GapMind for catabolism of small carbon sources

 

succinate catabolism in Desulfovibrio vulgaris Miyazaki F

Best path

dauA

Also see fitness data for the top candidates

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.

9 steps (4 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
dauA succinate:H+ symporter DauA DvMF_1575 DvMF_2017
Alternative steps:
dctA succinate:H+ symporter DctA
dctM succinate TRAP transporter, large permease protein DctM DvMF_1931 DvMF_2137
dctP succinate TRAP transporter, component DctP DvMF_2135 DvMF_1932
dctQ succinate TRAP transporter, small permease component DctQ
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
satP succinate:H+ symporter SatP DvMF_2076
sdc succinate:Na+ symporter Sdc

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

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