Table 5 Statistics of the benchmark datasets: homogeneous dataset, strictly one EC number per family
From: Combining specificity determining and conserved residues improves functional site prediction
Family ID | Family name | # sequences | Alignment length | EC | PDB | Bound ligand equivalent to natural substrate/product |
|---|---|---|---|---|---|---|
PF00303 | Thymidylat_ synt | 19 | 384 | 2.1.1.45 | 2G8O | 2'-deoxyuridine 5'-monophosphate, 10-propargyl-5,8-dideazafolic acid |
PF00693 | Herpes_TK | 15 | 305 | 2.7.1.21 | 1VTK | Adenosine-5'-diphosphate, thymidine-5'-phosphate |
PF00925 | GTP_ cyclohydro2 | 16 | 193 | 3.5.4.25 | 2BZ0 | Phosphomethylphosphonic acid guanylate ester |
PF01014 | Uricase | 17 | 196 | 1.7.3.3 | 2FXL | 1-(2,5-dioxo-2,5-dihydro-1h-imidazol-4-yl)urea |
PF01227 | GTP_ cyclohydroI | 16 | 107 | 3.5.4.16 | 1A8R | Guanosine-5'-triphosphate |
PF01293 | PEPCK_ATP | 12 | 495 | 4.1.1.49 | 1YTM | Adenosine-5'-triphosphate, oxalic acid |
PF01583 | APS_kinase | 20 | 166 | 2.7.1.25 | 1M7G | Adenosine-5'-phosphosulfate, adenosine-5'-diphosphate-2',3'-vanadate |
PF01656 | CbiA | 80 | 372 | 6.3.3.3 | 1A82 | Adenosine-5'-triphosphate, 7,8-diamino-nonanoic acid |
PF01702 | TGT | 13 | 256 | 2.4.2.29 | 1Q2S | 9-deazaguanine |
PF01747 | ATP- sulfurylase | 19 | 397 | 2.7.7.4 | 1G8H | Adenosine-5'-phosphosulfate, pyrophosphate 2- |
PF02110 | HK | 9 | 282 | 2.7.1.50 | 1ESQ | Adenosine-5'-triphosphate, 4-methyl-5-hydroxyethylthiazole phosphate |
PF02223 | Thymidylate_ kin | 26 | 209 | 2.7.4.9 | 1E9E | Adenosine-5'-diphosphate, thymidine-5'-phosphate |
PF02277 | DBI_PRT | 28 | 398 | 2.4.2.21 | 1L5L | 7-alpha-d-ribofuranosyl-purine-5'-phosphate, nicotinic acid |
PF02353 | CMAS | 12 | 304 | 2.1.1.79 | 1KPI | S-adenosyl-Ll-homocysteine |
PF02569 | Pantoate_ ligase | 7 | 311 | 6.3.2.1 | 2A86 | Adenosine monophosphate, beta-alanine |
PF02898 | NO_synthase | 8 | 374 | 1.14.13.39 | 1Q2O | L-n(omega)-nitroarginine-2,4-L-diaminobutyric amide |
PF02901 | PFL | 11 | 734 | 2.3.1.54 | 1MZO | Pyruvic acid |
PF03332 | PMM | 9 | 248 | 5.4.2.8 | 2FUE | Alpha-d-mannose 1-phosphate |