Table 3.
Comparison of gold and silver standard families to Pfam and SCOP families
| Gold/silver standard family | Pfam family* | SCOP family* | Reaction catalyzed |
| Enolase | enolase_n, enolase_c | Enolase N-terminal domain-like, enolase | Dehydration of 2-phospho-D-glycerate |
| Methylaspartate ammonia-lyase | maal_n, maal_c | Enolase N-terminal domain-like, D-glucarate dehydratase-like | Elimination of ammonia from methylaspartic acid |
| Mandelate racemase | mr_mle_n, mr_mle | Enolase N-terminal domain-like, D-glucarate dehydratase-like | Racemization of S-mandelate to R-mandelate |
| Dipeptide epimerase | mr_mle_n, mr_mle | Enolase N-terminal domain-like, D-glucarate dehydratase-like | Dipeptide epimerization |
| Chloromuconate cycloisomerase | mr_mle_n, mr_mle | Enolase N-terminal domain-like, D-glucarate dehydratase-like | Chloromuconate lactonization |
| Muconate cycloisomerase | mr_mle_n, mr_mle | Enolase N-terminal domain-like, D-glucarate dehydratase-like | Muconate lactonization |
| Ortho-succinylbenzoate synthase | mr_mle_n, mr_mle | Enolase N-terminal domain-like, D-glucarate dehydratase-like | Dehydration of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid |
| Glucarate dehydratase | mr_mle_n, mr_mle | Enolase N-terminal domain-like, D-glucarate dehydratase-like | Dehydration of D-glucarate |
| Galactonate dehydratase | mr_mle_n, mr_mle | NA | Dehydration of D-galactonate |
| Fosfomycin resistance protein FosA | Glyoxalase | Antibiotic resistance proteins | Addition of glutathione to the oxirane ring of fosfomycin |
| 2,3-Dihydroxybiphenyl dioxygenase | Glyoxalase | Extradiol dioxygenases | Extradiol cleavage of 2,3-dihydroxybiphenyl to 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate |
| 3,4-Dihydroxyphenylacetate 2,3-dioxygenase | Glyoxalase | Extradiol dioxygenases | extradiol cleavage of 3,4-dihydroxyphenylacetate to 2-hydroxy-5-carboxymethylmuconate semialdehyde |
| 3-Methylcatechol 2,3-dioxygenase | Glyoxalase | Extradiol dioxygenases | Extradiol cleavage of 3-methylcatechol to 2-hydroxy-6-oxo-2,4-heptadienoate |
| 4-Hydroxyphenylpyruvate dioxygenase | Glyoxalase | Extradiol dioxygenases | Conversion of 4-hydroxyphenylpyruvate to homogentisate |
| Glyoxalase I | Glyoxalase | Glyoxalase I | Conversion of methylglyoxal (hemithioacetal form) to S-D-lactoylglutathione |
| Methylmalonyl-CoA epimerase | Glyoxalase | Methylmalonyl-CoA epimerase | Epimerization of (2R)-methylmalonyl-CoA to (2S)-methylmalonyl-CoA |
| 1,2-Dihydroxynaphthalene dioxygenase | Glyoxalase | NA | Extradiol cleavage of 1,2-dihydroxynaphthalene |
| 2,2',3-Trihydroxybiphenyl dioxygenase | Glyoxalase | NA | Extradiol cleavage of 2,2',3-trihydroxybiphenyl to 2-hydroxy-6-oxo-(2-hydroxyphenyl)-hexa-2,4-dienoic acid |
| 2,3-Dihydroxy-p-cumate-3,4-dioxygenase | Glyoxalase | NA | Extradiol cleavage of 2,3-dihydroxy-p-cumate to 2-hydroxy-3-carboxy-6-oxo-7-methylocta-2,4-dienoate |
| 2,4,5-Trihydroxytoluene oxygenase | Glyoxalase | NA | Extradiol cleavage of 2,4,5-trihydroxytoluene |
| 2,6-Dichlorohydroquinone dioxygenase | Glyoxalase | NA | Extradiol cleavage of 2,6-dichlorohydroquinone |
| 3-Isopropylcatechol-2,3-dioxygenase | Glyoxalase | NA | Extradiol cleavage of 3-isopropylcatechol |
| 4-Hydroxymandelate synthase | Glyoxalase | NA | Conversion of p-hydroxyphenylpyruvate to L-p-hydroxymandelate |
| Catechol 2,3-dioxygenase | Glyoxalase | NA | Extradiol cleavage of catechol to alpha-hydroxymuconic semialdehyde |
| Fosfomycin resistance protein FosB | Glyoxalase | NA | Addition of L-cysteine to the oxirane ring of fosfomycin |
| Fosfomycin resistance protein FosX | Glyoxalase | NA | Addition of water to the oxirane ring of fosfomycin |
| Adenosine deaminase | A_deaminase | Adenosine deaminase (ADA) | Deamination of adenosine |
| AMP deaminase | A_deaminase | NA | Deamination of AMP |
| Cytosine deaminase | Amidohydro_1 | Cytosine deaminase catalytic domain; cytosine deaminase | Deamination of cytosine |
| N-acyl-D-amino-acid deacylase | Amidohydro_1 | D-aminoacylase, catalytic domain; D-aminoacylase | Hydrolysis of an N-acyl-D-amino-acid |
| Dihydroorotase3 | Amidohydro_1 | Dihydroorotase | Synthesis of dihydroorotate from carbamoyl aspartate |
| D-hydantoinase | Amidohydro_1 | Hydantoinase (dihydropyrimidinase), catalytic domain; hydantoinase (dihydropyrimidinase) | Hydrolytic ring cleavage of a dihydropyrimidine |
| L-hydantoinase | Amidohydro_1 | Hydantoinase (dihydropyrimidinase), catalytic domain; hydantoinase (dihydropyrimidinase) | Hydrolytic ring cleavage of a 5 membered cyclic diamide |
| Isoaspartyl dipeptidase | Amidohydro_1 | Isoaspartyl dipeptidase, catalytic domain; isoaspartyl dipeptidase | Hydrolysis of beta-l-isoaspartyl linkage of a dipeptide |
| Adenine deaminase | Amidohydro_1 | NA | Deamination of adenine |
| Allantoinase | Amidohydro_1 | NA | Hydrolysis of allantoin |
| Ammelide aminohydrolase | Amidohydro_1 | NA | Deamination of ammelide |
| Aryldialkylphosphatase | Amidohydro_1 | NA | Hydrolysis of an organophosphate |
| Atrazine chlorohydrolase | Amidohydro_1 | NA | Hydrolytic dechlorination of atrazine |
| Dihydroorotase1 | Amidohydro_1 | NA | Synthesis of dihydroorotate from carbamoyl aspartate |
| Dihydroorotase2 | Amidohydro_1 | NA | Synthesis of dihydroorotate from carbamoyl aspartate |
| Guanine deaminase | Amidohydro_1 | NA | Deamination of guanine |
| Hydroxydechloroatrazine ethylaminohydrolase | Amidohydro_1 | NA | Conversion of 4-(ethylamino)-2-hydroxy-6-(isopropylamino)-1,3,5-triazine to N-isopropylammelide |
| Imidazolonepropionase | Amidohydro_1 | NA | Hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate |
| Melamine deaminase | Amidohydro_1 | NA | Deamination of melamine |
| N-acetylgalactosamine-6-phosphate deacetylase | Amidohydro_1 | NA | Deacetylation of N-acetylgalactosamine-6-phosphate |
| N-isopropylammelide isopropylaminohydrolase | Amidohydro_1 | NA | Conversion of N-isopropylammelide to isopropylamine |
| S-triazine hydrolase | Amidohydro_1 | NA | Hydrolysis of a triazine |
| Trzn | Amidohydro_1 | NA | Hydrolysis of a triazine |
| N-acetylglucosamine-6-phosphate deacetylase | Amidohydro_1 | N-acetylglucosamine-6-phosphate deacetylase, catalytic domain; N-acetylglucosamine-6-phosphate deacetylase | Deacetylation of N-acetylglucosamine-6-phosphate |
| Urease | Amidohydro_1, urease | Alpha-subunit of urease, catalytic domain; alpha-subunit of urease; urease, beta-subunit; urease, gamma-subunit | Hydrolysis of urea to ammonia and carbon dioxide |
| 1-Aminocyclopropane-1-carboxylate deaminase | None | NA | Deamination of 1-aminocyclopropane-1-carboxylate |
| Phosphotriesterase | PTE | Phosphotriesterase-like | Hydrolysis of an organophosphate |
| Membrane dipeptidase | Renal_dipeptase | Renal dipeptidase | Hydrolysis of a dipeptide |
| Glucuronate isomerase | UxaC | Uronate isomerase TM0064 | Conversion of D-glucuronate to D-frucuronate |
| Delta(3,5)-delta(2,4)-dienoyl-CoA isomerase | ECH | Crotonase-like | Isomerization of 3,5-dienoyl-CoA to 2,4-dienoyl-CoA |
| Methylmalonyl-CoA decarboxylase | ECH | Crotonase-like | Decarboxylation of methylmalonyl CoA |
| Methylglutaconyl-CoA hydratase | ECH | Crotonase-like | Hydration of 3-methylglutaconyl-CoA |
| Enoyl-CoA hydratase | ECH | Crotonase-like | Hydration of trans-2-enoyl-CoA thiolester |
| 4-Chlorobenzoate dehalogenase | ECH | Crotonase-like | Hydrolytic dehalogenation of 4-chlorobenzoyl-CoA |
| Dodecenoyl-CoA delta-isomerase (peroxisomal) | ECH | Crotonase-like | Isomerization of 3-enoyl-CoA to 2-enoyl-CoA |
| Methylglutaconyl-CoA hydratase 2 | ECH | NA | Hydration of 3-methylglutaconyl-CoA |
| Histone acetyltransferase | ECH | NA | Acetylation of histone |
| 2-Ketocyclohexanecarboxyl-CoA hydrolase | ECH | NA | Cleavage of 2-ketocyclohexanecarboxyl-CoA to pimelyl-CoA |
| 1,4-Dihydroxy-2-napthoyl-CoA synthase | ECH | NA | Cyclization of o -succinylbenzoate-CoA thioester |
| Feruloyl-CoA hydratase/lyase | ECH | NA | Hydration and nonoxidative cleavage of feruloyl-SCoA to vanillin and acetyl-SCoA |
| Crotonobetainyl-CoA hydratase | ECH | NA | Hydration of crotonobetainyl-CoA |
| Cyclohex-1-enecarboxyl-CoA hydratase | ECH | NA | Hydration of cyclohex-1-enecarboxyl-CoA |
| Cyclohexa-1,5-dienecarbonyl-CoA hydratase | ECH | NA | Hydration of cyclohexa-1,5-diene-1-carboxyl-CoA |
| 3-Hydroxyisobutyryl-CoA hydrolase | ECH | NA | Hydrolysis of 3-hydroxyisobutyryl-CoA |
| Dodecenoyl-CoA delta-isomerase (mitochondrial) | ECH | NA | Isomerization of 3-enoyl-CoA to 2-enoyl-CoA |
| Beta-phosphoglucomutase | Hydrolase | Beta-phosphoglucomutase-like | Conversion of beta-glucose-1-phosphate to glucose-6-phosphate |
| P-type ATPase | Hydrolase | Calcium ATPase, catalytic domain P | Dephosphorylation of ATP to ADP |
| Epoxide hydrolase N-terminal phosphatase | Hydrolase | Epoxide hydrolase, N-terminal domain | Dephosphorylation |
| 2-Haloacid dehalogenase | Hydrolase | L-2-haloacid dehalogenase, HAD | Dehalogenation of (s)-2-haloacid |
| Phosphoserine phosphatase | Hydrolase | Phosphoserine phosphatase | Dephosphorylation of phosphoserine |
| Phosphonoacetaldehyde hydrolase | Hydrolase | Phosphonoacetaldehyde hydrolase | Hydrolysis of phosphonoacetaldehyde |
| 2-Deoxyglucose-6-phosphatase | Hydrolase | NA | Dephosphorylation of 2-deoxyglucose-6-phosphate |
| Phosphoglycolate phosphatase | Hydrolase | NA | Dephosphorylation of 2-phosphoglycolate |
| Phosphoglycolate phosphatase 2 | Hydrolase | NA | Dephosphorylation of 2-phosphoglycolate |
| Glycerol-3-phosphate phosphatase | Hydrolase | NA | Dephosphorylation of glycerol-3-phosphate |
| Pyridoxal phosphatase | Hydrolase | NA | Dephosphorylation of pyridoxal 5'-phosphate |
| Enolase-phosphatase | Hydrolase | NA | Oxidative cleavage |
| Histidinol-phosphatase | IGPD | NA | Dephosphorylation of L-histidinol-phosphate |
| Sucrose-phosphatase | S6PP | NA | Dephosphorylation of sucrose 6-phosphate |
| Trehalose-phosphatase | Trehalose_ PPase | NA | Dephosphorylation of trehalose 6-phosphate |
| 5'-Nucleotidase | None | 5' (3')-Deoxyribonucleotidase (dNT-2) | Dephosphorylation of 5' nucleotide |
| Deoxy-D-mannose-octulosonate 8-phosphate phosphatase | None | Probable phosphatase YrbI | Dephosphorylation of 3-deoxy-D-manno-octulosonate 8-phosphate |
| Polynucleotide 5'-hydroxyl-kinase carboxy-terminal phosphatase | None | Polynucleotide kinase, phosphatase domain | Dephosphorylation of 3' nucleotide |
| mdp-1 | None | NA | Dephosphorylation |
| Mannosyl-3-phosphoglycerate phosphatase | None | NA | Dephosphorylation of 2(alpha-D-mannosyl)-3-phosphoglycerate |
*Some gold standard families correspond to multiple Pfam and/or SCOP families because Pfam and SCOP divide the enzymes in question into multiple structural domains, each with a different family assignment. NA = Not applicable, IGPD, Pfam Imidazoleglycerol-phosphate dehydratase family; ECH, Pfam Enoyl-CoA hydratase/isomerase family; PTE, Pfam Phosphotriesterase family.