GapMind for catabolism of small carbon sources

 

Definition of D-sorbitol (glucitol) catabolism

As rules and steps, or see full text

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).

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

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

mtlA: PTS system for polyols, EII-CBA components

SOT: sorbitol:H+ co-transporter SOT1 or SOT2

sdh: sorbitol dehydrogenase

scrK: fructokinase

srlD: sorbitol 6-phosphate 2-dehydrogenase

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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