GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamF in Desulfovibrio vulgaris Hildenborough

Align Benzoyl-CoA reductase electron transfer protein, selenocysteine-containing, putative (characterized, see rationale)
to candidate 207892 DVU2401 hydrogenase, iron-sulfur cluster-binding subunit, putative

Query= uniprot:Q39TW2
         (255 letters)



>MicrobesOnline__882:207892
          Length = 494

 Score =  126 bits (316), Expect = 1e-33
 Identities = 55/124 (44%), Positives = 82/124 (66%), Gaps = 1/124 (0%)

Query: 11  VVGFLCTWUAYGAADLAGVSRLQYTTETKIIRVMCTGRVDLAFVLRAFSKGADGVFIGGC 70
           VVGFLC W +YG AD AGV R    T+ +I+RV C+GRVD  F+++A   GADGV + GC
Sbjct: 11  VVGFLCNWCSYGGADTAGVGRFSQPTDLRIVRVPCSGRVDPLFIIKALISGADGVLVSGC 70

Query: 71  WPGECHYVTEGNYDVLKNVHIAKKILERIGINPDRLRLEWIAASEGMRYAEVMNDFGKRL 130
            P +CHY + GN+   + +   K  L  +GI+P+R +  W++ASEG R+  V++ F +++
Sbjct: 71  HPRDCHY-SHGNFYARRRLETLKSFLPALGIDPERFQYTWVSASEGQRWKNVVSTFVEKV 129

Query: 131 KELG 134
            +LG
Sbjct: 130 HQLG 133


Lambda     K      H
   0.321    0.138    0.406 

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: 248
Number of extensions: 7
Number of successful extensions: 2
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: 255
Length of database: 494
Length adjustment: 29
Effective length of query: 226
Effective length of database: 465
Effective search space:   105090
Effective search space used:   105090
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: 49 (23.5 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