Align Phenylacetyl-CoA:acceptor oxidoreductase small subunit PadC (characterized, see rationale)
to candidate WP_011383654.1 AMB_RS06305 4Fe-4S dicluster domain-containing protein
Query= uniprot:A0A2R4BLY8 (215 letters) >NCBI__GCF_000009985.1:WP_011383654.1 Length = 217 Score = 325 bits (832), Expect = 5e-94 Identities = 145/213 (68%), Positives = 170/213 (79%) Query: 1 MTRYAMVADLRRCVGCQTCTAACKHTNATPPGVQWRWVLDVEAGEFPDVSRTFVPVGCQH 60 MT++A+VADL RCVGCQTCT AC+H NATPPGVQ+R VLD+E G FPDV R FVPVGC H Sbjct: 1 MTKWAIVADLGRCVGCQTCTTACRHANATPPGVQYRKVLDMEVGTFPDVRRVFVPVGCMH 60 Query: 61 CDEPPCETVCPTTATKKRADGLVTIDYDLCIGCAYCSVACPYNARYKVNFAEPAYGDRLM 120 CDEPPC VCPTTAT KRADG+V IDYD+CIGC YC VACPY ARYKV+ A+ D+ Sbjct: 61 CDEPPCRDVCPTTATTKRADGMVMIDYDICIGCGYCIVACPYQARYKVSKPTFAFKDQET 120 Query: 121 ANEKQRADPARVGVATKCTFCSDRIDYGVAHGLTPGVDPDATPACANACIANALTFGDID 180 NE+ R D +GVA KCTFC DR+DYG+A+GLTPGV P+ATPAC N+C++ ALTFGD D Sbjct: 121 QNERTRFDERLLGVAQKCTFCVDRVDYGLANGLTPGVAPEATPACVNSCLSKALTFGDTD 180 Query: 181 DPNSKASRLLRENEHFRMHEELGTGPGFFYLWE 213 +P+S S+LL+ + FRMHEELGTGP YLWE Sbjct: 181 NPDSNVSKLLKRYKSFRMHEELGTGPNIHYLWE 213 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: 321 Number of extensions: 15 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: 215 Length of database: 217 Length adjustment: 22 Effective length of query: 193 Effective length of database: 195 Effective search space: 37635 Effective search space used: 37635 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