Align benzoyl-CoA reductase (EC 1.3.7.8) (characterized)
to candidate WP_041101989.1 SUTH_RS08170 benzoyl-CoA reductase, bzd-type, subunit N
Query= BRENDA::Q8VUG3 (379 letters) >NCBI__GCF_000828635.1:WP_041101989.1 Length = 379 Score = 695 bits (1794), Expect = 0.0 Identities = 327/379 (86%), Positives = 353/379 (93%) Query: 1 MSDGLFDQFKTWYEKRHDYARDWKARTGGQVVATMCTYTPEELLIAAGMLPVRVLGAHEP 60 M+D LFDQFK WYEKRHDYARDWK RTGGQVVATMCTYT EELLIAAGMLPVRVLGAHEP Sbjct: 1 MADALFDQFKNWYEKRHDYARDWKQRTGGQVVATMCTYTAEELLIAAGMLPVRVLGAHEP 60 Query: 61 QNVTEPHIFGMFCPFCRDSLAQGLLGRFDYAEGVTLTQSCIQYRQTFGSWRLHVPTVKWD 120 QNVTEPHIFGMFCPFCRDSLAQGLLGRFDY EGVTLTQSCIQYRQTF SWR +VP+V+WD Sbjct: 61 QNVTEPHIFGMFCPFCRDSLAQGLLGRFDYCEGVTLTQSCIQYRQTFSSWRSNVPSVQWD 120 Query: 121 YYVPMPNEVQSQHSRKAHYEEVQSFRVFLQTLTGKEITDAMLKDALAVCDENRRLLRELY 180 YYVPMPN+VQS H+RKAHY E+QSFR FL LTGKE+TDAMLK+ALAV DENRRLLREL+ Sbjct: 121 YYVPMPNDVQSPHARKAHYAEIQSFRTFLSALTGKELTDAMLKEALAVVDENRRLLRELF 180 Query: 181 EYRKEADPKVTGVEALYASLTAQFIDKREHNEMLKKTLAALPTRKVERKTGARFMTIGSE 240 EYRKE +P+VTGVEALYAS+TAQF+DKREHNEMLKK LAALP+RK++RK G RFMTIGSE Sbjct: 181 EYRKEENPRVTGVEALYASITAQFVDKREHNEMLKKVLAALPSRKMDRKEGVRFMTIGSE 240 Query: 241 NDDIAFMGMVESVGATIVIDDQCSGSRYFWNASKSEGDVIKAIAERYCDRPACPTKDYPA 300 NDDIAFM MVESVG+TIVIDDQCSG+RYFWN SK E DVIKAIA+RYCDRPACPTKDYP+ Sbjct: 241 NDDIAFMAMVESVGSTIVIDDQCSGTRYFWNESKPEDDVIKAIADRYCDRPACPTKDYPS 300 Query: 301 HTRFDHVLGLAKDYGVQGAIFLQQKFCDPHEGDYPDLKRHLEDNGIPTLFLEFDITNPIG 360 HTRFDHVLGLAK++ + AIFLQQKFCDPHEGDYPDLK HLE NGIPTLFLEFDITNPIG Sbjct: 301 HTRFDHVLGLAKEFNARAAIFLQQKFCDPHEGDYPDLKEHLEKNGIPTLFLEFDITNPIG 360 Query: 361 PFRIRIEAFLETLSEEELF 379 PFRIRIEAFLET+S+EELF Sbjct: 361 PFRIRIEAFLETMSDEELF 379 Lambda K H 0.322 0.137 0.424 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: 619 Number of extensions: 12 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: 379 Length of database: 379 Length adjustment: 30 Effective length of query: 349 Effective length of database: 349 Effective search space: 121801 Effective search space used: 121801 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 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