Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family

Table 2 Partial phylogenetic profiling (PPP) results

Chlorobium luteolum
78186745	8	8	16	-16.124	NHLP
78186739	9	19	26	-13.212	Trans
78186738	9	22	29	-12.492	Trans-Cleave
78186736	8	16	17	12.045	Trans-Fuse
78187852	10	95	123	-7.475	(PAS domain)
Nostoc sp. PCC 7120
17229519	9	9	23	-18.140	NHLP
17229518	11	21	38	-16.662	NHLP
17229516	8	8	23	-16.124	NHLP
17233313	10	20	26	-14.927	Trans
17229512	10	20	26	-14.927	Trans
17229513	11	33	42	-13.969	Trans-Cleave
17233311	10	25	31	-13.698	Trans-Cleave
17229514	9	24	33	-12.080	Trans-Fuse
17233314	9	26	35	-11.709	Trans-Fuse
17228094	7	19	27	-9.451	(S-layer homol.)
Microscilla marina ATCC 23134
123986279	9	16	23	-14.108	Trans
123988060	9	21	28	-12.717	Trans-Cleave
123988059	7	10	14	-12.041	Trans-Fuse
123992175	8	29	54	-9.570	(HAMP domain)
Victivallis vadensis ATCC BAA-548
150259686	8	10	16	-14.479	Trans-Fuse
150259687	9	17	24	-13.784	Trans-Cleave
150259688	8	13	20	-13.033	Trans
150259679	6	6	15	-12.093	NHLP
150259681	5	6	8	-9.303	NHLP
150259680	4	4	6	-8.062	NHLP
150257768	10	88	119	-7.798	(GAF domain)

This table shows the results of PPP, where the profile contains 14 'YES' genomes having proteins recognized by TIGR03793, about 1% of genomes and 1437 'NO' genomes. PPP scores each protein by selecting a BLAST score cutoff that gives the best possible fit between YES genomes in the profile and the set of genomes in the BLAST hits list, then scoring the fit at that depth. Columns, from left to right, are gi number, number of YES genomes encountered at the optimal depth, the total number of genomes at that depth, and the number of proteins at that depth (which can differ from the total number of genomes because several proteins may come from the same genome), the PPP score (a negative logarithm from the binomial distribution), and the protein family abbreviation. As PPP scores are not corrected for taxonomic relationships between species, scores are for comparison within each genome only and are shown down to the first noise hit. Results are shown in boldface except for noise hits. Note: Microscilla marina ATCC 23134 contains the nitrile hydratase leader peptide (NHLP) protein, 123988058, which is not detected by PPP. This gene is found co-clustered with the transport proteins identified by PPP, as shown.

ISSN: 1741-7007