GapMind for catabolism of small carbon sources

 

D-sorbitol (glucitol) catabolism in Neiella marina J221

Best path

SOT, sdh, scrK

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 (6 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
SOT sorbitol:H+ co-transporter SOT1 or SOT2 CBE68_RS14625 CBE68_RS15430
sdh sorbitol dehydrogenase CBE68_RS14530 CBE68_RS14645
scrK fructokinase CBE68_RS08895 CBE68_RS14640
Alternative steps:
mtlA PTS system for polyols, EII-CBA components
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 CBE68_RS16350
mtlK ABC transporter for polyols MtlEFGK, permease component MtlK CBE68_RS16355 CBE68_RS09785
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 CBE68_RS17620 CBE68_RS16430
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 24 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:

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