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.
|
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 |
|
|
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 |
|
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 |
|
|
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) |
|
|
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 |
|
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) |
|
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 |