GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamG in Dinoroseobacter shibae DFL-12

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate 3607905 Dshi_1313 NADH-quinone oxidoreductase, E subunit (RefSeq)

Query= uniprot:Q39TW4
         (150 letters)



>FitnessBrowser__Dino:3607905
          Length = 402

 Score = 80.1 bits (196), Expect = 4e-20
 Identities = 41/133 (30%), Positives = 73/133 (54%), Gaps = 1/133 (0%)

Query: 16  EASSLIQILLDIQSEHNWLPKEALKRVCERLQVPMSRITHIATFYKAFSLVPKGR-HQVH 74
           +AS++I IL   Q +  WL K A++ V + L +P  R   +ATFY  F L P G    + 
Sbjct: 35  QASAIIPILWRAQEQEGWLSKPAIEYVADMLDMPYIRALEVATFYFMFQLQPVGSVAHIQ 94

Query: 75  VCMGTACHVRGAQRVLDTVQEVTGVKSGETDSDLKFSVETVNCLGCCALGPVMEVDGKHH 134
           +C  T+C + GA+ ++   +E    ++ +  +D KFS E V CLG CA  P+ ++   ++
Sbjct: 95  ICGTTSCMICGAEDLVAVCKEKIAPRAHQLSADGKFSWEEVECLGSCANAPMAQIGKDYY 154

Query: 135 GNIAPSQIASVLN 147
            ++     +++L+
Sbjct: 155 EDLTVESFSALLD 167


Lambda     K      H
   0.321    0.135    0.408 

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: 136
Number of extensions: 11
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: 150
Length of database: 402
Length adjustment: 23
Effective length of query: 127
Effective length of database: 379
Effective search space:    48133
Effective search space used:    48133
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: 46 (22.3 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