Table 1 Statistics of the benchmark datasets: diverse dataset, two or more EC numbers per family
From: Combining specificity determining and conserved residues improves functional site prediction
Family ID | Family name | # sequences | Alignment length | ECs | PDB | Bound ligand equivalent to natural substrate/product |
|---|---|---|---|---|---|---|
PF00108 | Thiolase_N | 22 | 291 | 2.3.1.9 2.3.1.16 2.3.1.176 | 1NL7 | Coenzyme A |
PF00128 | Alpha-amylase | 54 | 673 | 2.4.1.4 2.4.1.7 3.2.1.10 3.2.1.20 3.2.1.70 3.2.1.98 3.2.1.93 3.2.1.141 5.4.99.16 5.4.99.15 | 2D3N | Glucose |
PF00135 | COesterase | 129 | 889 | 3.1.1.1 3.1.1.3 3.1.1.7 3.1.1.8 3.1.1.13 3.1.1.59 | 1P0M | Choline ion |
PF00215 | OMPdecase | 92 | 402 | 4.1.1.23 4.1.1.85 | 2CZE | Uridine-5'-monophosphate |
PF00278 | Orn_DAP_Arg_deC | 55 | 220 | 4.1.1.17 4.1.1.18 4.1.1.19 4.1.1.20 | 1TWI | Lysine |
PF00293 | NUDIX | 205 | 314 | 2.7.7.1 3.6.1.13 3.6.1.17 3.6.1.52 3.6.1.52 5.3.3.2 | 2DSC | Adenosine-5-diphosphoribose |
PF00348 | Polyprenyl_synt | 16 | 289 | 2.5.1.10 2.5.1.29 | 2F8Z | Zoledronic acid, 3-methylbut-3-enyl trihydrogen diphosphate |
PF00351 | Biopterin_H | 6 | 332 | 1.14.16.1 1.14.16.2 1.14.16.4 | 1MMK | 5,6,7,8-tetrahydrobiopterin, beta(2-thienyl)alanine |
PF00579 | tRNA-synt_1b | 41 | 402 | 6.1.1.1 6.1.1.2 | 1WQ4 | Tyrosine |
PF00583 | Acetyltransf_1 | 244 | 150 | 2.3.1.1 2.3.1.4 2.3.1.48 2.3.1.57 2.3.1.59 2.3.1.82 2.3.1.87 2.3.1.88 2.3.1.128 | 1TIQ | Coenzyme A |
PF00590 | TP_methylase | 22 | 247 | 2.1.1.98 2.1.1.107 2.1.1.130 2.1.1.131 2.1.1.132 2.1.1.133 2.1.1.152 2.1.1.151 4.2.1.75 4.99.1.4 | 1S4D | S-adenosyl-L-homocysteine |
PF00755 | Carn_acyltransf | 22 | 867 | 2.3.1.6 2.3.1.7 2.3.1.21 2.3.1.137 | 1NDI | Coenzyme A |
PF00871 | Acetate_kinase | 12 | 405 | 2.7.2.1 2.7.2.7 2.7.2.15 | 1TUY | Adenosine-5'-diphosphate |
PF00896 | Mtap_PNP | 13 | 288 | 2.4.2.1 2.4.2.28 | 1V48 | 9-(5,5-difluoro-5-phosphonopentyl)guanine |
PF00962 | A_deaminase | 17 | 475 | 3.5.4.4 3.5.4.6 | 1NDZ | 1-((1r)-1-(hydroxymethyl)-3-(6-((3-(1-methyl- 1h-benzimidazol-2-yl)propanoyl)amino)-1h- indol-1-yl)propyl)-1h-imidazole-4-carboxamide |
PF01048 | PNP_UDP_1 | 16 | 276 | 2.4.2.1 2.4.2.3 2.4.2.28 3.2.2.4 3.2.2.9 | 1PK7 | Adenosine |
PF01112 | Asparaginase_2 | 7 | 365 | 3.5.1.1 3.5.1.26 | 1SEO | Aspartic acid |
PF01135 | PCMT | 9 | 232 | 2.1.1.77 2.1.1.36 | 1R18 | S-adenosyl-L-homocysteine |
PF01202 | SKI | 100 | 263 | 2.7.4.3 2.7.1.12 2.7.4.14 2.7.1.71 4.2.3.4 | 1WE2 | Adenosine-5'-diphosphate |
PF01234 | NNMT_PNMT_TEMT | 7 | 289 | 2.1.1.1 2.1.1.28 2.1.1.49 | 2AN4 | S-adenosyl-L-homocysteine |
PF01467 | CTP_transf_2 | 66 | 302 | 2.7.7.1 2.7.7.3 2.7.7.14 2.7.7.15 2.7.7.18 2.7.7.39 | 1N1D | [Cytidine-5'-phosphate] glycerylphosphoric acid ester |
PF01712 | dNK | 14 | 174 | 1.6.99.3 2.7.1.21 2.7.1.74 2.7.1.76 2.7.1.113 2.7.1.145 | 2A2Z | Uridine-5'-diphosphate, 2'-deoxycytidine |
PF02274 | Amidinotransf | 32 | 455 | 2.1.4.1 3.5.3.6 3.5.3.18 | 2A9G | Arginine |
PF03061 | 4HBT | 153 | 102 | 3.1.2.2 3.1.2.23 | 1LO7 | 2-oxyglutaric acid, 2-aminoethanesulfonic acid |
PF03171 | 2OG-FeII_Oxy | 147 | 183 | 1.14.11.2 1.14.11.4 1.14.11.7 1.14.11.9 1.14.11.11 1.14.11.13 1.14.11.19 1.14.11.20 1.14.11.23 1.14.11.26 1.14.17.4 1.14.20.1 1.21.3.1 | 2FDJ | 4-hydroxyphenacyl coenzyme A |
PF03414 | Glyco_transf_6 | 6 | 341 | 2.4.1.87 2.4.1.40 | 1LZJ | Succinic acid |