GapMind for catabolism of small carbon sources

 

fumarate catabolism in Shewanella amazonensis SB2B

Best path

dctM, dctP, dctQ

Also see fitness data for the top candidates

Rules

Overview: Since fumarate is a TCA cycle intermediate, GapMind represent its uptake only.

9 steps (6 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
dctM fumarate TRAP transporter, large permease component DctM Sama_2211
dctP fumarate TRAP transporter, substrate-binding component DctP Sama_2209
dctQ fumarate TRAP transporter, small permease component DctQ Sama_2210
Alternative steps:
dauA fumarate transporter DauA Sama_1067
dctA fumarate:H+ symporter DctA Sama_2768 Sama_1319
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
sdcL fumarate:Na+ symporter SdcL
SLC26dg fumarate transporter SLC26dg Sama_1990

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 (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 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