2 | 126 | Alpha adaptin AP2, N-terminal domain of C-terminal region |
| Alpha_adaptinC12 | 2 | 240 | Alpha adaptin AP2, C-terminal region (consists of 2 domains) |
| Alpha_adaptin_C | 2 | 113 | Alpha adaptin AP2, C-terminal domain of C-terminal region |
| alk_phosphatase | 2 | 464 | Alkaline phosphatase |
| Ald_Xan_dh_2 | 6 | 763 | Aldehyde oxidase and xanthine dehydrogenase, domains 3-4 |
| Ald_Xan_dh_1 | 6 | 171 | Aldehyde oxidase and xanthine dehydrogenase, domains 1-2 |
| Aldolase_II | 2 | 214 | Class II Aldolase |
| aldedh | 4 | 484 | Aldehyde dehydrogenase |
| ALBUMIN | 3 | 194 | albumin |
| Ala_racemase_N | 2 | 229 | Alanine racemase, N-terminal domain |
| AlaDh_PNT_D2 | 2 | 171 | Alanine dehydrogenase/pyridine nucleotide transhydrogenase domain 2 |
| AlaDh_PNT_D1 | 2 | 193 | Alanine dehydrogenase/pyridine nucleotide transhydrogenase domain 1 |
| AlaDh_PNT | 2 | 364 | Alanine dehydrogenase/pyridine nucleotide transhydrogenase |
| ALAD | 2 | 323 | Delta-aminolevulinic acid dehydratase |
| AhpC-TSA | 3 | 195 | AhpC/TSA family |
| Agglutinin | 2 | 149 | Agglutinin |
| AFOR | 2 | 608 | Aldehyde ferredoxin oxidoreductase |
| ADP_PFK_GK | 2 | 449 | ADP-specific Phosphofructokinase/Glucokinase conserved region |
| Adenylsucc_synt | 3 | 430 | Adenylosuccinate synthetase |
| adeno_fiber | 3 | 188 | Adenovirus fiber protein head domain (knob domain) |
| Activin_recp | 2 | 87 | Activin types I and II receptor domain |
| ACT | 2 | 90 | ACT domain |
| ACPS | 3 | 109 | 4'-phosphopantetheinyl transferase superfamily |
| aconitase | 2 | 445 | Aconitase family (aconitate hydratase) |
| acid_phosphat | 3 | 372 | Histidine acid phosphatase |
| Acetyltransf2 | 2 | 275 | N-acetyltransferase |
| Acetyltransf | 6 | 161 | Acetyltransferase (GNAT) family |
| ACBP | 2 | 87 | Acyl CoA binding protein |
| abhydrolase_2 | 2 | 223 | Phospholipase/Carboxylesterase |
| ABC_tran | 6 | 255 | ABC transporter |
| aakinase | 2 | 310 | Amino acid kinase family |
| AAA | 4 | 314 | ATPase family associated with various cellular activities (AAA) |
| A2M_B | 2 | 285 | Alpha-2-macroglobulin family B |
| A2M_A | 2 | 132 | Alpha-2-macroglobulin family A |
| 7kD_DNA_binding | 2 | 65 | 7kD DNA-binding domain |
| 6PGD | 2 | 475 | 6-phosphogluconate dehydrogenases |
| 6PF2K | 2 | 213 | 6-phosphofructo-2-kinase |
| 5_3_exonuclease | 2 | 265 | 5'-3' exonuclease |
| lipocalin | 15 | 161 | Lipocalin family |
| cytc | 11 | 111 | cytochrome c |
| FAD_binding_4 | 4 | 245 | FAD binding domain |
| PCI_1 | 2 | 52 | Plant proteinase inhibitors |
| GGL | 2 | 61 | G protein gamma subunit-like motifs |
| GBP_PSP | 3 | 23 | Paralytic/GBP/PSP peptide |
| biotin_lipoyl | 7 | 83 | Biotin-requiring enzymes |
| B | 3 | 50 | B domain |
| alpha-amylase_C | 21 | 85 | Alpha amylase, C-terminal domain |
