Align Uncharacterized protein (characterized, see rationale)
to candidate CA265_RS07800 CA265_RS07800 Fe-S oxidoreductase
Query= uniprot:B2TBW0 (256 letters) >FitnessBrowser__Pedo557:CA265_RS07800 Length = 245 Score = 172 bits (437), Expect = 4e-48 Identities = 98/246 (39%), Positives = 136/246 (55%), Gaps = 15/246 (6%) Query: 10 MKVALFIPCFIDAFYPEVGIATLELLERFGIQVDYPQEQTCCGQPMANSGAHAEAAGTER 69 MKV LF+PCF+D YPE TL LLE+ G V Y +QTCCGQP N+G EA Sbjct: 1 MKVELFVPCFVDQLYPETAFNTLRLLEKSGCDVTYNSKQTCCGQPAYNAGYWDEAKEVGT 60 Query: 70 VFARNFAGYDYIVGPSASCIHHVR----EHLTALEQTDEVKKVRANAYELVEFLHDVVGA 125 F +F Y+V PSASC+ V+ + T ++ + +++N +EL +FL + V Sbjct: 61 KFLNDFTENTYVVAPSASCVGMVKGGFNDLFTNTIVHNKCRSLQSNIWELSDFLIN-VAK 119 Query: 126 REFPWAEFPHRVGLHNSCSALRHLKEASISEVAGAPFSKPRTLLEGVKGIEFVKPARPDE 185 R++ AE + H+SCSALR K +PR LL V G+E ++ D Sbjct: 120 RDYFGAELEGKAVYHDSCSALRECKIK----------DEPRQLLSKVHGLEMIEMEDTDM 169 Query: 186 CCGFGGTFSVTEEPVSVRMGQDKVRDHLNAGAEYIVSGDMSCLMHQQGCAERMKADARFI 245 CCGFGGTF+V + +S M + KV L A+YI+S D+SCL+H QG E+ + + Sbjct: 170 CCGFGGTFAVKFDAISSAMAEQKVNHALAQQADYIISTDLSCLLHLQGYIEKNNLPIKTM 229 Query: 246 HIAQVL 251 HIA VL Sbjct: 230 HIADVL 235 Lambda K H 0.323 0.137 0.422 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 173 Number of extensions: 7 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 256 Length of database: 245 Length adjustment: 24 Effective length of query: 232 Effective length of database: 221 Effective search space: 51272 Effective search space used: 51272 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory