ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process

Table 3 Top 10 hits from DPPP at in Shewanella sp. MR-4, with the [FeFe] hydrogenase maturation GTP-binding protein HydF (GI:113971588) as query, at a query protein BLAST hits depth of 210 (finding 200 genomes)

GI number¹	YES genomes²	Total genomes³	BLAST depth⁴	Score⁵	HMM-based protein annotation⁶
113971588	200	200	209	172.61	[FeFe] hydrogenase H-cluster maturation GTPase HydF (TIGR03918)
113971587	189	189	206	163.11	[FeFe] hydrogenase H-cluster radical SAM maturase HydE (TIGR03956)
113971585	179	180	187	152.29	[FeFe] hydrogenase H-cluster radical SAM maturase HydG (TIGR03955)
113971582	191	218	485	132.19	iron hydrogenase, large subunit (TIGR02512)
113971583	159	176	272	115.03	iron hydrogenase, small subunit (PF02256)
113970224	194	336	613	78.43	thiazole biosynthesis protein ThiH (TIGR02351)
113971167	169	320	480	60.69	hydroxylamine reductase (TIGR01703)
113971205	181	374	603	57.37	radical SAM protein (TIGR01212)
113971473	161	327	484	52.43	peptidase, U32 family (PF01136)
113971082	132	240	843	50.34	MATE domain protein (PF01554)

Proteins related to [FeFe]-hydrogenase are marked in boldface.
¹NCBI GI. ²"YES" denotes number of unique taxa common to query profile and the target BLAST hit list. ³The total number of unique taxa found in the target BLAST list at the level that gives the best PPP score. ⁴The depth in the target BLAST list that give the best PPP score, which may reflect multiple hits in some genomes. ⁵Score reported by PPP as the negative logarithm of P-value. ⁶TIGRFAMs and Pfam models were used because existing GenBank annotations were out of date.

ISSN: 1471-2105