Align Phenylacetyl-CoA:acceptor oxidoreductase small subunit PadC (characterized, see rationale)
to candidate 7023405 Shewana3_0635 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein (RefSeq)
Query= uniprot:A0A2R4BLY8 (215 letters) >FitnessBrowser__ANA3:7023405 Length = 251 Score = 140 bits (353), Expect = 2e-38 Identities = 77/214 (35%), Positives = 106/214 (49%), Gaps = 38/214 (17%) Query: 3 RYAMVADLRRCVGCQTCTAACKHTNATPPGVQWRWVLDVEAGEFPDVSRT---FVPVGCQ 59 RY MV DLRRCVGCQ CT AC N P G V E + + +P C Sbjct: 40 RYGMVIDLRRCVGCQACTVACTFENLPPLGQFRTTVQQYEVSQQDSATPPAFLMLPRLCN 99 Query: 60 HCDEPPCETVCPTTATKKRADGLVTIDYDLCIGCAYCSVACPYNARYKVNFAEPAYGDRL 119 HC+ PPC +CPT AT +R DG+V ++ + C+GC YC ACPY+AR+ Sbjct: 100 HCENPPCIPICPTGATFQRPDGIVVVNNEWCVGCGYCVQACPYDARF------------- 146 Query: 120 MANEKQRADPARVGVATKCTFCSDRIDYGVAHGLTPGVDPDATPACANACIANALTFGDI 179 + +E AD KCTFC+ R++ G+ PAC C+ A GD+ Sbjct: 147 INHETNTAD--------KCTFCAHRLEAGL------------LPACVETCVGEARVIGDL 186 Query: 180 DDPNSKASRLLRENEH--FRMHEELGTGPGFFYL 211 +DP+S S+LL+ N+ + + T P FY+ Sbjct: 187 NDPHSHISQLLKANQADIKVLKPDANTAPRVFYI 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: 254 Number of extensions: 22 Number of successful extensions: 6 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: 251 Length adjustment: 23 Effective length of query: 192 Effective length of database: 228 Effective search space: 43776 Effective search space used: 43776 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