Align Benzoyl-CoA oxygenase component A; Benzoyl-CoA 2,3-dioxygenase subunit A; Benzoyl-CoA dioxygenase reductase component; EC 1.14.13.208 (characterized)
to candidate WP_009547107.1 CCE_RS04725 phycobilisome linker polypeptide
Query= SwissProt::Q9AIX6 (414 letters) >NCBI__GCF_000017845.1:WP_009547107.1 Length = 408 Score = 191 bits (486), Expect = 3e-53 Identities = 108/288 (37%), Positives = 158/288 (54%), Gaps = 10/288 (3%) Query: 137 VNLYTPANPITATVTGNYRLTAEDASSDIHHIVLDFGTTPFPVLEGQSIGIIPPGVDEKG 196 VN+Y P +P NY L AE S + H+ D LEGQSIGIIPPG D+ G Sbjct: 121 VNIYKPKDPFIGKCIENYPLVAEGGSGIVQHLTFDLSGGDLHYLEGQSIGIIPPGTDDNG 180 Query: 197 KPHLLRMYSVASPRDGERPHYNNLSLTVKRVVEDH-EGNPT-RGVASNYVCDLKKGDKVQ 254 KPH LR+YS+AS R G++ +SL V+++ H E N T GV S ++C+L+ G V Sbjct: 181 KPHKLRLYSIASTRHGDKGDDKTVSLCVRQLEYQHPETNETVYGVCSTHLCNLEVGADVA 240 Query: 255 VTGPYGSTYLMPNHPGSSIMMICTGTGSAPMRAMTERR--RRRMDRKEGGELVLFFGARA 312 +TGP G L+P+ ++I+M+ TGTG AP RA R + D K G+ L FG Sbjct: 241 ITGPVGKEMLLPDDEDANIVMLATGTGIAPFRAFLWRMFFEKHEDYKFKGKSWLIFGVPY 300 Query: 313 PEELPYFGPLQKLPKEFID---INFAFSRVPGEP---KRYVQDAIRERADKVFQMLQDDN 366 + Y L+++ + D + +A SR + Y+Q + E+A+K++ MLQD Sbjct: 301 TANILYKDKLEEIETNYPDNFELTYAISREQKNSEGGRMYIQHRVAEQAEKLWTMLQDPK 360 Query: 367 CYIYICGLKGMEAGVLEAFRDICRAKGADWDALRPQLLSKARFHVETY 414 ++Y+CGLKGME+G+ E +G +W +L + R+HVE Y Sbjct: 361 THLYMCGLKGMESGIEEGLSPFAAKQGVEWSDFVKKLKKEHRWHVEVY 408 Lambda K H 0.319 0.136 0.425 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: 438 Number of extensions: 23 Number of successful extensions: 3 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: 414 Length of database: 408 Length adjustment: 31 Effective length of query: 383 Effective length of database: 377 Effective search space: 144391 Effective search space used: 144391 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 (21.8 bits) S2: 50 (23.9 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