GapMind for catabolism of small carbon sources

 

Protein Ga0059261_2250 in Sphingomonas koreensis DSMZ 15582

Annotation: Ga0059261_2250 ABC-type multidrug transport system, ATPase component

Length: 307 amino acids

Source: Korea in FitnessBrowser

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 38% 57% 135.6 uncharacterized ABC transporter ATP-binding protein yadG 42% 238.0
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 95% 125.9 uncharacterized ABC transporter ATP-binding protein yadG 42% 238.0
L-leucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 95% 125.9 uncharacterized ABC transporter ATP-binding protein yadG 42% 238.0
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 95% 125.9 uncharacterized ABC transporter ATP-binding protein yadG 42% 238.0
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 95% 125.9 uncharacterized ABC transporter ATP-binding protein yadG 42% 238.0
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 95% 125.9 uncharacterized ABC transporter ATP-binding protein yadG 42% 238.0
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 95% 125.9 uncharacterized ABC transporter ATP-binding protein yadG 42% 238.0
D-galactose catabolism BPHYT_RS16930 lo Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 30% 57% 120.2 uncharacterized ABC transporter ATP-binding protein yadG 42% 238.0
L-arabinose catabolism araVsh lo ABC transporter related (characterized, see rationale) 30% 65% 116.3 uncharacterized ABC transporter ATP-binding protein yadG 42% 238.0
L-alanine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 95% 109.8 uncharacterized ABC transporter ATP-binding protein yadG 42% 238.0
L-serine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 95% 109.8 uncharacterized ABC transporter ATP-binding protein yadG 42% 238.0
L-threonine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 95% 109.8 uncharacterized ABC transporter ATP-binding protein yadG 42% 238.0
L-valine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 95% 109.8 uncharacterized ABC transporter ATP-binding protein yadG 42% 238.0

Sequence Analysis Tools

View Ga0059261_2250 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

MSDAAIEIEGLSKVYQGGKQALDDVSFTVPRGQIFGLLGPNGAGKSTLINILAGLVNKTA
GRASIWGFDIDQHPRNAKRAIGIVNQEILFDPFFTPVETLEIQAGLYGVPKAQRRSMELL
RAVHLEDKAHAYSRTLSGGMKRRLMVAKAMVHSPPVLVLDEPTAGVDIELRQQLWAYVRS
LNERGVTVVLTTHYLEEAEELCDRIAIINHGKLIANEPTRELVGKTQEKAVEVTVDRDIA
AVPDSRCFQKIEVKGDRTLVITYAKDQANAGEVLGAVQAAGFGIVDVSTREADLEDVFLS
LTRAANC

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