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 Ac3H11_3083 Benzoyl-CoA oxygenase component A
Query= SwissProt::Q9AIX6 (414 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3083 Length = 422 Score = 508 bits (1308), Expect = e-148 Identities = 245/419 (58%), Positives = 299/419 (71%), Gaps = 9/419 (2%) Query: 5 AEHANLARQHLIDPEICIRCNTCEEICPVDAITHDSRNYVVKFETCNGCLACISPCPTGA 64 A A + +QHLIDPEICIRCNTCE CPV AITHD NYVV+ + CNGC+ACISPCPTG+ Sbjct: 4 AVEAAVIKQHLIDPEICIRCNTCEATCPVGAITHDDNNYVVRADVCNGCMACISPCPTGS 63 Query: 65 IDSWRNVDKATPHSLADQYSWDYLPDTTELDQF--EATVMGAAELP-----AEVQQITEV 117 ID+WR + A +++ +Q +W+ LP D E A +P A V+ T+ Sbjct: 64 IDNWRTMPLARAYTIEEQLTWEELPPELPPDALAAEGVAPSADAVPPTTPAAPVEPGTQA 123 Query: 118 ATAGQGGPAMAPWSASHPYVNLYTPANPITATVTGNYRLTAEDASSDIHHIVLDFGTTPF 177 + Q G + PWSA+HPY NL+ P +P ATV GN+ T ++ HH+VLDFG+ PF Sbjct: 124 FRSAQYGATVPPWSAAHPYTNLFPPKSPTEATVVGNFNCTEAGFENETHHVVLDFGSMPF 183 Query: 178 PVLEGQSIGIIPPGVDEKGKPHLLRMYSVASPRDGERPHYNNLSLTVKRVVEDHEGNPTR 237 PVLEGQSIGIIPPG D GK H R YS+ASPR+GERP YNNL+LTVKRV DH+GN R Sbjct: 184 PVLEGQSIGIIPPGTDALGKEHHARQYSIASPRNGERPGYNNLALTVKRVTTDHDGNAVR 243 Query: 238 GVASNYVCDLKKGDKVQVTGPYGSTYLMPNHPGSSIMMICTGTGSAPMRAMTE--RRRRR 295 G+ASN+VCDLK GDKVQV GP+GS++LMPNHP S I+MICTGTGSAPMRAMTE RR R Sbjct: 244 GIASNFVCDLKVGDKVQVVGPFGSSFLMPNHPRSHIVMICTGTGSAPMRAMTEWRRRLRS 303 Query: 296 MDRKEGGELVLFFGARAPEELPYFGPLQKLPKEFIDINFAFSRVPGEPKRYVQDAIRERA 355 + EGG+L+LFFGAR +ELPYFGPLQ LPK+FIDIN AFSR G+PKRYVQD +RERA Sbjct: 304 SGKFEGGKLMLFFGARTQQELPYFGPLQNLPKDFIDINLAFSRTAGQPKRYVQDLMRERA 363 Query: 356 DKVFQMLQDDNCYIYICGLKGMEAGVLEAFRDICRAKGADWDALRPQLLSKARFHVETY 414 + +L+D + + Y+CGLK ME GV+ A RDI G DWD + L + R H+ETY Sbjct: 364 ADLAALLRDGSGHFYVCGLKSMEEGVVMALRDIASEAGLDWDTVGAALQREGRLHLETY 422 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: 624 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: 422 Length adjustment: 32 Effective length of query: 382 Effective length of database: 390 Effective search space: 148980 Effective search space used: 148980 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