GapMind for catabolism of small carbon sources


Finding step gtrB for L-glutamate catabolism in Azospirillum brasilense Sp245

3 candidates for gtrB: tripartite L-glutamate:Na+ symporter, large membrane component GtrB

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med AZOBR_RS20015 C4-dicarboxylate ABC transporter GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized) 55% 97% 505 Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids 57% 515.0
med AZOBR_RS29760 C4-dicarboxylate ABC transporter GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized) 44% 75% 251.9 TRAP C4-dicarboxylate transport system permease, DctM-2 subunit, component of The 2-ketomonocarboxylate transporter (presented in order of affinity - 2-oxovalerate [highest affinity, KD=0.1 μM], 2-oxoisovalerate, 2-oxobutyrate, 2-oxoisocaproate, 2-oxo-3-methylvalerate, pyruvate [lowest affinity, KD=3 μM]) 47% 479.9
lo AZOBR_RS14700 C4-dicarboxylate ABC transporter permease GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized) 31% 98% 224.6 Putative uncharacterized protein, component of The malonate uptake transporter, MatPQM. Regulated by the GtrA transcriptional activator (Chen et al. 2010). MatM is fused in a single protein C-terminal to MatA (malonyl-CoA decarboxylase) 37% 284.6

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

Also see fitness data for the candidates

Definition of step gtrB

Or cluster all characterized gtrB proteins

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



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 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