GapMind for catabolism of small carbon sources


Definition of succinate catabolism

As rules and steps, or see full text


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.


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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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