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 H281DRAFT_00375 H281DRAFT_00375 benzoyl-CoA oxygenase, component A
Query= SwissProt::Q9AIX6 (414 letters) >FitnessBrowser__Burk376:H281DRAFT_00375 Length = 413 Score = 524 bits (1350), Expect = e-153 Identities = 255/415 (61%), Positives = 301/415 (72%), Gaps = 3/415 (0%) Query: 1 MNAPAEHANLARQHLIDPEICIRCNTCEEICPVDAITHDSRNYVVKFETCNGCLACISPC 60 MN P + RQHLIDPEICIRCNTCEE CP+DAITHD NYVVK + CNGC+AC+ PC Sbjct: 1 MNGPVS-IEVLRQHLIDPEICIRCNTCEETCPIDAITHDENNYVVKADVCNGCMACVPPC 59 Query: 61 PTGAIDSWRNVDKATPHSLADQYSWDYLPDTTELDQFEATVMGAAELPAEVQ-QITEVAT 119 PTGAID+WR V KA + + +Q++WD LP+ + AA+ + + + Sbjct: 60 PTGAIDNWRTVLKADAYPVEEQFTWDVLPEQNTMAAPAVEESPAADTTGDAAANASGIEV 119 Query: 120 AGQGGPAMAPWSASHPYVNLYTPANPITATVTGNYRLTAEDASSDIHHIVLDFGTTPFPV 179 G + PWSA+ PYVNLYT P TATV GNYRLT SDIHHIVLDFGT PFPV Sbjct: 120 DTVRGSVVPPWSAAKPYVNLYTHKTPTTATVVGNYRLTDVSTESDIHHIVLDFGTMPFPV 179 Query: 180 LEGQSIGIIPPGVDEKGKPHLLRMYSVASPRDGERPHYNNLSLTVKRVVEDHEGNPTRGV 239 LEGQSIGI+PPG G+ H R YS+ASPRDGERP YNN+SLTVKRV + H G+ GV Sbjct: 180 LEGQSIGILPPGASADGRVHHARQYSIASPRDGERPGYNNVSLTVKRVAQRH-GDSIDGV 238 Query: 240 ASNYVCDLKKGDKVQVTGPYGSTYLMPNHPGSSIMMICTGTGSAPMRAMTERRRRRMDRK 299 SNY+CDLKKGD V V GP+GST+LMPNHP S ++MICTGTGSAPMRAMTE RRRR + Sbjct: 239 CSNYLCDLKKGDVVTVIGPFGSTFLMPNHPNSHLLMICTGTGSAPMRAMTEYRRRRRLKG 298 Query: 300 EGGELVLFFGARAPEELPYFGPLQKLPKEFIDINFAFSRVPGEPKRYVQDAIRERADKVF 359 G+L+LFFGAR EELPYFGPL LPK+FID N AFSR PG+PKRYVQDA+RERA V Sbjct: 299 ATGKLMLFFGARTKEELPYFGPLTNLPKDFIDTNLAFSRTPGQPKRYVQDAMRERAVDVS 358 Query: 360 QMLQDDNCYIYICGLKGMEAGVLEAFRDICRAKGADWDALRPQLLSKARFHVETY 414 QML+DDN +IY+CGLKGME GVL+A ++I DW+AL +L + R H+ETY Sbjct: 359 QMLKDDNTHIYVCGLKGMEDGVLQALKEIGEQHQLDWEALWAKLKKEGRLHLETY 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: 589 Number of extensions: 20 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