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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)

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

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)
  1. Proteins related to [FeFe]-hydrogenase are marked in boldface.
  2. 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PPP as the negative logarithm of P-value. 6TIGRFAMs and Pfam models were used because existing GenBank annotations were out of date.