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Comparison of gold and silver standard families to Pfam and SCOP families |
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| Gold/silver standard family |
Pfam family* |
SCOP family* |
Reaction catalyzed |
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| 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 |
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*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. | |||
Brown et al. Genome Biology 2006 7:R8 doi:10.1186/gb-2006-7-1-r8 |
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