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 BPHYT_RS13335 BPHYT_RS13335 benzoyl-CoA oxygenase
Query= SwissProt::Q9AIX6 (414 letters) >FitnessBrowser__BFirm:BPHYT_RS13335 Length = 413 Score = 522 bits (1345), Expect = e-153 Identities = 259/420 (61%), Positives = 302/420 (71%), Gaps = 13/420 (3%) Query: 1 MNAPAEHANLARQHLIDPEICIRCNTCEEICPVDAITHDSRNYVVKFETCNGCLACISPC 60 MN P + RQHLIDPEICIRCNTCEE CPVDAITHD NYVVK E CNGC+AC+ PC Sbjct: 1 MNGPVS-IEVLRQHLIDPEICIRCNTCEETCPVDAITHDDNNYVVKAEICNGCMACVPPC 59 Query: 61 PTGAIDSWRNVDKATPHSLADQYSWDYLPDTTELDQFEATVMGAAELPAEVQQITEVATA 120 PTGAID+WR V KA + + +Q++WD LP+ + V A ELP VA A Sbjct: 60 PTGAIDNWRTVLKADAYPIEEQFTWDVLPEQNTM-----AVPAADELPGAGASGDTVAEA 114 Query: 121 GQ------GGPAMAPWSASHPYVNLYTPANPITATVTGNYRLTAEDASSDIHHIVLDFGT 174 G + PWSA+ PYVNLYT P +ATV GNYRLT SDIHHIVLDFG+ Sbjct: 115 SGIEVDTVRGSVVPPWSAAKPYVNLYTHKEPTSATVVGNYRLTDGSTDSDIHHIVLDFGS 174 Query: 175 TPFPVLEGQSIGIIPPGVDEKGKPHLLRMYSVASPRDGERPHYNNLSLTVKRVVEDHEGN 234 PFPVLEGQSIGI+PPG G+ H R YS+ASPRDGERP YNN+SLTVKRV + H G+ Sbjct: 175 MPFPVLEGQSIGILPPGTAADGRAHHARQYSIASPRDGERPGYNNVSLTVKRVSQQH-GD 233 Query: 235 PTRGVASNYVCDLKKGDKVQVTGPYGSTYLMPNHPGSSIMMICTGTGSAPMRAMTERRRR 294 GV SNY+CDLKKGD V+V GP+G T+LMPNHP S ++MICTGTGSAPMRAMTE RRR Sbjct: 234 SLDGVCSNYLCDLKKGDVVKVIGPFGGTFLMPNHPNSHLLMICTGTGSAPMRAMTEYRRR 293 Query: 295 RMDRKEGGELVLFFGARAPEELPYFGPLQKLPKEFIDINFAFSRVPGEPKRYVQDAIRER 354 R + G+L+LFFGAR EELPYFGPL LPK+FID N AFSR PG+PKRYVQDA+RER Sbjct: 294 RRLKGATGKLMLFFGARTKEELPYFGPLTNLPKDFIDTNLAFSRTPGQPKRYVQDAMRER 353 Query: 355 ADKVFQMLQDDNCYIYICGLKGMEAGVLEAFRDICRAKGADWDALRPQLLSKARFHVETY 414 A V ML+DDN +IY+CGLKGME GVL+A ++I DW+AL +L + R H+ETY Sbjct: 354 AVDVAHMLKDDNTHIYVCGLKGMEDGVLQALKEIGERHQLDWEALWVKLKKEGRLHLETY 413 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: 586 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: 414 Length of database: 413 Length adjustment: 31 Effective length of query: 383 Effective length of database: 382 Effective search space: 146306 Effective search space used: 146306 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