Align Phenylacetyl-CoA:acceptor oxidoreductase small subunit PadC (characterized, see rationale)
to candidate AZOBR_RS23550 AZOBR_RS23550 tetrathionate reductase subunit B
Query= uniprot:A0A2R4BLY8 (215 letters) >FitnessBrowser__azobra:AZOBR_RS23550 Length = 250 Score = 152 bits (385), Expect = 4e-42 Identities = 82/209 (39%), Positives = 107/209 (51%), Gaps = 33/209 (15%) Query: 3 RYAMVADLRRCVGCQTCTAACKHTNATPPGVQWRWVLDVEAGEFPDVSRTFVPVGCQHCD 62 R+AMV D+R+CVGCQ CT AC N P V E E +P C HC+ Sbjct: 45 RWAMVVDVRKCVGCQACTVACIMENDVPENSFRTIVSTYEVTEQGKAGSYMLPRLCNHCE 104 Query: 63 EPPCETVCPTTATKKRADGLVTIDYDLCIGCAYCSVACPYNARYKVNFAEPAYGDRLMAN 122 +PPC VCPT AT +R DG+V +D +C+GCAYC ACPY+AR+ + + Sbjct: 105 DPPCIPVCPTGATFQRRDGIVVVDNTVCVGCAYCVQACPYDARF-------------INH 151 Query: 123 EKQRADPARVGVATKCTFCSDRIDYGVAHGLTPGVDPDATPACANACIANALTFGDIDDP 182 E Q AD KCTFC R++ G+ PAC C+ A FGD++DP Sbjct: 152 ETQTAD--------KCTFCVHRVEAGL------------LPACVETCVGGARIFGDLNDP 191 Query: 183 NSKASRLLRENEHFRMHEELGTGPGFFYL 211 +S + L+RE + E GT P FYL Sbjct: 192 DSAVATLVREENPKVLKPEQGTQPRVFYL 220 Lambda K H 0.323 0.137 0.461 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: 278 Number of extensions: 19 Number of successful extensions: 5 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: 215 Length of database: 250 Length adjustment: 23 Effective length of query: 192 Effective length of database: 227 Effective search space: 43584 Effective search space used: 43584 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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