GapMind for catabolism of small carbon sources

 

D-sorbitol (glucitol) catabolism in Pseudomonas fluorescens FW300-N2C3

Best path

mtlE, mtlF, mtlG, mtlK, sdh, scrK

Also see fitness data for the top candidates

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 (8 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
mtlE ABC transporter for polyols MtlEFGK, substrate-binding component MtlE AO356_00025 AO356_27670
mtlF ABC transporter for polyols MtlEFGK, permease component MtlF AO356_00020 AO356_27675
mtlG ABC transporter for polyols MtlEFGK, permease component MtlG AO356_00015 AO356_27680
mtlK ABC transporter for polyols MtlEFGK, permease component MtlK AO356_00010 AO356_27685
sdh sorbitol dehydrogenase AO356_27985 AO356_27690
scrK fructokinase AO356_00035 AO356_27700
Alternative steps:
mtlA PTS system for polyols, EII-CBA components
SOT sorbitol:H+ co-transporter SOT1 or SOT2 AO356_27270
srlA PTS system for sorbitol SrlABE, EII-C2 component SrlA
srlB PTS system for sorbitol SrlABE, EII-A component SrlB
srlD sorbitol 6-phosphate 2-dehydrogenase AO356_22455 AO356_18385
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 (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