GapMind for catabolism of small carbon sources

 

D-sorbitol (glucitol) catabolism in Desulfovibrio vulgaris Hildenborough

Best path

mtlA, srlD

Rules

Overview: D-sorbitol is also known as D-glucitol. D-sorbitol degradation in GapMind is based on MetaCyc pathways D-sorbitol degradation I (via sorbitol dehydrogenase, link) and pathway II (via sorbitol-6-phosphate 2-dehydrogenase, link).

12 steps (3 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
mtlA PTS system for polyols, EII-CBA components
srlD sorbitol 6-phosphate 2-dehydrogenase 206645
Alternative steps:
mtlE ABC transporter for polyols MtlEFGK, substrate-binding component MtlE
mtlF ABC transporter for polyols MtlEFGK, permease component MtlF
mtlG ABC transporter for polyols MtlEFGK, permease component MtlG
mtlK ABC transporter for polyols MtlEFGK, permease component MtlK DVU3161 DVU0098
scrK fructokinase
sdh sorbitol dehydrogenase 206645 DVU3137
SOT sorbitol:H+ co-transporter SOT1 or SOT2
srlA PTS system for sorbitol SrlABE, EII-C2 component SrlA
srlB PTS system for sorbitol SrlABE, EII-A component SrlB
srlE PTS system for sorbitol SrlABE, EII-BC1 component SrlE

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