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_RS35120 RR42_RS35120 benzoyl-CoA oxygenase
Query= SwissProt::Q9AIX6 (414 letters) >FitnessBrowser__Cup4G11:RR42_RS35120 Length = 426 Score = 517 bits (1331), Expect = e-151 Identities = 250/417 (59%), Positives = 301/417 (72%), Gaps = 14/417 (3%) Query: 12 RQHLIDPEICIRCNTCEEICPVDAITHDSRNYVVKFETCNGCLACISPCPTGAIDSWRNV 71 RQHLIDPEICIRCNTCE CPV AITHD+RNYVV + CNGC+ACISPCPTG+ID+WR + Sbjct: 10 RQHLIDPEICIRCNTCEATCPVAAITHDARNYVVDADKCNGCMACISPCPTGSIDNWRTM 69 Query: 72 DKATPHSLADQYSWDYLPDTTELDQFEATVMGAAELP----AEVQQITEVA-----TAGQ 122 +A + + +Q+ WD LPD +Q A + A P A + V + Q Sbjct: 70 PRAMAYGIVEQFGWDTLPDELSSEQLAAQGVAADAEPVLESAPASSLAAVTGEDGFNSAQ 129 Query: 123 GGPAMAPWSASHPYVNLY---TPANPITATVTGNYRLTAEDASSDIHHIVLDFGTTPFPV 179 G + PWSA+H Y NLY A +TATV GN R+T D HHIVLDFG+ PFPV Sbjct: 130 YGATVPPWSAAHAYTNLYGAKAAARSVTATVVGNARVTEVGRDYDTHHIVLDFGSAPFPV 189 Query: 180 LEGQSIGIIPPGVDEKGKPHLLRMYSVASPRDGERPHYNNLSLTVKRVVEDHEGNPTRGV 239 LEGQSIGI+PPGVD G+ H R YS+ASPR+GERP YNN+SLT+KRV+EDH+GNP RGV Sbjct: 190 LEGQSIGIVPPGVDASGRQHHARQYSLASPRNGERPGYNNISLTIKRVLEDHQGNPVRGV 249 Query: 240 ASNYVCDLKKGDKVQVTGPYGSTYLMPNHPGSSIMMICTGTGSAPMRAMTE--RRRRRMD 297 ASNY+CDL+ GDKV V GP+G+++LMPNHP S I+MICTGTGSAPMRAMTE RR R+ Sbjct: 250 ASNYMCDLQVGDKVDVIGPFGASFLMPNHPRSHIVMICTGTGSAPMRAMTEWRRRLRKSG 309 Query: 298 RKEGGELVLFFGARAPEELPYFGPLQKLPKEFIDINFAFSRVPGEPKRYVQDAIRERADK 357 + EGG+L+LFFGAR EELPYFGPLQ LPK+FIDINFAFSR PG+PKRYVQD +RERA Sbjct: 310 KFEGGKLMLFFGARTQEELPYFGPLQSLPKDFIDINFAFSRTPGQPKRYVQDVMRERAAD 369 Query: 358 VFQMLQDDNCYIYICGLKGMEAGVLEAFRDICRAKGADWDALRPQLLSKARFHVETY 414 + +L D N Y+CGLK ME GV+ A RD+ + G WDA+ L + R H+ETY Sbjct: 370 LGPLLADPNTCFYVCGLKSMEEGVVLALRDVAQQAGLSWDAVGAALKKEGRLHLETY 426 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: 591 Number of extensions: 15 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: 426 Length adjustment: 32 Effective length of query: 382 Effective length of database: 394 Effective search space: 150508 Effective search space used: 150508 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