Align benzoyl-CoA reductase (EC 1.3.7.8) (characterized)
to candidate 18358 b4334 putative enzyme (VIMSS)
Query= BRENDA::Q8VUG0 (301 letters) >FitnessBrowser__Keio:18358 Length = 255 Score = 160 bits (404), Expect = 4e-44 Identities = 94/251 (37%), Positives = 139/251 (55%), Gaps = 8/251 (3%) Query: 41 GIDVGSVSSQAVLVCDGELYGYNSMRTGNNSPDSAKNALQGIMDKIGMKLEDINYVVGTG 100 GID GS +++ +L+ DG + + R +P A+ + + LE ++ TG Sbjct: 6 GIDSGSTATKGILLADGVI----TRRFLVPTPFRPATAITEAWETLREGLETTPFLTLTG 61 Query: 101 YGRVNVPFAHKAITEIACHARGANYMGGNKVRTILDMGGQDCKAIHCDDKGKVTNFLMND 160 YGR V FA K +TEI+CH GA ++ R ++D+GGQD K I DD G + +FLMND Sbjct: 62 YGRQLVDFADKQVTEISCHGLGARFLAP-ATRAVIDIGGQDSKVIQLDDDGNLCDFLMND 120 Query: 161 KCAAGTGRGMEVISDLMQIPIAELGPRSFDVETEPEAVSSICVVFAKSEALGLLKAGYTK 220 KCAAGTGR +EVIS + + +L S P A++S+C VFA+SEA+ L AG Sbjct: 121 KCAAGTGRFLEVISRTLGTSVEQLD--SITENVTPHAITSMCTVFAESEAISLRSAGVAP 178 Query: 221 NMVIAAYCQAMAERVVSLLERIGVEEGFFITGGIAKNPGVVKRIERLLGIKQLETKIDSQ 280 ++A AMA R + + R+ E TGG++ + +E L + + T D+Q Sbjct: 179 EAILAGVINAMARRSANFIARLSCEAPILFTGGVSHCQKFARMLESHLRM-PVNTHPDAQ 237 Query: 281 IAGALGAALFG 291 AGA+GAA+ G Sbjct: 238 FAGAIGAAVIG 248 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: 195 Number of extensions: 18 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: 301 Length of database: 255 Length adjustment: 25 Effective length of query: 276 Effective length of database: 230 Effective search space: 63480 Effective search space used: 63480 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: 47 (22.7 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