Align Phenylacetyl-CoA:acceptor oxidoreductase small subunit PadC (characterized, see rationale)
to candidate WP_084207294.1 SUTH_RS07125 4Fe-4S dicluster domain-containing protein
Query= uniprot:A0A2R4BLY8 (215 letters) >NCBI__GCF_000828635.1:WP_084207294.1 Length = 260 Score = 124 bits (312), Expect = 1e-33 Identities = 70/214 (32%), Positives = 98/214 (45%), Gaps = 27/214 (12%) Query: 3 RYAMVADLRRCV-GCQTCTAACKHTNATP-----PGVQWRWVLDVEAGEFPDVSRTFVPV 56 R+ ++ D RC GC C AC N P +W+ +E + + +T +P+ Sbjct: 65 RWGLLIDATRCAPGCTKCIDACHTENGVSEKLPDPRQNSQWIRKIELTDRRNGKKTELPM 124 Query: 57 GCQHCDEPPCETVCPTTATKKRADGLVTIDYDLCIGCAYCSVACPYNARYKVNFAEPAYG 116 CQHC PPC VCPT A+ KRADG+V +D CIGC YC +ACPY AR V+ Sbjct: 125 MCQHCANPPCVDVCPTGASMKRADGIVLVDRHTCIGCRYCMMACPYKARSFVH------- 177 Query: 117 DRLMANEKQRADPARVGVATKCTFCSDRIDYGVAHGLTPGVDPDATPACANACIANALTF 176 E+ P G CT C R+D G PAC +C A+ F Sbjct: 178 --APLTEQNPEVPRGQGCVESCTLCVHRVDKG------------QQPACVESCPEGAMLF 223 Query: 177 GDIDDPNSKASRLLRENEHFRMHEELGTGPGFFY 210 GD++DP S ++ + ++ +L G Y Sbjct: 224 GDLNDPASAIAKRIASVPTTQVRSDLRLNQGVRY 257 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: 307 Number of extensions: 26 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: 260 Length adjustment: 23 Effective length of query: 192 Effective length of database: 237 Effective search space: 45504 Effective search space used: 45504 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 Apr 09 2024. 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