GapMind for catabolism of small carbon sources

 

Protein 6938983 in Shewanella amazonensis SB2B

Annotation: Sama_3081 ABC transporter, ATP-binding protein, putative (RefSeq)

Length: 270 amino acids

Source: SB2B in FitnessBrowser

Candidate for 10 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 35% 59% 146.4 Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- 66% 357.8
L-histidine catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 37% 78% 136.7 Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- 66% 357.8
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 37% 78% 136.7 Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- 66% 357.8
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 99% 134.8 Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- 66% 357.8
L-leucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 99% 134.8 Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- 66% 357.8
L-valine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 99% 134.8 Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- 66% 357.8
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 33% 62% 129.8 Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- 66% 357.8
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 33% 68% 127.1 Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- 66% 357.8
D-alanine catabolism AZOBR_RS08245 lo Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 32% 90% 110.2 Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- 66% 357.8
L-proline catabolism AZOBR_RS08245 lo Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 32% 90% 110.2 Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- 66% 357.8

Sequence Analysis Tools

View 6938983 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MNHESDVLVEVRNLGFSRGERVIYEDISLSIPKGKVTAIMGPSGIGKTTLLKLIAGQLVP
DHGEVLFDGVNIHDISRSELFELRKRMSMLFQSGALFTDMNVFDNIAFALREHSGLDEAI
IRRIVLMKLEAVGLRGAAMLMPSELSGGMQRRVALARAIALEPEMVMYDEPFAGQDPISM
GVLVKLIRELSDALNLTSVVVSHDVGEVLGIADYVYVIAEKRIIAQGTPAQLKSSHDPRL
RQFIGGEPDGPVPFHYPANDYMKELTGGAN

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, 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