Align Benzoyl-CoA reductase subunit D; 3-hydroxybenzoyl-CoA reductase subunit delta; EC 1.3.7.8; EC 1.3.99.n1 (characterized)
to candidate WP_011384537.1 AMB_RS10805 benzoyl-CoA reductase subunit D
Query= SwissProt::O87877 (282 letters) >NCBI__GCF_000009985.1:WP_011384537.1 Length = 279 Score = 404 bits (1037), Expect = e-117 Identities = 203/273 (74%), Positives = 233/273 (85%) Query: 3 ITAGIDIGTGAVKTVLFRVEGDKTEWLAKRNDRIRQRDPFKLAEEAYNGLLEEAGLKASD 62 IT G+DIG+G +KTV+F+V GDK EWL K RIR RDPF+L EAY+ +L+ AG+ D Sbjct: 5 ITTGVDIGSGCIKTVVFKVNGDKVEWLGKETARIRNRDPFQLTNEAYDHMLKTAGVDRKD 64 Query: 63 VDYVATTGEGESLAFHTGHFYSMTTHARGAVYLNPEARAVLDIGALHGRAIRNDERGKVE 122 V YVA+TG+ E+L+F TGHFYSMTTH RG +YLNPEARAVLDIGAL+GRAIR D GKV Sbjct: 65 VAYVASTGDAENLSFATGHFYSMTTHGRGGLYLNPEARAVLDIGALNGRAIRMDGVGKVL 124 Query: 123 TYKMTSQCASGSGQFLENIARYLGIAQDEIGSLSTQADNPEVVSSICAVLAETDVINMVS 182 +YKMTSQCASGSGQFLENIARYLGIAQDEIGSLS +AD+PE VSSICAVLAETDVINMVS Sbjct: 125 SYKMTSQCASGSGQFLENIARYLGIAQDEIGSLSMKADDPEKVSSICAVLAETDVINMVS 184 Query: 183 RGISAPNILKGIHISMAGRLAKLLKSVGARDGVVLCTGGLALDEGLLKTLNESIQEQKMA 242 RGISA NILKGIH+SMA RLAKLLKS+GA DG+V TGGLALD GL+ LNE+ +++K+ Sbjct: 185 RGISASNILKGIHVSMAVRLAKLLKSIGAVDGIVQVTGGLALDTGLVAALNEAAEQEKVN 244 Query: 243 VVAYNHPDSPYAGAIGAALWGAFRHEKLARLGQ 275 + A +HPDS YAGAIGAALWGAFRHEKLARLGQ Sbjct: 245 LKAVSHPDSIYAGAIGAALWGAFRHEKLARLGQ 277 Lambda K H 0.316 0.133 0.376 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: 340 Number of extensions: 6 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: 282 Length of database: 279 Length adjustment: 26 Effective length of query: 256 Effective length of database: 253 Effective search space: 64768 Effective search space used: 64768 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 (21.6 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