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Table 2 Summary of gold and silver standard families

From: A gold standard set of mechanistically diverse enzyme superfamilies

Superfamily

Family

EC number*

Number of sequences (gold/silver)

Number of structures

Amidohydrolase

Aryldialkylphosphatase

3.1.8.1

2/3

0

 

Phosphotriesterase

3.1.8.1

7/8

12

 

Membrane dipeptidase

3.4.13.19

1/1

2

 

N-acetylglucosamine-6-phosphate deacetylase

3.5.1.25

1/54

2

 

Urease

3.5.1.5

100/107

35

 

N-acyl-D-amino-acid deacylase

3.5.1.81

3/11

8

 

D-hydantoinase

3.5.2.2

10/25

4

 

L-hydantoinase

3.5.2.2

3/3

1

 

Dihydroorotase1

3.5.2.3

3/79

0

 

Dihydroorotase2

3.5.2.3

13/13

0

 

Dihydroorotase3

3.5.2.3

7/43

1

 

Allantoinase

3.5.2.5

4/7

0

 

Imidazolonepropionase

3.5.2.7

1/29

0

 

Cytosine deaminase

3.5.4.1

9/24

7

 

Adenine deaminase

3.5.4.2

1/24

0

 

Guanine deaminase

3.5.4.3

11/34

0

 

Adenosine deaminase

3.5.4.4

10/20

17

 

AMP deaminase

3.5.4.6

28/31

0

 

Hydroxydechloroatrazine ethylaminohydrolase

3.5.99.3

1/2

0

 

N-isopropylammelide isopropylaminohydrolase

3.5.99.4

1/1

0

 

1-Aminocyclopropane-1-carboxylate deaminase

3.5.99.7

1/1

0

 

Atrazine chlorohydrolase

3.8.1.8

1/1

0

 

Glucuronate isomerase

5.3.1.12

1/2

1

 

Ammelide aminohydrolase

NA

2/2

0

 

Isoaspartyl dipeptidase

NA

5/5

5

 

Melamine deaminase

NA

1/1

0

 

N-acetylgalactosamine-6-phosphate deacetylase

NA

3/5

0

 

S-triazine hydrolase

NA

1/1

0

 

TrzN

NA

1/1

0

Crotonase

Histone acetyltransferase

2.3.1.48

11/12

0

 

3-Hydroxyisobutyryl-CoA hydrolase

3.1.2.4

2/70

0

 

4-Chlorobenzoate dehalogenase

3.8.1.7

1/7

2

 

Methylmalonyl-CoA decarboxylase

4.1.1.41

1/6

2

 

Cyclohexa-1,5-dienecarbonyl-CoA hydratase

4.2.1.100

1/3

0

 

Enoyl-CoA hydratase

4.2.1.17

54/293

7

 

Methylglutaconyl-CoA hydratase

4.2.1.18

2/5

1

 

Methylglutaconyl-CoA hydratase 2

4.2.1.18

2/11

0

 

Dodecenoyl-CoA delta-isomerase (mitochondrial)

5.3.3.8

2/13

1

 

Dodecenoyl-CoA delta-isomerase (peroxisomal)

5.3.3.8

1/3

4

 

Cyclohex-1-enecarboxyl-CoA hydratase

NA

1/2

0

 

1,4-Dihydroxy-2-napthoyl-CoA synthase

NA

2/56

4

 

2-Ketocyclohexanecarboxyl-CoA hydrolase

NA

1/1

0

 

Crotonobetainyl-CoA hydratase

NA

2/15

0

 

Delta(3,5)-delta(2,4)-dienoyl-CoA isomerase

NA

3/24

1

 

Feruloyl-CoA hydratase/lyase

NA

5/18

0

Enolase

Enolase

4.2.1.11

215/375

20

 

Glucarate dehydratase

4.2.1.40

26/31

7

 

Galactonate dehydratase

4.2.1.6

5/27

0

 

Methylaspartate ammonia-lyase

4.3.1.2

5/8

4

 

Mandelate racemase

5.1.2.2

2/3

6

 

Muconate cycloisomerase

5.5.1.1

14/26

5

 

Chloromuconate cycloisomerase

5.5.1.7

10/15

3

 

Dipeptide epimerase

NA

2/57

3

 

Ortho-succinylbenzoate synthase

NA

6/75

4

Haloacid dehalogenase

Polynucleotide 5'-hydroxyl-kinase carboxy-terminal phosphatase

2.7.1.78

1/1

1

 

Trehalose-phosphatase

3.1.3.12

1/2

0

 

Histidinol-phosphatase

3.1.3.15

1/2

0

 

Phosphoglycolate phosphatase

3.1.3.18

1/14

0

 

Phosphoglycolate phosphatase 2

3.1.3.18

1/10

0

 

Sucrose-phosphatase

3.1.3.24

5/13

0

 

Phosphoserine phosphatase

3.1.3.3

2/56

9

 

Deoxy-D-mannose-octulosonate 8-phosphate phosphatase

3.1.3.45

2/16

2

 

5'-Nucleotidase

3.1.3.5

1/1

3

 

2-Deoxyglucose-6-phosphatase

3.1.3.68

1/2

0

 

Mannosyl-3-phosphoglycerate phosphatase

3.1.3.70

1/3

0

 

Phosphonoacetaldehyde hydrolase

3.11.1.1

3/9

6

 

P-type atpase

3.6.3.-

91/735

8

 

2-Haloacid dehalogenase

3.8.1.2

7/20

8

 

Beta-phosphoglucomutase

5.4.2.6

1/21

3

 

Pyridoxal phosphatase

NA

1/1

0

 

Enolase-phosphatase

NA

1/20

0

 

Epoxide hydrolase N-terminal phosphatase

NA

2/2

6

 

Glycerol-3-phosphate phosphatase

NA

1/3

0

 

mdp-1

NA

1/2

2

Vicinal oxygen chelate

3,4-Dihydroxyphenylacetate 2,3-dioxygenase

1.13.11.15

4/9

6

 

Catechol 2,3-dioxygenase

1.13.11.2

32/53

0

 

4-Hydroxyphenylpyruvate dioxygenase

1.13.11.27

26/69

7

 

2,3-Dihydroxybiphenyl dioxygenase

1.13.11.39

23/26

16

 

4-Hydroxymandelate synthase

1.13.11.46

1/6

0

 

Fosfomycin resistance protein FosA

2.5.1.18

2/4

6

 

Glyoxalase I

4.4.1.5

12/58

9

 

Methylmalonyl-CoA epimerase

5.1.99.1

5/9

2

 

3-Methylcatechol 2,3-dioxygenase

NA

7/10

1

 

2,6-Dichlorohydroquinone dioxygenase

NA

3/3

0

 

2,3-Dihydroxy-p-cumate-3,4-dioxygenase

NA

2/3

0

 

2,2',3-Trihydroxybiphenyl dioxygenase

NA

4/4

0

 

1,2-Dihydroxynaphthalene dioxygenase

NA

6/17

0

 

3-Isopropylcatechol-2,3-dioxygenase

NA

2/3

0

 

2,4,5-Trihydroxytoluene oxygenase

NA

2/3

0

 

Fosfomycin resistance protein FosB

NA

1/9

0

 

Fosfomycin resistance protein FosX

NA

2/4

1

  1. *Enzyme Commission Number for the primary reaction catalyzed by the family. Some families catalyze a characterized reaction for which no EC number has yet been assigned. The EC numbers for these families are designated as NA (not available).