GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcrD in Desulfovibrio vulgaris Miyazaki F

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.

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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 (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:

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. 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