GapMind for catabolism of small carbon sources

 

Definition of succinate catabolism

As rules and steps, or see full text

Rules

Overview: GapMind represents succinate uptake only, as succinate is part of central metabolism. Specifically, succinate can be consumed by the TCA cycle enzymes succinate dehydrogenase, fumarase (forming L-malate), and malate dehydrogenase (either decarboxylating, with pyruvate as the product, or not, with oxalacetate with the product; both compounds are central metabolic intermediates). It's also possible that malate could be decarboxylated to lactate, as in malolactic fermentation by lactic acid bacteria.

Steps

sdc: succinate:Na+ symporter Sdc

dctA: succinate:H+ symporter DctA

dauA: succinate:H+ symporter DauA

satP: succinate:H+ symporter SatP

dctQ: succinate TRAP transporter, small permease component DctQ

dctM: succinate TRAP transporter, large permease protein DctM

dctP: succinate TRAP transporter, component DctP

Dshi_1194: TRAP transporter for succinate, fumarate, L-malate, and 2-oxoglutarate, fused 4TM/12TM components

Dshi_1195: TRAP transporter for succinate, fumarate, L-malate, and 2-oxoglutarate, substrate-binding component

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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, 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