GapMind for catabolism of small carbon sources

 

Finding step gltK for L-glutamate catabolism in Pseudomonas fluorescens FW300-N1B4

4 candidates for gltK: L-glutamate ABC transporter, permease component 1 (gltK/aatM)

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi Pf1N1B4_773 Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4) ABC transporter for L-asparagine and L-glutamate, permease subunit 2 (characterized) 100% 100% 435.3 Glutamine ABC transporter permease and substrate binding protein protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity 36% 139.8
lo Pf1N1B4_915 Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4) ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) 34% 96% 141 ABC transporter for D-Alanine, permease component 1 96% 708.0
lo Pf1N1B4_772 Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4) ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) 31% 98% 126.3 ABC transporter for L-asparagine and L-glutamate, permease component 1 100% 495.4
lo Pf1N1B4_4805 ABC transporter permease protein Glutamate/aspartate import permease protein GltK (characterized) 31% 99% 110.9 L-cystine transport system permease protein YecS 41% 145.6

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 gltK

Or cluster all characterized gltK proteins

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