GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Shewanella loihica PV-4

Align glucose transporter, ATPase component (characterized)
to candidate 5210659 Shew_3087 lipid ABC transporter ATPase/inner membrane protein (RefSeq)

Query= reanno::Phaeo:GFF3641
         (260 letters)



>FitnessBrowser__PV4:5210659
          Length = 620

 Score = 89.7 bits (221), Expect = 1e-22
 Identities = 66/216 (30%), Positives = 107/216 (49%), Gaps = 20/216 (9%)

Query: 27  GIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRVNGDKVEITNPRD 86
           G++ +  +S+ + PGE V L+G +GAGKSTL ++L   Y +D+G I ++G  +    P+D
Sbjct: 391 GVEVIRGLSLHIAPGERVALVGASGAGKSTLFELLQRFYVLDSGVIALDGIDIASLRPQD 450

Query: 87  ARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAMEAECRKIMNRLNPNFQK 146
            R        +++  A ++    N+  GR         D S  E +   +  R +     
Sbjct: 451 LRQQYALVPQESVIFATSV--LENVRYGRP--------DASLEEVQAACVAARADEFIAD 500

Query: 147 FSEPVSA--------LSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQMVAELIQQ 198
           FSE            LSGGQ+Q +AIARA+  +  +L++DE T+AL     Q V + +  
Sbjct: 501 FSEGYQTYLGERGVRLSGGQKQRIAIARAILADRPVLLLDEATSALDAVSEQKVKQALDV 560

Query: 199 LKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVGT 234
           L  QG    +I H +  V+   DR  VM  G+L+ +
Sbjct: 561 L-MQGRTTLIIAHRLATVLN-ADRILVMDKGELIAS 594


Lambda     K      H
   0.317    0.135    0.373 

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: 288
Number of extensions: 17
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: 260
Length of database: 620
Length adjustment: 31
Effective length of query: 229
Effective length of database: 589
Effective search space:   134881
Effective search space used:   134881
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: 50 (23.9 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