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Table 3 Comparison of gold and silver standard families to Pfam and SCOP families

From: A gold standard set of mechanistically diverse enzyme superfamilies

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
  1. *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.