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 RR42_RS07500 RR42_RS07500 benzoyl-CoA oxygenase
Query= SwissProt::Q9AIX6 (414 letters) >FitnessBrowser__Cup4G11:RR42_RS07500 Length = 411 Score = 515 bits (1327), Expect = e-151 Identities = 249/418 (59%), Positives = 309/418 (73%), Gaps = 11/418 (2%) Query: 1 MNAPAEHANLARQHLIDPEICIRCNTCEEICPVDAITHDSRNYVVKFETCNGCLACISPC 60 M AP ++ +QHLIDPEICIRCNTCE+ CP+DAITHD RNYVV+ + CNGC AC+ PC Sbjct: 1 MGAP----DIIKQHLIDPEICIRCNTCEDTCPIDAITHDDRNYVVRADVCNGCGACLGPC 56 Query: 61 PTGAIDSWRNVDKATPHSLADQYSWDYLPDTTELDQFEATVMGAAELPA----EVQQITE 116 PTGAID+WR + K+ + + Q WD LP + L +A + A + + + Q + Sbjct: 57 PTGAIDNWRTMLKSEAYPIEAQLLWDELPASLPLPA-DAGIDDAPDTASPQTGQEPQTQQ 115 Query: 117 VATAGQGGPAMAPWSASHPYVNLYTPANPITATVTGNYRLTAEDASSDIHHIVLDFGTTP 176 V T+ P APWSA+HPYVNL+ P+TATV GNYRLTA+DASSD+HHIVLDFG Sbjct: 116 VETSRHTSPK-APWSAAHPYVNLHGVRAPVTATVAGNYRLTADDASSDVHHIVLDFGQHF 174 Query: 177 FPVLEGQSIGIIPPGVDEKGKPHLLRMYSVASPRDGERPHYNNLSLTVKRVVEDHEGNPT 236 FPVLEGQ+IGI+PPG D GKPH +RMYS+ASPRDGERP YNNL+LTVKRV +DHEG P Sbjct: 175 FPVLEGQAIGIVPPGTDANGKPHYIRMYSIASPRDGERPGYNNLALTVKRVEQDHEGQPV 234 Query: 237 RGVASNYVCDLKKGDKVQVTGPYGSTYLMPNHPGSSIMMICTGTGSAPMRAMTERRRRRM 296 RGVASN++CDL +GD+V+V GP+G+T+LMPNH +S+MMICTGTGSAPMRAMTE RR + Sbjct: 235 RGVASNFLCDLARGDEVRVVGPFGTTFLMPNHREASVMMICTGTGSAPMRAMTEHMRRNV 294 Query: 297 DRKEGGELVLFFGARAPEELPYFGPLQKLPKEFIDINFAFSRVPGEPKRYVQDAIRERAD 356 + +G L LFFGAR ELPYFGPL KLP F+DI+ AFSR PG+P+RYVQDAIRE Sbjct: 295 GQFDGQRL-LFFGARNARELPYFGPLMKLPPSFLDIHLAFSRDPGQPRRYVQDAIREAGA 353 Query: 357 KVFQMLQDDNCYIYICGLKGMEAGVLEAFRDICRAKGADWDALRPQLLSKARFHVETY 414 +V +L D + ++YICGLKGME GVL AF ++C G W L + ++ R H+ETY Sbjct: 354 RVAALLNDPHGHVYICGLKGMEDGVLAAFAEVCAGAGLAWGELEAAMKTEGRLHIETY 411 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: 618 Number of extensions: 28 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: 414 Length of database: 411 Length adjustment: 31 Effective length of query: 383 Effective length of database: 380 Effective search space: 145540 Effective search space used: 145540 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