Definition of D-sorbitol (glucitol) catabolism

GapMind for catabolism of small carbon sources

Definition of D-sorbitol (glucitol) catabolism

# 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, metacyc:PWY-4101)
# and pathway II (via sorbitol-6-phosphate 2-dehydrogenase, metacyc:SORBDEG-PWY).

mtlE	ABC transporter for polyols MtlEFGK, substrate-binding component MtlE	curated:TCDB::O30491	curated:reanno::BFirm:BPHYT_RS16115	curated:reanno::Phaeo:GFF1305	curated:reanno::WCS417:GFF2493	curated:reanno::acidovorax_3H11:Ac3H11_2944	curated:reanno::pseudo5_N2C3_1:AO356_00025	curated:reanno::pseudo6_N2E2:Pf6N2E2_1963	curated:TCDB::O30831	ignore:reanno::pseudo3_N2E3:AO353_25880	ignore:reanno::pseudo13_GW456_L13:PfGW456L13_3042

mtlF	ABC transporter for polyols MtlEFGK, permease component MtlF	curated:TCDB::O30492	curated:reanno::BFirm:BPHYT_RS16110	curated:reanno::Phaeo:GFF1304	curated:reanno::WCS417:GFF2492	curated:reanno::acidovorax_3H11:Ac3H11_2943	curated:reanno::pseudo5_N2C3_1:AO356_00020	curated:reanno::pseudo6_N2E2:Pf6N2E2_1962	curated:TCDB::O30832	ignore:reanno::pseudo3_N2E3:AO353_25885	ignore:reanno::pseudo13_GW456_L13:PfGW456L13_3041

mtlG	ABC transporter for polyols MtlEFGK, permease component MtlG	curated:TCDB::O30493	curated:reanno::BFirm:BPHYT_RS16105	curated:reanno::Phaeo:GFF1303	curated:reanno::WCS417:GFF2491	curated:reanno::acidovorax_3H11:Ac3H11_2942	curated:reanno::pseudo5_N2C3_1:AO356_00015	curated:reanno::pseudo6_N2E2:Pf6N2E2_1961	ignore:reanno::pseudo3_N2E3:AO353_25890	ignore:reanno::pseudo13_GW456_L13:PfGW456L13_3040	ignore:TCDB::O30833

mtlK	ABC transporter for polyols MtlEFGK, permease component MtlK	curated:TCDB::O30494	curated:reanno::BFirm:BPHYT_RS16095	curated:reanno::Phaeo:GFF1302	curated:reanno::WCS417:GFF2490	curated:reanno::acidovorax_3H11:Ac3H11_2941	curated:reanno::pseudo5_N2C3_1:AO356_00010	curated:reanno::pseudo6_N2E2:Pf6N2E2_1960	ignore:reanno::pseudo3_N2E3:AO353_25895	ignore:reanno::pseudo13_GW456_L13:PfGW456L13_3039	ignore:TCDB::P54933

# 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.
mtlEFGK: mtlE mtlF mtlG mtlK

srlA	PTS system for sorbitol SrlABE, EII-C2 component SrlA	curated:SwissProt::O32332	curated:SwissProt::O32521	curated:SwissProt::P56579

# A complication in Erwinia -- srlB is present in Erwinia amylovora (O32523_ERWAM, 50% identical)
# but is not curated, probably because PMID:9435786 do not report a mutant in it.
# Since it is in a characterized cluster, decided to include it.
# PMID:9435786 also suggests that EII-BC1 is split into srlA/srlE but I think this is not correct.
srlB	PTS system for sorbitol SrlABE, EII-A component SrlB	curated:CharProtDB::CH_090883	curated:TCDB::O32334	uniprot:O32523

srlE	PTS system for sorbitol SrlABE, EII-BC1 component SrlE	curated:SwissProt::O32333	curated:SwissProt::O32522	curated:SwissProt::P56580

# 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.
srlABE: srlA srlB srlE

# polyol PTS system with EII-CBA all fused, known as mtlA in E. coli (TC 4.A.2.1.2).
# Also includes TC 4.A.2.1.12 (Q9KKQ7).
# TC 4.A.2.1.5 (P42956) is the B. subtilis mannitol transporter but probably has weak activity no sorbitol (PMC222339).
# so exclude it. Not known if the homologs from Geobacillus stearothermophilus (P50852) or Clostridium acetobutylicum
# (O65989) [which lack the A component], which are mannitol transporters, are capable of sorbitol transport
mtlA	PTS system for polyols, EII-CBA components	curated:BRENDA::P00550	curated:TCDB::Q9KKQ7	ignore:TCDB::P42956

# Various monomeric transporters related to SOT1 or SOT2
SOT	sorbitol:H+ co-transporter SOT1 or SOT2	curated:CharProtDB::CH_091483	curated:TCDB::AGG19156.1	curated:TCDB::AIU41385.1

# TakP from Rhodobacter sphaeroides (Q3J1R2) was originally misannotated as SmoM, ignored.

# PTS systems form sorbitol 6-phosphate
sorbitol-PTS: mtlA
sorbitol-PTS: srlABE

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

sdh	sorbitol dehydrogenase	EC:1.1.1.14	term:sorbitol dehydrogenase

import fructose.steps:scrK # fructokinase

# In pathway I, sorbitol dehydrogenase (sdh) forms fructose and a fructokinase forms fructose 6-phosphate,
# a central metabolite.
all: sorbitol-transport sdh scrK

srlD	sorbitol 6-phosphate 2-dehydrogenase	EC:1.1.1.140	term:sorbitol-6-phosphate dehydrogenase

# In pathway II, the PTS uptake system forms sorbitol 6-phosphate,
# and dehydrogenase srlD forms fructose 6-phosphate.
all: sorbitol-PTS srlD

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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:

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