Align Phenylacetyl-CoA:acceptor oxidoreductase small subunit PadC (characterized, see rationale)
to candidate BWI76_RS15930 BWI76_RS15930 dimethylsulfoxide reductase, chain B
Query= uniprot:A0A2R4BLY8 (215 letters) >FitnessBrowser__Koxy:BWI76_RS15930 Length = 205 Score = 109 bits (272), Expect = 4e-29 Identities = 61/195 (31%), Positives = 85/195 (43%), Gaps = 41/195 (21%) Query: 3 RYAMVADLRRCVGCQTCTAACKHTNATPPGVQWRWVLDVEAGEFPD--------VSRTFV 54 +Y D RC GC+TC ACK P V + + + G++ + V ++ Sbjct: 4 QYGFFIDSARCTGCKTCELACKDYKNLTPDVSFHRIYEYAGGDWQEDNGVWNQNVFAYYL 63 Query: 55 PVGCQHCDEPPCETVCPTTATKKRADGLVTIDYDLCIGCAYCSVACPYNARYKVNFAEPA 114 + C HC++P C VCP+ A KR DG V ++ ++CIGC YC +ACPY A P Sbjct: 64 SIACNHCEDPACTKVCPSGAMHKRDDGFVVVNEEVCIGCRYCHMACPYGA--------PQ 115 Query: 115 YGDRLMANEKQRADPARVGVATKCTFCSDRIDYGVAHGLTPGVDPDATPACANACIANAL 174 Y A G TKC C DR+ G P C +C AL Sbjct: 116 YN-------------AAKGHMTKCDGCYDRVADG------------KKPICVESCPLRAL 150 Query: 175 TFGDIDDPNSKASRL 189 FG I++ K +L Sbjct: 151 DFGPIEELREKHGQL 165 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: 248 Number of extensions: 23 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: 205 Length adjustment: 21 Effective length of query: 194 Effective length of database: 184 Effective search space: 35696 Effective search space used: 35696 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: 45 (21.9 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