GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mtlF in Phaeobacter inhibens BS107

Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate GFF1304 PGA1_c13200 ABC transporter permease protein

Query= reanno::Phaeo:GFF1304
         (288 letters)



>lcl|FitnessBrowser__Phaeo:GFF1304 PGA1_c13200 ABC transporter
           permease protein
          Length = 288

 Score =  563 bits (1452), Expect = e-165
 Identities = 288/288 (100%), Positives = 288/288 (100%)

Query: 1   MATQHSRSAARIMMAPAVILLLGWMLVPLTMTLYFSFKKYLPLRGGDLGWVGFDNYARFL 60
           MATQHSRSAARIMMAPAVILLLGWMLVPLTMTLYFSFKKYLPLRGGDLGWVGFDNYARFL
Sbjct: 1   MATQHSRSAARIMMAPAVILLLGWMLVPLTMTLYFSFKKYLPLRGGDLGWVGFDNYARFL 60

Query: 61  SSSAFWPSVQATLVIVGGVLAITVILGVFLALLLNQPMWGQGIVRILVIAPFFVMPTVSA 120
           SSSAFWPSVQATLVIVGGVLAITVILGVFLALLLNQPMWGQGIVRILVIAPFFVMPTVSA
Sbjct: 61  SSSAFWPSVQATLVIVGGVLAITVILGVFLALLLNQPMWGQGIVRILVIAPFFVMPTVSA 120

Query: 121 LVWKNMFMDPVNGLFAHLWKAFGAEPVSWLSEASLQSIILIVSWQWLPFATLILLTAIQS 180
           LVWKNMFMDPVNGLFAHLWKAFGAEPVSWLSEASLQSIILIVSWQWLPFATLILLTAIQS
Sbjct: 121 LVWKNMFMDPVNGLFAHLWKAFGAEPVSWLSEASLQSIILIVSWQWLPFATLILLTAIQS 180

Query: 181 LDSEQLEAAEMDGAPPVARFGYITLPHLSRAITVVVLIQTIFLLSIFAEIFVTTQGSFGT 240
           LDSEQLEAAEMDGAPPVARFGYITLPHLSRAITVVVLIQTIFLLSIFAEIFVTTQGSFGT
Sbjct: 181 LDSEQLEAAEMDGAPPVARFGYITLPHLSRAITVVVLIQTIFLLSIFAEIFVTTQGSFGT 240

Query: 241 KTLTYLIYQRVLESQNVGLGSAGGVYAIILANIVAIFLMRIVGKNLDA 288
           KTLTYLIYQRVLESQNVGLGSAGGVYAIILANIVAIFLMRIVGKNLDA
Sbjct: 241 KTLTYLIYQRVLESQNVGLGSAGGVYAIILANIVAIFLMRIVGKNLDA 288


Lambda     K      H
   0.328    0.140    0.430 

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: 480
Number of extensions: 11
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: 288
Length of database: 288
Length adjustment: 26
Effective length of query: 262
Effective length of database: 262
Effective search space:    68644
Effective search space used:    68644
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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