GapMind for catabolism of small carbon sources

 

D-sorbitol (glucitol) catabolism in Cronobacter universalis NCTC 9529

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 (8 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
mtlA PTS system for polyols, EII-CBA components AFK65_RS00440
srlD sorbitol 6-phosphate 2-dehydrogenase AFK65_RS09920 AFK65_RS04585
Alternative steps:
mtlE ABC transporter for polyols MtlEFGK, substrate-binding component MtlE
mtlF ABC transporter for polyols MtlEFGK, permease component MtlF AFK65_RS05685 AFK65_RS15765
mtlG ABC transporter for polyols MtlEFGK, permease component MtlG AFK65_RS05690 AFK65_RS17625
mtlK ABC transporter for polyols MtlEFGK, permease component MtlK AFK65_RS02825 AFK65_RS17610
scrK fructokinase AFK65_RS04815 AFK65_RS02370
sdh sorbitol dehydrogenase AFK65_RS04555 AFK65_RS07725
SOT sorbitol:H+ co-transporter SOT1 or SOT2 AFK65_RS04490 AFK65_RS16050
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 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