D-sorbitol (glucitol) catabolism in Saccharomonospora marina XMU15

GapMind for catabolism of small carbon sources

D-sorbitol (glucitol) catabolism in Saccharomonospora marina XMU15

Best path

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).

all:

sorbitol-transport, sdh and scrK
or sorbitol-PTS and srlD
Comment: In pathway I, sorbitol dehydrogenase (sdh) forms fructose and a fructokinase forms fructose 6-phosphate, a central metabolite. In pathway II, the PTS uptake system forms sorbitol 6-phosphate, and dehydrogenase srlD forms fructose 6-phosphate.

sorbitol-transport:

SOT
or mtlEFGK
Comment: Rules for sorbitol transport were built using curated clusters for transporters and PTS systems of sorbitol / D-sorbitol / glucitol / D-glucitol

sorbitol-PTS:

mtlA
or srlABE
Comment: PTS systems form sorbitol 6-phosphate

srlABE: srlA, srlB and srlE

Comment: sorbitol-specific PTS system with an unusual split EII-C, known as srlABE in Escherichia coli (TC 4.A.4.1.1). Because enzyme I and HPR are usually not specific, they are not represented. srlA = EII-C2 component; srlB = EII-A component; srlE = EII-BC1 components.

mtlEFGK: mtlE, mtlF, mtlG and mtlK

Comment: A polyol ABC transporter, known as MtlEFGK in Pseudomonas fluorescens (TC 3.A.1.1.49). Pseudomonas fluorescens FW300-N2E3 and Pseudomonas fluorescens GW456-L13 have very similar systems, but FW300-N2E3 does not grow on sorbitol as the sole carbon source, and we have no fitness data for GW456-L13 on sorbitol, so it is uncertain whether they transport sorbitol or not. They are marked as ignore. A related system in Rhodobacter sphaeroides, smoEFGK, appears in TCDB (as TC 3.A.1.1.5) but there does not seem to be any experimental evidence that it tranpsorts sorbitol, so it is also ignored.

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	SACMADRAFT_RS22755
mtlF	ABC transporter for polyols MtlEFGK, permease component MtlF	SACMADRAFT_RS22750	SACMADRAFT_RS06535
mtlG	ABC transporter for polyols MtlEFGK, permease component MtlG	SACMADRAFT_RS22745	SACMADRAFT_RS06540
mtlK	ABC transporter for polyols MtlEFGK, permease component MtlK	SACMADRAFT_RS04690	SACMADRAFT_RS15515
sdh	sorbitol dehydrogenase	SACMADRAFT_RS27250	SACMADRAFT_RS08725
scrK	fructokinase	SACMADRAFT_RS23105	SACMADRAFT_RS29575
Alternative steps:
mtlA	PTS system for polyols, EII-CBA components	SACMADRAFT_RS17490
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	SACMADRAFT_RS15760	SACMADRAFT_RS10135
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources