Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function

Table 1 Top scoring Partial Phylogenetic Profiling results for urea utilization vs. Corynebacterium glutamicum ATCC 13032, based on 117 TRUE genomes and 235 FALSE genomes.

PPP score^a	TRUE	Depth	Locus	Protein
45.4	95	95	NCgl0083	urease, gamma subunit UreA
45.4	95	95	NCgl0085	urease, alpha subunit UreC
45.4	95	95	NCgl0088	urease accessory protein UreG
44.9	94	95	NCgl0084	urease, beta subunit UreB
39.2	82	82	NCgl0087	urease accessory protein UreF
34.9	73	73	NCgl0089	urease accessory protein UreH
28.5	66	68	NCgl0894	urea ABC transporter, permease subunit UrtB
28.2	59	59	NCgl0895	urea ABC transporter, permease subunit UrtC
26.9	65	68	NCgl0893	urea ABC transporter, substrate-binding UrtA
24.1	59	62	NCgl0896	urea ABC transporter, ATPase subunit UrtD
19.5	55	61	NCgl0897	urea ABC transporter, ATPase subunit UrtE

a) PPP scores are reported as the optimal negative log odds against observing the indicated number of hits to the TRUE profile at the indicated search depth.

ISSN: 1471-2105