Align Benzoyl-CoA reductase subunit C; 3-hydroxybenzoyl-CoA reductase subunit gamma; EC 1.3.7.8; EC 1.3.99.n1 (characterized)
to candidate WP_011384540.1 AMB_RS10820 benzoyl-CoA reductase subunit C
Query= SwissProt::O87874 (386 letters) >NCBI__GCF_000009985.1:WP_011384540.1 Length = 391 Score = 530 bits (1365), Expect = e-155 Identities = 244/385 (63%), Positives = 316/385 (82%) Query: 2 STADIIARCEALYEDLDFTAARQWKEADPSRKVIAYMPVYVPREIIHAAGMLPLGIMGGG 61 S ADI+A C+ ++EDL+FT AR+WK+A P RKVI ++PVY P E+IHAAG LPLGI GGG Sbjct: 7 SVADIMAVCQEMFEDLNFTYARKWKDAKPGRKVIGFLPVYSPIEMIHAAGCLPLGIFGGG 66 Query: 62 DGLEVIHGDAFYQSYICRIPRSTIELGLSKRMDFVDGMLFPSICDVIRNLSGMWKLMFPG 121 D +EVIHGDA+YQSYICRIPRSTIELG++ R+DFVDGM+FP +CDVIRNLSG+WKLMFP Sbjct: 67 DQMEVIHGDAYYQSYICRIPRSTIELGVTNRLDFVDGMIFPFVCDVIRNLSGIWKLMFPN 126 Query: 122 KYVRYFDVPQNYRDDVGGNYYTAELNELREGLEHLSGRKITDDALRASIKVYNENRKLVQ 181 + ++FD PQNY +GG YY EL+EL+EGLE L+GRKI+D ++ SI +YNENR+L++ Sbjct: 127 VWSKFFDTPQNYDKSIGGTYYIQELHELKEGLETLTGRKISDADIQRSIGLYNENRRLIR 186 Query: 182 DVYGLRSREPWKVPSADVYLLMRAGLVLPVEEHNQMLKDYLAAAVKVEAQKRDNCRVIIN 241 +VY R+++PW P+++VY+LMRAGL++ VEEHNQMLKDY+AAA + KRDN R+ I Sbjct: 187 EVYAFRAKQPWLAPTSEVYVLMRAGLMMDVEEHNQMLKDYMAAAANEDRPKRDNVRISIY 246 Query: 242 GSFCEQPPLNLIKSIELSGCYIVDDDYMIVHRFLRNEVSTAGDPMQNLSLAFLHESISTA 301 GSFCEQPPLNLIKSIE++GCY+VDDDY + +RFL +V T G+P++ L++ +L S+ T+ Sbjct: 247 GSFCEQPPLNLIKSIEMAGCYVVDDDYSLNNRFLMVDVPTTGNPLEALAMTYLENSVETS 306 Query: 302 AKYDDKEEDKGKYLLEQVRTNAAEGVIFAAPSFCDPALLERPMLADRCSENKVPYISFKY 361 KY + KG++ ++ V+ AEGVI+A PSFCDPALL+RPM+ ++ SE +PYI+FKY Sbjct: 307 CKYVPDGKVKGQFHVDAVKACGAEGVIYATPSFCDPALLDRPMVCNKLSEAGIPYIAFKY 366 Query: 362 AENSGQMQPIREQAGTFADSIKLWS 386 AENSGQMQPIREQAGTFADSIKLWS Sbjct: 367 AENSGQMQPIREQAGTFADSIKLWS 391 Lambda K H 0.321 0.138 0.412 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: 506 Number of extensions: 9 Number of successful extensions: 1 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: 386 Length of database: 391 Length adjustment: 30 Effective length of query: 356 Effective length of database: 361 Effective search space: 128516 Effective search space used: 128516 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