Alignments for a candidate for AZOBR_RS08240 in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for AZOBR_RS08240 in Azospirillum brasilense Sp245

Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate AZOBR_RS08240 AZOBR_RS08240 ABC transporter permease

Query= uniprot:G8ALI9
         (505 letters)



>FitnessBrowser__azobra:AZOBR_RS08240
          Length = 505

 Score =  984 bits (2545), Expect = 0.0
 Identities = 505/505 (100%), Positives = 505/505 (100%)

Query: 1   MTAISMSSPRAIAWPSILKEAAMTAFVALLLTIPLVGLRTVDRPTGLGLETRWNEVAAAV 60
           MTAISMSSPRAIAWPSILKEAAMTAFVALLLTIPLVGLRTVDRPTGLGLETRWNEVAAAV
Sbjct: 1   MTAISMSSPRAIAWPSILKEAAMTAFVALLLTIPLVGLRTVDRPTGLGLETRWNEVAAAV 60

Query: 61  GLVFLGRLGLCLIREGHAVTVLVLAAAATAAGFFIAMPTEALRVILIAGGAVIAIRAVLA 120
           GLVFLGRLGLCLIREGHAVTVLVLAAAATAAGFFIAMPTEALRVILIAGGAVIAIRAVLA
Sbjct: 61  GLVFLGRLGLCLIREGHAVTVLVLAAAATAAGFFIAMPTEALRVILIAGGAVIAIRAVLA 120

Query: 121 IRTGRSKLSQAERDKRMDHIAAQVQHASRWLGPIAVVVALAFPFTPLADRQLLDIGILLL 180
           IRTGRSKLSQAERDKRMDHIAAQVQHASRWLGPIAVVVALAFPFTPLADRQLLDIGILLL
Sbjct: 121 IRTGRSKLSQAERDKRMDHIAAQVQHASRWLGPIAVVVALAFPFTPLADRQLLDIGILLL 180

Query: 181 TYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAMSG 240
           TYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAMSG
Sbjct: 181 TYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAMSG 240

Query: 241 VLLGFPVLRLRGDYFAIVTLGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRT 300
           VLLGFPVLRLRGDYFAIVTLGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRT
Sbjct: 241 VLLGFPVLRLRGDYFAIVTLGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRT 300

Query: 301 PAEGTAAFHEMFGLEFSPLHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDI 360
           PAEGTAAFHEMFGLEFSPLHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDI
Sbjct: 301 PAEGTAAFHEMFGLEFSPLHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDI 360

Query: 361 ACASLGINRTNMKLAAFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGM 420
           ACASLGINRTNMKLAAFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGM
Sbjct: 361 ACASLGINRTNMKLAAFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGM 420

Query: 421 GSQIGVVVAAFLVIGLPEAFRELADYRMLAFGMGMVLIMLWRPRGLLAHRDPTILLHGRP 480
           GSQIGVVVAAFLVIGLPEAFRELADYRMLAFGMGMVLIMLWRPRGLLAHRDPTILLHGRP
Sbjct: 421 GSQIGVVVAAFLVIGLPEAFRELADYRMLAFGMGMVLIMLWRPRGLLAHRDPTILLHGRP 480

Query: 481 KGGAGGPAAGSAAAGGQGIAGGSAK 505
           KGGAGGPAAGSAAAGGQGIAGGSAK
Sbjct: 481 KGGAGGPAAGSAAAGGQGIAGGSAK 505


Lambda     K      H
   0.329    0.144    0.438 

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: 990
Number of extensions: 30
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: 505
Length of database: 505
Length adjustment: 34
Effective length of query: 471
Effective length of database: 471
Effective search space:   221841
Effective search space used:   221841
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: 52 (24.6 bits)

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources