Align benzoyl-CoA reductase (EC 1.3.7.8) (characterized)
to candidate WP_041098441.1 SUTH_RS08185 benzoyl-CoA reductase, bzd-type, subunit Q
Query= BRENDA::Q8VUG0 (301 letters) >NCBI__GCF_000828635.1:WP_041098441.1 Length = 301 Score = 555 bits (1429), Expect = e-163 Identities = 272/300 (90%), Positives = 287/300 (95%) Query: 1 MNAEVAAATAAPEKKEFWRWQENTWYDETKNWKDAKIITCGIDVGSVSSQAVLVCDGELY 60 MNAEV AA APEKKEFWRWQENTW DETK+WK AKIITCGIDVGSVSSQAVLV DGELY Sbjct: 1 MNAEVTAAPTAPEKKEFWRWQENTWVDETKDWKTAKIITCGIDVGSVSSQAVLVVDGELY 60 Query: 61 GYNSMRTGNNSPDSAKNALQGIMDKIGMKLEDINYVVGTGYGRVNVPFAHKAITEIACHA 120 G+NSMRTGNNSPDSA NALQG+MDK GMKLEDI+YVVGTGYGRVNVPFAHKAITEIACHA Sbjct: 61 GFNSMRTGNNSPDSATNALQGVMDKCGMKLEDIHYVVGTGYGRVNVPFAHKAITEIACHA 120 Query: 121 RGANYMGGNKVRTILDMGGQDCKAIHCDDKGKVTNFLMNDKCAAGTGRGMEVISDLMQIP 180 RGANYMGGN VRTILDMGGQDCKAIHCD+KGKVTNFLMNDKCAAGTGRGMEVISDLMQIP Sbjct: 121 RGANYMGGNGVRTILDMGGQDCKAIHCDEKGKVTNFLMNDKCAAGTGRGMEVISDLMQIP 180 Query: 181 IAELGPRSFDVETEPEAVSSICVVFAKSEALGLLKAGYTKNMVIAAYCQAMAERVVSLLE 240 IAELGPRSFD++++ EAVSS+CVVFAKSEALGLLKAGYTKN VIAAYCQAMAERVVSLLE Sbjct: 181 IAELGPRSFDIDSDVEAVSSVCVVFAKSEALGLLKAGYTKNKVIAAYCQAMAERVVSLLE 240 Query: 241 RIGVEEGFFITGGIAKNPGVVKRIERLLGIKQLETKIDSQIAGALGAALFGYTLMQKQAA 300 RIGVEEGFFITGGIAKNPGVVKRIE+LLGIK ++TK+DSQIAGALGAALFGYTLM K+AA Sbjct: 241 RIGVEEGFFITGGIAKNPGVVKRIEKLLGIKAIDTKVDSQIAGALGAALFGYTLMSKKAA 300 Lambda K H 0.318 0.134 0.395 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: 430 Number of extensions: 8 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: 301 Length of database: 301 Length adjustment: 27 Effective length of query: 274 Effective length of database: 274 Effective search space: 75076 Effective search space used: 75076 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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