GapMind for catabolism of small carbon sources

 

Definition of pyruvate catabolism

As rules and steps, or see full text

Rules

Overview: Pyruvate is a central metabolite, so GapMind represents transport only.

Steps

actP: large subunit of pyruvate transporter (actP-like)

yjcH: putative small subunit of pyruvate transporter (yjcH-like)

cstA: large subunit of pyruvate transporter (CstA)

ybdD: small subunit of pyruvate transporter (YbdD)

SLC5A8: sodium-coupled pyruvate transporter

dctP: pyruvate TRAP transporter, substrate-binding component

dctQ: pyruvate TRAP transporter, small permease component

dctM: pyruvate TRAP transporter, large permease component

JEN1: pyruvate symporter JEN1

btsT: pyruvate symporter BtsT

mctC: pyruvate symporter MctC

MCT4: pyruvate symporter MCT4 (SLC16A3)

mctP: pyruvate permease MctP

Links

Downloads

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, the preprint on GapMind for carbon sources, 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