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 Synpcc7942_0978 Synpcc7942_0978 ferredoxin-NADP oxidoreductase
Query= SwissProt::Q9AIX6 (414 letters) >FitnessBrowser__SynE:Synpcc7942_0978 Length = 403 Score = 190 bits (483), Expect = 6e-53 Identities = 115/325 (35%), Positives = 166/325 (51%), Gaps = 16/325 (4%) Query: 103 GAAELPAEVQQITEVATAGQGGPAMAPWSASHPYVNLYTPANPITATVTGNYRLTAEDAS 162 GAA L A + E A A PA SA VN+Y P P V N L E Sbjct: 82 GAAPLQAAAE---EPAAAPTPAPAAKKHSAEDVPVNIYRPNKPFVGKVLSNEPLVQEGGI 138 Query: 163 SDIHHIVLDFGTTPFPVLEGQSIGIIPPGVDEKGKPHLLRMYSVASPRDGERPHYNNLSL 222 + H+ D +EGQSIGIIP G D+KGKPH LR+YS+AS R G+ +SL Sbjct: 139 GVVQHLTFDISEGDLRYIEGQSIGIIPDGTDDKGKPHKLRLYSIASTRHGDHVDDKTVSL 198 Query: 223 TVKRVVEDHE-GNPTRGVASNYVCDLKKGDKVQVTGPYGSTYLMPNHPGSSIMMICTGTG 281 V+++ +E G GV S ++C LK GD V++TGP G L+P ++++M+ TGTG Sbjct: 199 CVRQLQYQNEAGETINGVCSTFLCGLKPGDDVKITGPVGKEMLLPADTDANVIMMGTGTG 258 Query: 282 SAPMRAMTERRRRRMDR------KEGGELVLFFGARAPEELPYFGPLQKLPKEFID---I 332 AP RA R + +R + G+ L FG + Y L+ L ++ D + Sbjct: 259 IAPFRAYLWRMFKDNERAINSEYQFNGKAWLIFGIPTTANILYKEELEALQAQYPDNFRL 318 Query: 333 NFAFSRVPGEP---KRYVQDAIRERADKVFQMLQDDNCYIYICGLKGMEAGVLEAFRDIC 389 +A SR + Y+QD + E AD+++ +L+D+ ++YICGL+GME G+ +A Sbjct: 319 TYAISREQKNEAGGRMYIQDRVAEHADEIWNLLKDEKTHVYICGLRGMEDGIDQAMTVAA 378 Query: 390 RAKGADWDALRPQLLSKARFHVETY 414 + W + L R+HVETY Sbjct: 379 AKEDVVWSDYQRTLKKAGRWHVETY 403 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: 416 Number of extensions: 24 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: 403 Length adjustment: 31 Effective length of query: 383 Effective length of database: 372 Effective search space: 142476 Effective search space used: 142476 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 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