GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bcrD in Magnetospirillum magneticum AMB-1

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)



>lcl|NCBI__GCF_000009985.1:WP_011384537.1 AMB_RS10805 benzoyl-CoA
           reductase subunit D
          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.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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