Align Phenylacetyl-CoA:acceptor oxidoreductase small subunit PadC (characterized, see rationale)
to candidate WP_041100019.1 SUTH_RS13740 ferredoxin
Query= uniprot:A0A2R4BLY8 (215 letters) >NCBI__GCF_000828635.1:WP_041100019.1 Length = 243 Score = 151 bits (382), Expect = 9e-42 Identities = 88/231 (38%), Positives = 114/231 (49%), Gaps = 43/231 (18%) Query: 1 MTRYAMVADLRRCVGCQTCTAACKHTN---------------ATPPGVQWRWVLDVEAGE 45 MT+ A+V DL CVGCQ C +CK N A P G + V E GE Sbjct: 1 MTQLALVIDLNVCVGCQACVTSCKEWNTSGSAGPMGDQNPYGADPTGTFFNRVQTFEVGE 60 Query: 46 FPDVSRTFVPVGCQHCDEPPCETVCPTTAT-KKRADGLVTIDYDLCIGCAYCSVACPYNA 104 FP P C HC++PPC VCPT A+ K++ DG+V ++YD CIGC YCS ACPY A Sbjct: 61 FPTTETVHFPKSCLHCEDPPCVPVCPTGASYKRKEDGIVLVNYDKCIGCKYCSWACPYGA 120 Query: 105 RYKVNFAEPAYGDRLMANEKQRADPARVGVATKCTFCSDRIDYGVAHGLTPGVDPDATPA 164 R +E+Q+ V KCT C DRI + +T + D P+ Sbjct: 121 R--------------ELDEQQQ-------VMKKCTLCVDRI-----YDMTM-AEADRKPS 153 Query: 165 CANACIANALTFGDIDDPNSKASRLLRENEHFRMHEELGTGPGFFYLWEKK 215 C AC +A FGD+ DP S S +RE+ + + E GT P YL +K Sbjct: 154 CVKACPTSARLFGDVHDPESAVSVAIRESGGYALMPEWGTHPANHYLPRRK 204 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: 275 Number of extensions: 23 Number of successful extensions: 7 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: 243 Length adjustment: 23 Effective length of query: 192 Effective length of database: 220 Effective search space: 42240 Effective search space used: 42240 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 24 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