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