Predicting genes for orphan metabolic activities using phylogenetic profiles

Table 1 Performance of our method with Escherichia coli orphan activities without independent sequence homology information

EC number	Description	Responsible gene	Rank
1.14.11.17	Taurine dioxygenase	b0368/tauD	1,143
1.1.1.251	Fructose 6-phosphate aldolase	b0825/fsa	1
1.1.1.264	L-idonate 5-dehydrogenase	b4267/idnD	44.5
1.2.1.22	Lactaldehyde dehydrogenase	b0356/adhC	1
1.2.1.22	Lactaldehyde dehydrogenase	b1241/adhE	18
1.2.1.22	Lactaldehyde dehydrogenase	b3588/aldB	208
1.2.1.22	Lactaldehyde dehydrogenase	b1415/aldA	654
1.2.2.2	Pyruvate oxidase	b0871/poxB	1,451
1.2.1.39	Phenylacetaldehyde dehydrogenase	b1385/feaB	1
1.1.1.57	Mannonate oxidoreductase	b4323/uxuB	71.5
1.1.1.77	Lacaldehyde reductase	b2799/fucO	10
2.7.1.130	Tetraacyldisaccharide 4'kinase	b0915/lpxK	1,507
2.6.1.66	Valine-pyruvate aminotransferase	b3572/avtA	70.5
2.7.1.58	2-Dehydro-3-deoxygalactonokinase	b3693/dgoK	68
2.7.1.73	Insosine kinase	b0477/gsk	1,041
3.2.2.4	AMP nucleosidase	b1982/amn	69
2.7.7.58	2,3-Dihydroxybenzoate adenylate synthase	b0594/entE	30
4.1.2.20	5-Dehydro-4-deoxyglucarate aldolase	b3126/garL	2,057.5
4.1.1.41	Methylmalonyl-CoA decarboxylase	b2919/ygfG	889
4.1.1.47	Glyoxalate carboligase	b0507/gcl	1
4.2.1.42	Galactarate dehydratase	b3128/garD	757
4.2.1.6	galactonate dehydratase	b3692/dgoA	1,841.5
4.2.1.7	Altronate hydrolase	b3091/uxaA	25
5.3.1.22	Hydroxypyruvate isomerase	b0508/hyi	33
6.2.1.30	Phenylacetate-CoA ligase	b1398/paaK	9

The subset of orphan activities, identified using the SWISS-PROT database [37], includes EC numbers with representative sequences exclusively from E. coli. We also included EC numbers with representative sequences in the TrEMBL database, but only if these were computationally annotated from E. coli sequences.

ISSN: 1474-760X