GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08250 in Pseudomonas fluorescens FW300-N1B4

Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate Pf1N1B4_1079 Lipopolysaccharide ABC transporter, ATP-binding protein LptB

Query= uniprot:G8ALJ1
         (236 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1079
          Length = 241

 Score =  116 bits (291), Expect = 3e-31
 Identities = 74/240 (30%), Positives = 126/240 (52%), Gaps = 11/240 (4%)

Query: 2   LKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITFE 61
           LK   +   Y + + ++ V + I +G+IV L+G NGAGK+T    I G  +A  GR+  +
Sbjct: 4   LKAQHLAKSYKSRQVVRDVSLSIDSGQIVGLLGPNGAGKTTCFYMIVGLVQADQGRVLID 63

Query: 62  GQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITAKPGSFA---NELERVLT 118
             D++  P +   + GI   P+   IF ++SV +N+     T K    A    ELE +L 
Sbjct: 64  DLDVSHQPMHGRAKAGIGYLPQEASIFRKLSVADNIMAILETRKELDQAGRRQELESLLQ 123

Query: 119 LF--PRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAV 176
            F    +++ +     ++SGGE++ + I RAL + P+ +LLDEP  G+ P+ V  I Q +
Sbjct: 124 EFHIHHIRDNLGM---SLSGGERRRVEIARALATNPKFILLDEPFAGVDPISVGDIKQII 180

Query: 177 KDINREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYLEGGH 236
             + + + + V + + N    L +    Y++ +G++   G  A +LANE V+  YL  GH
Sbjct: 181 HHL-KAKGIGVLITDHNVRETLDICETAYIVNDGQLIAEGDSATILANELVKEVYL--GH 237


Lambda     K      H
   0.320    0.136    0.377 

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: 113
Number of extensions: 5
Number of successful extensions: 3
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: 236
Length of database: 241
Length adjustment: 23
Effective length of query: 213
Effective length of database: 218
Effective search space:    46434
Effective search space used:    46434
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 (21.8 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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