Align benzoyl-CoA reductase (EC 1.3.7.8) (characterized)
to candidate WP_041098439.1 SUTH_RS08180 acyl-CoA dehydratase activase
Query= BRENDA::Q8VUG1 (269 letters) >NCBI__GCF_000828635.1:WP_041098439.1 Length = 269 Score = 427 bits (1097), Expect = e-124 Identities = 213/269 (79%), Positives = 245/269 (91%) Query: 1 MITAGIDMGSRSVKVVLLEQIKVEGAKAPSFAVKKAHLMLPGDLDADQAAEKAFDAALAE 60 MITAGIDMGSRS+KV+LLE++KV+GA A + VKKAH+M+PGDLD D AA+KA++ AL Sbjct: 1 MITAGIDMGSRSIKVILLEELKVDGAPALKYGVKKAHIMMPGDLDQDVAADKAYNEALEA 60 Query: 61 AGVTRDQVKSVFATGAGRGQVAFATEGITEMTAGARGAVFMYPQARTVVDVGAEEGRGIK 120 AG+ R+ VK+VFATGAGR QVAFA EGITEMTAGA+GA FM+PQ RTVVDVGAEEGRG+K Sbjct: 61 AGLKREDVKAVFATGAGRKQVAFAAEGITEMTAGAKGANFMFPQGRTVVDVGAEEGRGMK 120 Query: 121 TDPDGKAIDFAGNEKCAAGAGSFAEAMSRALQLSLKEFGEASLRSDKSIPMNAQCTVFAE 180 TD +G+A+DFAGNEKCAAGAGSFAEAMSRALQ++LKEFG+ASL+SDK+IPMNAQCTVFAE Sbjct: 121 TDAEGRAVDFAGNEKCAAGAGSFAEAMSRALQMTLKEFGDASLKSDKTIPMNAQCTVFAE 180 Query: 181 SEVVSLIHSSTPKEDIAKAVLDAVASRVCAMVRRVGIEGNVVLIGGMGHNPGFVQSLKTA 240 SEVVSLIHS+TPK DIAKAVLDAVASRVCAMVRRVGIEG VVLIGGM HN GFVQSLKTA Sbjct: 181 SEVVSLIHSATPKNDIAKAVLDAVASRVCAMVRRVGIEGEVVLIGGMVHNAGFVQSLKTA 240 Query: 241 MDVDQVLLPELPEFVSALGCALIAAERVH 269 M VD + LP++PE++SALGCA+IAAER H Sbjct: 241 MGVDAISLPDMPEYISALGCAMIAAERQH 269 Lambda K H 0.317 0.131 0.363 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: 332 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: 269 Length of database: 269 Length adjustment: 25 Effective length of query: 244 Effective length of database: 244 Effective search space: 59536 Effective search space used: 59536 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