Align Phenylacetyl-CoA:acceptor oxidoreductase small subunit PadC (characterized, see rationale)
to candidate WP_011385651.1 AMB_RS16595 4Fe-4S dicluster domain-containing protein
Query= uniprot:A0A2R4BLY8 (215 letters) >NCBI__GCF_000009985.1:WP_011385651.1 Length = 242 Score = 134 bits (338), Expect = 1e-36 Identities = 75/211 (35%), Positives = 99/211 (46%), Gaps = 35/211 (16%) Query: 3 RYAMVADLRRCVGCQTCTAACKHTNATPPGVQWRWVLDVEAGEFPDVSRTFVPVGCQHCD 62 R+AMV DL +C+GCQ CT C N P +V E E V +P C HC Sbjct: 42 RWAMVVDLGKCIGCQACTIGCIMENRVPADSFRTFVSTYEVTEGDKVGTYVLPRLCNHCS 101 Query: 63 EPPCETVCPTTATKKRADGLVTIDYDLCIGCAYCSVACPYNARYKVNFAEPAYGDRLMAN 122 +PPC VCP AT ++ DG V +D D C+GCAYC ACPY+AR+ + + Sbjct: 102 DPPCVGVCPVGATFQQKDGAVMVDSDRCVGCAYCVQACPYDARF-------------INH 148 Query: 123 EKQRADPARVGVATKCTFCSDRIDYGVAHGLTPGVDPDATPACANACIANALTFGDIDDP 182 E AD KCTFC R+ G+ PAC C+ A FGD+++ Sbjct: 149 ETNTAD--------KCTFCGHRVAAGL------------LPACVETCVGGARVFGDLNET 188 Query: 183 NSKASRLLRENEHFR--MHEELGTGPGFFYL 211 RLL N+ + E GT P +Y+ Sbjct: 189 EGAVRRLLDANKGRTKVLKPEQGTAPNVYYI 219 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: 262 Number of extensions: 21 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: 242 Length adjustment: 23 Effective length of query: 192 Effective length of database: 219 Effective search space: 42048 Effective search space used: 42048 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