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Table 2
*List of ORFs in E. coli* with updated annotations based on sequence similarity**
EC number	Bnum	Gene	Published annotation [12]	Suggested annotation

1.1.1.48	b1315	ycjS	Putative NADH-dependent dehydrogenase	D-Galactose 1-dehydrogenase
1.1.1.48	b1624	*ydgJ*	Putative NAD(P)-binding dehydrogenase	D-Galactose 1-dehydrogenase
1.1.1.48	b3440	*yhhX*	Putative NAD(P)-binding dehydrogenase	D-Galactose 1-dehydrogenase
1.1.1.5	b2426	ucpA	Putative oxidoreductase, NAD(P)-binding	Acetoin dehydrogenase, diacetyl reductase
1.1.1.5	b2137	yohF	Putative oxidoreductase	Acetoin dehydrogenase, diacetyl reductase
1.1.1.5	b4266	idnO	5-Keto-D-gluconate-5-reductase	Acetoin dehydrogenase, diacetyl reductase
1.2.1.19	b1385	feaB	Phenylacetaldehyde dehydrogenase	Aminobutyraldehyde dehydrogenase
1.2.1.19	b1444	ydcW	Putative aldehyde dehydrogenase	Aminobutyraldehyde dehydrogenase
1.2.1.19	b3588	aldB	Aldehyde dehydrogenase B (lactaldehyde dehydrogenase)	Aminobutyraldehyde dehydrogenase
1.2.1.24	b1385	feaB	Phenylacetaldehyde dehydrogenase	Succinate-semialdehyde dehydrogenase
1.2.1.24	b1444	ydcW	Putative aldehyde dehydrogenase	Succinate-semialdehyde dehydrogenase
1.2.1.24	b1415	aldA	Aldehyde dehydrogenase A, NAD-linked	Succinate-semialdehyde dehydrogenase
1.2.7.1	b1378	nifJ	Putative pyruvate-flavodoxin oxidoreductase	Pyruvate synthase
1.3.1.2	b2146	*yeiT*	Putative glutamate synthase	Dihydrothymine dehydrogenase
1.3.1.2	b2147	*yeiA*	Putative dihydropyrimidine dehydrogenase, FMN-linked	Dihydrothymine dehydrogenase
1.3.1.2	b2878	*b2878*	Putative oxidoreductase	Dihydrothymine dehydrogenase
1.3.99.3	b1695	ydiO	Putative acyl-CoA dehydrogenase	Acyl-CoA dehydrogenase
1.3.99.3	b0039	caiA	Putative acyl-CoA dehydrogenase, carnitine metabolism	Acyl-CoA dehydrogenase
1.3.99.3	b4187	aidB	Putative acyl-CoA dehydrogenase; adaptive response (transcription activated by Ada)	Acyl-CoA dehydrogenase
1.6.6.9	b3551	bisC	Biotin sulfoxide reductase	Trimethylamine-N-oxide reductase (TMAO reductase II)
1.6.6.9	b1587	b1587	Putative reductase	Trimethylamine-N-oxide reductase (TMAO reductase II)
1.6.6.9	b1588	b1588	Putative reductase	Trimethylamine-N-oxide reductase (TMAO reductase II)
1.6.99.2	b0046	yabF	Putative electron transfer flavoprotein-NAD/FAD/quinone oxidoreductase, subunit for KefC K+ efflux system	NAD(P)H dehydrogenase
1.6.99.2	b3351	yheR	Putative electron transfer flavoprotein-NAD/FAD/quinone oxidoreductase	NAD(P)H dehydrogenase
1.6.99.2	b0901	ycaK	Putative electron transfer flavoprotein-NAD/FAD/quinone oxidoreductase	NAD(P)H dehydrogenase
2.3.3.11 (formerly 4.1.3.9)	b2264	*menD*	Bifunctional modular MenD: 2-oxoglutarate decarboxylase and SHCHC synthase	2-Hydroxyglutarate synthase
2.3.3.11 (formerly 4.1.3.9)	b3671	*ilvB*	Acetolactate synthase I, large subunit, valine-sensitive, FAD and thiamine PPi binding	2-Hydroxyglutarate synthase
2.7.1.23	b2615	yfjB	Conserved protein	NAD+ kinase
2.7.1.23	b3916	pfkA	6-phosphofructokinase I	NAD+ kinase
2.7.2.1	b3115	tdcD	Propionate kinase/acetate kinase II, anaerobic	Acetate kinase (ackB)
2.7.8.2	b1408	*b1408*	Putative enzyme	Diacylglycerol cholinephosphotransferase
2.8.1.2	b2521	sseA	Putative sulfurtransferase	3-Mercaptopyruvate sulfurtransferase
2.8.1.2	b1757	ynjE	Putative thiosulfate sulfur transferase	3-Mercaptopyruvate sulfurtransferase
2.8.3.8	b2222	atoA	Acetyl-CoA:acetoacetyl-CoA transferase, beta subunit	Acetate CoA-transferase
2.8.3.8	b2221	atoD	Acetyl-CoA:acetoacetyl-CoA transferase, alpha subunit	Acetate CoA-transferase
2.8.3.8	b1694	ydiF	Putative acetyl-CoA:acetoacetyl-CoA transferase alpha subunit	Acetate CoA-transferase
3.1.1.31	b0678	nagB	Glucosamine-6-phosphate deaminase	6-Phosphogluconolactonase (Pgl)
3.1.1.31	b3718	yieK	Putative isomerase	6-Phosphogluconolactonase (Pgl)
3.1.1.31	b3141	agaI	Putative galactosamine-6-phosphate isomerase	6-Phosphogluconolactonase (Pgl)
3.2.1.68	b3431	glgX	Glycosyl hydrolase	Isoamylase
3.5.1.2	b1524	yneH	Putative glutaminase	Glutaminase A or B
3.5.1.2	b0485	ybaS	Putative glutaminase	Glutaminase A or B
3.6.1.19	b2954	*yggV*	Conserved hypothetical protein	Nucleoside-triphosphate (ITP) diphosphatase
3.6.1.22	b3996	yjaD	Conserved hypothetical protein, MutT-like protein	NAD+ diphosphatase
3.6.1.5	b3615	*yibD*	Putative glycosyltransferase	Inosine triphosphate diphosphatase
3.6.1.6	b3614	*yibQ*	Conserved hypothetical protein	Nucleoside (IDP) diphosphatase
4.1.1.39	b3615	*yibD*	Putative glycosyltransferase	Ribulose-bisphosphate carboxylase (2-phosphoglycolate forming)
4.1.2.10	b0311	*betA*	Choline dehydrogenase, a flavoprotein	Hydroxynitrile lyase
4.1.2.10	b3168	*infB*	Protein chain initiation factor IF-2	Hydroxynitrile lyase
4.2.1.66	b3022	*ygiU*	Conserved protein	Cyanide hydratase
6.2.1.12	b4069	*acs*	Acetyl-CoA synthetase	Hydroxycinnamate-CoA ligase
6.2.1.12	b1701	*ydiD*	Putative CoA-dependent ligase	Hydroxycinnamate-CoA ligase
6.2.1.12	b2836	*aas*	bifunctional multimodular Aas: 2-acylglycerophospho-ethanolamine acyl transferase	Hydroxycinnamate-CoA ligase
6.2.1.4	b0728	*sucC*	Succinyl-CoA synthetase, beta subunit	Succinate-CoA ligase (ITP forming)
6.2.1.4	b0729	*sucD*	Succinyl-CoA synthetase, alpha subunit, NAD(P) binding	Succinate-CoA ligase (ITP forming)

Annotations shown in bold arose from analyzing the network gaps in iJR904.
Reed et al. Genome Biology 2003 4:R54 doi:10.1186/gb-2003-4-9-r54

Table 2