GapMind for catabolism of small carbon sources

 

D-sorbitol (glucitol) catabolism in Pseudomonas fluorescens FW300-N1B4

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 (7 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
mtlE ABC transporter for polyols MtlEFGK, substrate-binding component MtlE Pf1N1B4_4850 Pf1N1B4_5038
mtlF ABC transporter for polyols MtlEFGK, permease component MtlF Pf1N1B4_4849 Pf1N1B4_5113
mtlG ABC transporter for polyols MtlEFGK, permease component MtlG Pf1N1B4_4848 Pf1N1B4_5114
mtlK ABC transporter for polyols MtlEFGK, permease component MtlK Pf1N1B4_4847 Pf1N1B4_5115
sdh sorbitol dehydrogenase Pf1N1B4_5039 Pf1N1B4_4846
scrK fructokinase Pf1N1B4_4844 Pf1N1B4_4765
Alternative steps:
mtlA PTS system for polyols, EII-CBA components
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
srlD sorbitol 6-phosphate 2-dehydrogenase Pf1N1B4_730 Pf1N1B4_512
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 Aug 02 2021. The underlying query database was built on Aug 02 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