GapMind for catabolism of small carbon sources


Finding step AZOBR_RS08260 for L-proline catabolism in Pseudomonas fluorescens GW456-L13

2 candidates for AZOBR_RS08260: proline ABC transporter, substrate-binding component

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med PfGW456L13_124 Branched-chain amino acid ABC transporter, amino acid-binding protein (TC 3.A.1.4.1) Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale) 49% 99% 347.1 BraC, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC 49% 337.4
med PfGW456L13_4606 High-affinity leucine-specific transport system, periplasmic binding protein LivK (TC 3.A.1.4.1) Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale) 41% 98% 275.8 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 71% 545.8

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 AZOBR_RS08260

Or cluster all characterized AZOBR_RS08260 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