Align benzoyl-CoA reductase (EC 1.3.7.8) (characterized)
to candidate 8500230 DvMF_0987 CoA-substrate-specific enzyme activase (RefSeq)
Query= BRENDA::Q8VUG1 (269 letters) >FitnessBrowser__Miya:8500230 Length = 269 Score = 166 bits (419), Expect = 6e-46 Identities = 97/267 (36%), Positives = 147/267 (55%), Gaps = 11/267 (4%) Query: 2 ITAGIDMGSRSVKVVLLEQIKVEGAKAPSFAVKKAHLMLPGDLDADQAAEKAFDAALAEA 61 + AG+D+GS + K V+L+ S AV + P + + + DAAL EA Sbjct: 6 LVAGVDVGSTAAKAVVLD--------TASRAVLGV-AVTPTGWNPRETGQAVLDAALREA 56 Query: 62 GVTRDQVKSVFATGAGRGQVAFATEGITEMTAGARGAVFMYPQARTVVDVGAEEGRGIKT 121 G D+V V TG GR + F +TE+T ARGA + P RTV+DVG ++ + + Sbjct: 57 GTGIDRVARVVGTGYGRISLPFLHRTVTEITCHARGAQHLAPDTRTVLDVGGQDSKVVAV 116 Query: 122 DPDGKAIDFAGNEKCAAGAGSFAEAMSRALQLSLKEFGEASLRSDKSIPMNAQCTVFAES 181 D G DF N+KCAAG G F + M+ L ++L E G+A+LR +P+N+ C VFAE+ Sbjct: 117 DERGNVRDFVMNDKCAAGTGRFLQVMTGVLDMTLDEMGDAALRG-TPVPLNSMCAVFAET 175 Query: 182 EVVSLIHSSTPKEDIAKAVLDAVASRVCAMVRRVGIEGNVVLIGGMGHNPGFVQSLKTAM 241 EV+ LI K+D+A +++ +VA R+ A+ RV + GG+ NP F + + Sbjct: 176 EVIGLIAQGVSKDDLAASIVASVARRLKALTGRVPLVPGCAFTGGLATNPAFARIFSDTL 235 Query: 242 DVDQVLLPELPEFVSALGCALIAAERV 268 + V + ++P+ ALG ALIAA+ V Sbjct: 236 GL-AVTVSDMPQATGALGAALIAAQDV 261 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: 209 Number of extensions: 17 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: 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 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