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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