Suplementary information for:   

                                               

David M. Kristensen*, R. Matthew Ward*, Andreas Martin Lisewski, Serkan Erdin, Brian Y. Chen, Viacheslav Y. Fofanov, Marek Kimmel, Lydia E. Kavraki, and Olivier Lichtarge. (2007). "Prediction of Enzyme Function Based on 3D Templates of Evolutionarily Important Amino Acids". BMC Bioinformatics. (Accepted).
*These authors contributed equally to this work.

 

Table 1 - Training Set:

Protein

E.C. #

SCOP Class

SCOP Fold

Function

1rie_

1.10.2.2

b

ISP domain

RIESKE IRON-SULFUR PROTEIN

1mgtA

2.1.1.63

a,a/b

DNA/RNA-binding 3-helical bundle Ribonuclease H-like motif

O6-METHYLGUANINE-DNA METHYLTRANSFERASE

1eg2A

2.1.1.72

a/b

S-adenosyl-L-methionine-dependent methyltransferases

MODIFICATION METHYLASE RSRI

7mhtA

2.1.1.73

a/b

S-adenosyl-L-methionine-dependent methyltransferases

CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI

1jg1A

2.1.1.77

a/b

S-adenosyl-L-methionine-dependent methyltransferases

PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE

1kpgA

2.1.1.79

a/b

S-adenosyl-L-methionine-dependent methyltransferases

CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 1

1inlB

2.5.1.16

a/b

S-adenosyl-L-methionine-dependent methyltransferases

SPERMIDINE SYNTHASE

1g64B

2.5.1.17

a/b

P-loop containing nucleoside triphosphate hydrolases

COB(I)ALAMIN ADENOSYLTRANSFERASE

1e6bA

2.5.1.18

a,a/b

Glutathione S-transferase (GST), C-terminal domain Thioredo

GLUTATHIONE S-TRANSFERASE

1f2eA

2.5.1.18

a,a/b

Glutathione S-transferase (GST), C-terminal domain Thioredo

GLUTATHIONE S-TRANSFERASE

1gsfA

2.5.1.18

a,a/b

Glutathione S-transferase (GST), C-terminal domain Thioredo

GLUTATHIONE TRANSFERASE A1-1

6gsvA

2.5.1.18

a,a/b

Glutathione S-transferase (GST), C-terminal domain Thioredo

MU CLASS GLUTATHIONE S-TRANSFERASE OF ISOENZYME 3-3

1bdyA

2.7.1.37

b

PH domain-like

PROTEIN KINASE C

1iasA

2.7.1.37

small

Cystine-knot cytokines

TGF-BETA RECEPTOR TYPE I

1qf8A

2.7.1.37

b

Galactose-binding domain-like

CASEIN KINASE II

1rgs_

2.7.1.37

b

C2 domain-like

CAMP DEPENDENT PROTEIN KINASE

1b55B

2.7.1.112

a+b

Protein kinase-like (PK-like)

TYROSINE-PROTEIN KINASE BTK

1fltW

2.7.1.112

small

Rubredoxin-like

VASCULAR ENDOTHELIAL GROWTH FACTOR

1nukA

2.7.1.112

 

 

TYROSINE-PROTEIN KINASE RECEPTOR EPH

1nksA

2.7.4.3

a/b

P-loop containing nucleoside triphosphate hydrolases

ADENYLATE KINASE

1nskL

2.7.4.6

a+b

Ferredoxin-like

NUCLEOSIDE DIPHOSPHATE KINASE

1jxiA

2.7.4.7

a/b

Ribokinase-like

PHOSPHOMETHYLPYRIMIDINE KINASE

1c25_

3.1.3.48

a/b

Rhodanese/Cell cycle control phosphatase

CDC25A

1gwz_

3.1.3.48

a/b

(Phosphotyrosine protein) phosphatases II

SHP-1

1j4xA

3.1.3.48

a/b

(Phosphotyrosine protein) phosphatases II

DUAL SPECIFICITY PROTEIN PHOSPHATASE 3

1cen_

3.2.1.4

b,a/b

WW domain-like TIM beta/alpha-barrel FKBP-like

CELLULASE CELC

1edg_

3.2.1.4

b

Single-stranded right-handed beta-helix

ENDOGLUCANASE A

2nlrA

3.2.1.4

a+b

Lysozyme-like

ENDOGLUCANASE

7a3hA

3.2.1.4

a+b

Lysozyme-like

ENDOGLUCANASE

1i8a_

3.2.1.8

b

6-bladed beta-propeller

ENDO-1,4-BETA-XYLANASE A

1ukrA

3.2.1.8

a/b

TIM beta/alpha-barrel

ENDO-1,4-B-XYLANASE I

1goiA

3.2.1.14

a/b

TIM beta/alpha-barrel

CHITINASE B

1czfA

3.2.1.15

b

Concanavalin A-like lectins/glucanases

POLYGALACTURONASE II

1d9uA

3.2.1.17

a/b

TIM beta/alpha-barrel

BACTERIOPHAGE LAMBDA LYSOZYME

3lzt_

3.2.1.17

 

 

LYSOZYME

1f8eA

3.2.1.18

b

Concanavalin A-like lectins/glucanases

NEURAMINIDASE

1fr6A

3.5.2.6

mult

beta-lactamase/transpeptidase-like

BETA-LACTAMASE

1k55A

3.5.2.6

mult

beta-lactamase/transpeptidase-like

BETA LACTAMASE OXA-10

1pioA

3.5.2.6

mult

beta-lactamase/transpeptidase-like

BETA-LACTAMASE

1juk_

4.1.1.48

a/b

TIM beta/alpha-barrel

INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE

1ayl_

4.1.1.49

 

 

PHOSPHOENOLPYRUVATE CARBOXYKINASE

1jl0B

4.1.1.50

a+b

S-adenosylmethionine decarboxylase

S-ADENOSYLMETHIONINE DECARBOXYLASE PROENZYME

2ahjA

4.2.1.84

a+b

Nitrile hydratase alpha chain

NITRILE HYDRATASE

1dcpA

4.2.1.96

a+b

DCoH-like

DCOH

1ep0A

5.1.3.13

b

Double-stranded beta-helix

DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE

1eq2H

5.1.3.20

a/b

NAD(P)-binding Rossmann-fold domains

ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE

1a41_

5.99.1.2

a+b

DNA breaking-rejoining enzymes

TOPOISOMERASE I

1cy4A

5.99.1.2

mult

Prokaryotic type I DNA topoisomerase

DNA TOPOISOMERASE I

1ej9A

5.99.1.2

a+b,mult

DNA breaking-rejoining enzymes Eukaryotic DNA topoisomerase

DNA TOPOISOMERASE I

1vcc_

5.99.1.2

a+b

DNA topoisomerase I domain

DNA TOPOISOMERASE I

1fpmA

6.3.4.3

a/b

P-loop containing nucleoside triphosphate hydrolases

FORMATE--TETRAHYDROFOLATE LIGASE

1dj3A

6.3.4.4

a/b

P-loop containing nucleoside triphosphate hydrolases

ADENYLOSUCCINATE SYNTHETASE

1k92A

6.3.4.5

a/b,a+b

Adenine nucleotide alpha hydrolase-like Argininosuccinate s

ARGININOSUCCINATE SYNTHASE

                                               

Table 2 - PDB Set:

Protein

E.C. #

SCOP Class

SCOP Fold

Function

1hdoA

1.3.1.24

a/b

NAD(P)-binding Rossmann-fold domains

BILIVERDIN IX BETA REDUCTASE

1b26A

1.4.1.3

a/b

NAD(P)-binding Rossmann-fold domains

GLUTAMATE DEHYDROGENASE

1kmvA

1.5.1.3

a/b

Dihydrofolate reductases

DIHYDROFOLATE REDUCTASES, EUKARYOTIC TYPE

1l1dA

1.8.4.5

b

Mss4-like

C-TERMINAL MSRB DOMAIN OF PEPTIDE METHIONINE SULFOXIDE REDUCTASE PILB

1v54J

1.9.3.1

mem

Single transmembrane helix

MITOCHONDRIAL CYTOCHROME C OXIDASE SUBUNIT VIIA

1eb7A

1.11.1.5

a

Cytochrome c

DI-HEME CYTOCHROME C PEROXIDASE

1lycA

1.11.1.7

a

Heme-dependent peroxidases

FUNGAL PEROXIDASE (LIGNINASE)

1hqi_

1.14.13.7

a+b

Monooxygenase (hydroxylase) regulatory protein

PHENOL HYDROXYLASE P2 PROTEIN

1oykA

1.14.99.3

a

Heme oxygenase-like

HEME OXYGENASE-1 (HO-1)

1m1nA

1.18.6.1

a/b

Chelatase-like

NITROGENASE IRON-MOLYBDENUM PROTEIN, ALPHA CHAIN

1orhA

2.1.1.125

a/b

S-adenosyl-L-methionine-dependent methyltransferases

PROTEIN ARGININE N-METHYLTRANSFERASE 1, PRMT1

1ib1A

2.3.1.87

a

alpha-alpha superhelix

14-3-3 PROTEIN, ZETA ISOFORM

1o7qA

2.4.1.151

a/b

Nucleotide-diphospho-sugar transferases

ALPHA-1,3-GALACTOSYLTRANSFERASE CATALYTIC DOMAIN

1nh7A

2.4.2.17

a/b

Periplasmic binding protein-like II

ATP PHOSPHORIBOSYLTRANSFERASE (ATP-PRTASE, HISG), CATALYTIC DOMAIN

1fsgA

2.4.2.8

a/b

PRTase-like

HYPOXANTHINE-GUANINE-XANTHINE PRTASE

6pfkA

2.7.1.11

a/b

Phosphofructokinase

ATP-DEPENDENT PHOSPHOFRUCTOKINASE

1r79A

2.7.1.107

small

Cysteine-rich domain

DIACYLGLYCEROL KINASE DELTA

1bx4A

2.7.1.20

a/b

Ribokinase-like

ADENOSINE KINASE

1rdqE

2.7.1.37

a+b

Protein kinase-like (PK-like)

CAMP-DEPENDENT PK, CATALYTIC SUBUNIT

1pdo_

2.7.1.69

a/b

IIA domain of mannose transporter, IIA-Man

IA DOMAIN OF MANNOSE TRANSPORTER, IIA-MAN

1m15A

2.7.3.3

a

Guanido kinase N-terminal domain

ARGININE KINASE, N-DOMAIN

1jxiA

2.7.4.7

a/b

Ribokinase-like

HMP-PHOSPHATE KINASE, THID

1ef4A

2.7.7.6

a

DNA/RNA-binding 3-helical bundle

RNA POLYMERASE SUBUNIT RPB10

1p16A

2.7.7.50

a+b

ATP-grasp

MRNA CAPPING ENZYME ALPHA SUBUNIT

1f7lA

2.7.8.7

a+b

4'-phosphopantetheinyl transferase

HOLO-(ACYL CARRIER PROTEIN) SYNTHASE ACPS

1okgA

2.8.1.2

a+b

FKBP-like

3-MERCAPTOPYRUVATE SULFURTRANSFERASE

1ksjB

3.1.4.17

b

Immunoglobulin-like beta-sandwich

GMP-PDE DELTA

1jl1A

3.1.26.4

a/b

Ribonuclease H-like motif

RNASE H (RNASE HI)

1i0vA

3.1.27.3

a+b

Microbial ribonucleases

RNASE T1

1hx0A

3.2.1.1

a/b

TIM beta/alpha-barrel

ANIMAL ALPHA-AMYLASE

1ks8A

3.2.1.4

a

alpha/alpha toroid

ENDO-B-1,4-GLUCANASE

3sil_

3.2.1.18

b

6-bladed beta-propeller

SALMONELLA SIALIDASE

1es5A

3.4.16.4

mult

beta-lactamase/transpeptidase-like

D-ALA CARBOXYPEPTIDASE/TRANSPEPTIDASE

1bcrA

3.4.16.6

a/b

alpha/beta-Hydrolases

SERINE CARBOXYPEPTIDASE II

1pq7A

3.4.21.4

b

Trypsin-like serine proteases

TRYPSIN(OGEN)

2hrvA

3.4.22.29

b

Trypsin-like serine proteases

2A CYSTEINE PROTEINASE

1gk9A

3.5.1.11

a+b

Ntn hydrolase-like

PENICILLIN ACYLASE

1uf4A

3.5.1.77

a+b

Carbon-nitrogen hydrolase

N-CARBAMOYL-D-AMINOACID AMIDOHYDROLASE

1sg3A

3.5.3.4

b

Galactose-binding domain-like

ALLANTOICASE

1i40A

3.6.1.1

b

OB-fold

INORGANIC PYROPHOSPHATASE

1opzA

3.6.3.4

a+b

Ferredoxin-like

POTENTIAL COPPER-TRANSLOCATING P-TYPE ATPASE COPA (YVGX)

1hxgA

4.1.99.7

a

alpha/alpha toroid

5-EPI-ARISTOLOCHENE SYNTHASE

1iv3A

4.6.1.12

a+b

Bacillus chorismate mutase-like

2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE ISPF

1pinA

5.2.1.8

a+b

FKBP-like

MITOTIC ROTAMASE PIN1, DOMAIN 2

1dl3A

5.3.1.24

a/b

TIM beta/alpha-barrel

N-(5'PHOSPHORIBOSYL)ANTRANILATE ISOMERASE, PRAI

1fztA

5.4.2.1

a/b

Phosphoglycerate mutase-like

PHOSPHOGLYCERATE MUTASE

1n3lA

6.1.1.1

a/b

Adenine nucleotide alpha hydrolase-like

TYROSYL-TRNA SYNTHETASE (TYRRS)

1pfvA

6.1.1.10

a/b

Adenine nucleotide alpha hydrolase-like

METHIONYL-TRNA SYNTHETASE (METRS)

1sbqA

6.3.3.2

a/b

NagB/RpiA/CoA transferase-like

5,10-METHENYLTETRAHYDROFOLATE SYNTHETASE HOMOLOG MPN348

                                               

Table 3 - PSI Set:

Protein

E.C. #

SCOP Class

SCOP Fold

Function

1z82A

1.1.1.8

-

not available

GLYCEROL-3-PHOSPHATE DEHYDROGENASE

1nvtA

1.1.1.25

a/b

Aminoacid dehydrogenase-like, N-terminal domain

SHIKIMATE 5-DEHYDROGENASE AROE

1zejA

1.1.1.35

-

not available

3-HYDROXYACYL-COA DEHYDROGENASE

1spxA

1.1.1.47

a/b

NAD(P)-binding Rossmann-fold domains

GLUCOSE DEHYDROGENASE

1yb4A

1.1.1.60

-

not available

TARTRONIC SEMIALDEHYDE REDUCTASE

2amfA

1.2.1.5

-

not available

1-PYRROLINE-5-CARBOXYLATE REDUCTASE

1txnA

1.3.3.3

-

not available

COPROPORPHYRINOGEN III OXIDASE

1vllA

1.4.1.1

a/b

NAD(P)-binding Rossmann-fold domains

ARCHAEAL ALANINE DEHYDROGENASE

1ooeA

1.6.99.7

a/b

NAD(P)-binding Rossmann-fold domains

DIHYDROPTERIDIN REDUCTASE (PTERIDINE REDUCTASE)

1nni1

1.7.1.6

a/b

Flavodoxin-like

AZOBENZENE REDUCTASE

1p91A

2.1.1.51

a/b

S-adenosyl-L-methionine-dependent methyltransferases

RRNA METHYLTRANSFERASE RLMA

2ar0A

2.1.1.72

-

not available

TYPE I RESTRICTION ENZYME ECOKI M PROTEIN

1vloA

2.1.2.10

a+b

Aminomethyltransferase folate-binding domain

GLYCINE CLEAVAGE SYSTEM T PROTEIN, GCVT

1vlvA

2.1.3.3

a/b

ATC-like

ORNITHINE TRANSCARBAMOYLASE

1vmiA

2.3.1.8

-

not available

PUTATIVE PHOSPHATE ACETYLTRANSFERASE

1vlpA

2.4.2.11

a+b

alpha/beta-Hammerhead

NICOTINATE PHOSPHORIBOSYLTRANSFERASE, C-TERMINAL DOMAIN

1yirA

2.4.2.11

-

not available

NICOTINATE PHOSPHORIBOSYLTRANSFERASE 2

1xi3A

2.5.1.3

a/b

TIM beta/alpha-barrel

THIAMIN PHOSPHATE SYNTHASE

1iy9A

2.5.1.16

a/b

S-adenosyl-L-methionine-dependent methyltransferases

SPERMIDINE SYNTHASE

1vjoA

2.6.1.44

a/b

PLP-dependent transferases

ALANINE-GLYOXYLATE AMINOTRANSFERASE

1xx6A

2.7.1.21

-

not available

THYMIDINE KINASE

1kagA

2.7.1.71

a/b

P-loop containing nucleoside triphosphate hydrolases

SHIKIMATE KINASE (AROK)

2akoA

2.7.2.11

-

not available

GLUTAMATE 5-KINASE

1ej2A

2.7.7.1

a/b

Adenine nucleotide alpha hydrolase-like

NICOTINAMIDE MONONUCLEOTIDE (NMN) ADENYLYLTRANSFERASE

1r1dA

3.1.1.1

a/b

alpha/beta-Hydrolases

CARBOXYLESTERASE

1vl1A

3.1.1.31

a/b

NagB/RpiA/CoA transferase-like

6-PHOSPHOGLUCONOLACTONASE

1vjvA

3.1.2.15

a+b

Cysteine proteinases

UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 6

1xm8A

3.1.2.6

-

not available

GLYOXALASE II

1vr0A

3.1.3.71

-

not available

PROBABLE 2-PHOSPHOSULFOLACTATE PHOSPHATASE

1nxcA

3.2.1.113

a

alpha/alpha toroid

CLASS I ALPHA-1;2-MANNOSIDASE, CATALYTIC DOMAIN

1o0xA

3.4.11.18

a+b

Creatinase/aminopeptidase

METHIONINE AMINOPEPTIDASE

1o59A

3.5.3.4

b

Galactose-binding domain-like

ALLANTOICASE

1xfkA

3.5.3.8

-

not available

FORMIMIDOYLGLUTAMASE

1xsrA

3.5.3.19

-

not available

UREIDOGLYCOLATE HYDROLASE

1yvwA

3.6.1.31

-

not available

PHOSPHORIBOSYL-ATP PYROPHOSPHATASE

1tufA

4.1.1.20

a/b

TIM beta/alpha-barrel

DIAMINOPIMELATE DECARBOXYLASE LYSA

1fi4A

4.1.1.33

a+b

Ribosomal protein S5 domain 2-like

MEVALONATE 5-DIPHOSPHATE DECARBOXYLASE

1vpjA

4.2.1.2

-

not available

FUMARASE

1kmjA

4.4.1.16

a/b

PLP-dependent transferases

NIFS-LIKE PROTEIN/SELENOCYSTEINE LYASE

1kmkA

4.4.1.16

a/b

PLP-dependent transferases

NIFS-LIKE PROTEIN/SELENOCYSTEINE LYASE

1y0eA

5.1.3.9

-

not available

PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE

1o8bA

5.3.1.6

a/b

NagB/RpiA/CoA transferase-like

D-RIBOSE-5-PHOSPHATE ISOMERASE (RPIA), CATALYTIC DOMAIN

1x8mA

5.3.1.17

b

Double-stranded beta-helix

5-KETO-4-DEOXYURONATE ISOMERASE KDUI

1ou0A

5.4.1.2

a/b

Flavodoxin-like

PRECORRIN-8X METHYLMUTASE RELATED PROTEIN

1m0tA

6.3.2.3

a+b

ATP-grasp

EUKARYOTIC GLUTATHIONE SYNTHETASE

1kutA

6.3.2.6

a+b

SAICAR synthase-like

SAICAR SYNTHASE

1pzvA

6.3.2.19

a+b

UBC-like

UBIQUITIN CONJUGATING ENZYME, UBC

1vl2A

6.3.4.5

a+b

Argininosuccinate synthetase, C-terminal domain

ARGININOSUCCINATE SYNTHETASE

1vkzA

6.3.4.13

a+b

ATP-grasp

GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE (GAR-SYN)

 

Table 4: PSI Set Voting as sequence identity threshold of matched target pairs decreases.

Sequence Identity Cutoff

Correct Votes

Incorrect Votes

No Vote Winners

100

22

6

21

80

22

6

21

60

22

5

22

40

20

5

24

35

20

5

24

30

20

5

24

25

20

6

23

20

19

6

24

15

19

7

23

10

21

13

15

5

21

13

15