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 WP_011382623.1 AMB_RS00895 benzoyl-CoA 2,3-epoxidase subunit BoxA
Query= SwissProt::Q9AIX6 (414 letters) >NCBI__GCF_000009985.1:WP_011382623.1 Length = 393 Score = 479 bits (1232), Expect = e-140 Identities = 238/409 (58%), Positives = 284/409 (69%), Gaps = 22/409 (5%) Query: 10 LARQHLIDPEICIRCNTCEEICPVDAITHDSRNYVVKFETCNGCLACISPCPTGAIDSWR 69 L RQHLIDP +CIRCNTCEE CPVDAITHD NYVV ++ C GC C+SPCPTGAID+W Sbjct: 3 LKRQHLIDPVVCIRCNTCEEACPVDAITHDGTNYVVSYDKCTGCRTCVSPCPTGAIDNWL 62 Query: 70 NVDKATPHSLADQYSWDYLPDTTELDQFEATVMGAAEL----PAEVQQITEVATAGQGGP 125 VD+ P S+ DQ+ W+ LP T G AE P EV + ATA G Sbjct: 63 LVDQ--PWSIDDQFGWEELP-------LGQTGPGPAEPAPLPPGEVSDLLAAATATTGPS 113 Query: 126 AMAPWSASHPYVNLYTPANPITATVTGNYRLTAEDASSDIHHIVLDFGTTPFPVLEGQSI 185 P SA+ PY NLY+ P+TA V GN R+T E SDIHH+VLDF FP LEGQSI Sbjct: 114 VPPPASAAKPYFNLYSRDTPVTARVAGNMRITGEGTDSDIHHVVLDFSHNAFPFLEGQSI 173 Query: 186 GIIPPGVDEKGKPHLLRMYSVASPRDGERPHYNNLSLTVKRVVEDHEGNPTRGVASNYVC 245 GI+PPG D KG+ H +R+YS+ASPR+GER NNL+LTVKRV GV SNYVC Sbjct: 174 GIVPPGTDAKGRAHNIRLYSIASPREGERSGCNNLALTVKRVAG--------GVGSNYVC 225 Query: 246 DLKKGDKVQVTGPYGSTYLMPNHPGSSIMMICTGTGSAPMRAMTERRRRRMDRKEGGELV 305 DLKKGD+V+V GP+G +LMP+ P ++I+MICTGTGSAP RA TERRRR + G+L+ Sbjct: 226 DLKKGDEVRVAGPFGQAFLMPDAPNANIIMICTGTGSAPFRAFTERRRRNA-QDASGKLM 284 Query: 306 LFFGARAPEELPYFGPLQKLPKEFIDINFAFSRVPGEPKRYVQDAIRERADKVFQMLQDD 365 LFFGAR PEELPYFGPL KLPK ID+N AFSRVP PK+YVQD IRER+D + +L Sbjct: 285 LFFGARTPEELPYFGPLMKLPKSLIDVNLAFSRVPDRPKQYVQDKIRERSDDLAALLASA 344 Query: 366 NCYIYICGLKGMEAGVLEAFRDICRAKGADWDALRPQLLSKARFHVETY 414 + +++ICGLKGME G EAF DICR G DW LRP++ + R+HVETY Sbjct: 345 DTHVFICGLKGMEQGCDEAFADICRLHGLDWADLRPRMREEGRYHVETY 393 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: 596 Number of extensions: 18 Number of successful extensions: 6 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: 393 Length adjustment: 31 Effective length of query: 383 Effective length of database: 362 Effective search space: 138646 Effective search space used: 138646 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