Align benzoyl-CoA reductase (EC 1.3.7.8) (characterized)
to candidate WP_041098439.1 SUTH_RS08180 acyl-CoA dehydratase activase
Query= BRENDA::Q8VUG0 (301 letters) >NCBI__GCF_000828635.1:WP_041098439.1 Length = 269 Score = 134 bits (336), Expect = 3e-36 Identities = 80/264 (30%), Positives = 141/264 (53%), Gaps = 13/264 (4%) Query: 37 IITCGIDVGSVSSQAVLVCDGELYGYNSMRTGNNSPD-----------SAKNALQGIMDK 85 +IT GID+GS S + +L+ + ++ G +++ G +A A ++ Sbjct: 1 MITAGIDMGSRSIKVILLEELKVDGAPALKYGVKKAHIMMPGDLDQDVAADKAYNEALEA 60 Query: 86 IGMKLEDINYVVGTGYGRVNVPFAHKAITEIACHARGANYMGGNKVRTILDMGGQDCKAI 145 G+K ED+ V TG GR V FA + ITE+ A+GAN+M RT++D+G ++ + + Sbjct: 61 AGLKREDVKAVFATGAGRKQVAFAAEGITEMTAGAKGANFMFPQG-RTVVDVGAEEGRGM 119 Query: 146 HCDDKGKVTNFLMNDKCAAGTGRGMEVISDLMQIPIAELGPRSFDVETEPEAVSSICVVF 205 D +G+ +F N+KCAAG G E +S +Q+ + E G S + + +++ C VF Sbjct: 120 KTDAEGRAVDFAGNEKCAAGAGSFAEAMSRALQMTLKEFGDASLKSD-KTIPMNAQCTVF 178 Query: 206 AKSEALGLLKAGYTKNMVIAAYCQAMAERVVSLLERIGVEEGFFITGGIAKNPGVVKRIE 265 A+SE + L+ + KN + A A+A RV +++ R+G+E + GG+ N G V+ ++ Sbjct: 179 AESEVVSLIHSATPKNDIAKAVLDAVASRVCAMVRRVGIEGEVVLIGGMVHNAGFVQSLK 238 Query: 266 RLLGIKQLETKIDSQIAGALGAAL 289 +G+ + + ALG A+ Sbjct: 239 TAMGVDAISLPDMPEYISALGCAM 262 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: 196 Number of extensions: 13 Number of successful extensions: 4 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: 269 Length adjustment: 26 Effective length of query: 275 Effective length of database: 243 Effective search space: 66825 Effective search space used: 66825 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 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