GapMind for catabolism of small carbon sources


Definition of D-mannitol catabolism

As text, or see rules and steps

# Mannitol degradation in GapMind is based on MetaCyc pathway
# mannitol degradation I via a phosphotransferase system (metacyc:MANNIDEG-PWY),
# pathway II via mannitol 1-dehydrogenase (metacyc:PWY-3861),
# or another oxidative pathway with mannitol 2-dehydrogenase (PMID:8254318).

# Unified EII-CBA in Escherichia coli (mtlA) and Vibrio cholerae. Ignore similarity to the II-CB only systems.
mtlA	mannitol phosphotransferase system, EII-CBA components	curated:BRENDA::P00550	curated:TCDB::Q9KKQ7	ignore:TCDB::P42956	ignore:SwissProt::P50852	ignore:SwissProt::O65989	ignore:SwissProt::P69826	ignore:SwissProt::P28008

# PTS systems forming mannitol 1-phosphate
mannitol-PTS: mtlA

# Two-part PTS, with EII-CB (cmtA/mtlA) separate from EII-A (cmtB/mtlF), in
# Escherichia coli (cmt system), Bacillus subtilis, Staphylococcus
# carnosus, Clostridium acetobutylicum, and Geobacillus stearothermophilus.
# Ignore similarity to the unified systems.
cmtA	mannitol phosphotransferase system, EII-CB component CmtA/MtlF	curated:SwissProt::P69826	curated:TCDB::P42956	curated:SwissProt::P28008	curated:SwissProt::O65989	curated:SwissProt::P50852	ignore:BRENDA::P00550	ignore:TCDB::Q9KKQ7

# For C. acetobutylicum, the mtlF component is is uniprot:O65991
# (see PMID:11160802); and in Geobacillus it is uniprot:Q45420 (PMID:824601;
# Genbank U18943.1).
# There is also a paper about the EII-A and EII-BC system from S. aureus, see PMID:3064811 and
# SwissProt uniprot:P0A0E0, but I'm not sure this is the correct accession, so ignore it.
cmtB	mannitol phosphotransferase system, EII-A component CmtB/MtlF	curated:ecocyc::CMTB-MONOMER	curated:SwissProt::P17876	curated:TCDB::C0H3V2	uniprot:O65991	uniprot:Q45420	ignore:SwissProt::P0A0E0

mannitol-PTS: cmtA cmtB

# EII-A, EII-BC1, and EII-C2 -- the sorbitol/glucitol system in E. coli, which also transports mannitol.
gutB	mannitol PTS system, EII-A component GutB	curated:CharProtDB::CH_090883
# Ignore similarity to close homolog in Erwinia, annotated as transporting sorbitol only
gutE	mannitol PTS system, EII-BC1 component GutE	curated:SwissProt::P56580	ignore:SwissProt::O32522
# Ignore similarity to close homolog in Erwinia, annotated as transporting sorbitol only
gutA	mannitol PTS system, EII-C2 component GutA	curated:SwissProt::P56579	ignore:SwissProt::O32521
mannitol-PTS: gutB gutE gutA

# ABC transporters

# MtlEFGK in several strains of Pseudomonas fluorescens or Pseudomonas simiae, or smoEFGK in Rhodopseudomonas sphaeroides.
# (The Rhodopseudomonas system was missed by the query; it is annotated as a hexitol transporter.)
# For all components, ignore simlarity to close homologs in FW300-N2C3 or FW300-N2E2, annotated as transporting sorbitol only.
mtlE	polyol ABC transporter, substrate-binding component MtlE/SmoE	curated:TCDB::O30491	curated:reanno::WCS417:GFF2493	curated:reanno::pseudo13_GW456_L13:PfGW456L13_3042	curated:reanno::pseudo3_N2E3:AO353_25880	ignore:reanno::pseudo5_N2C3_1:AO356_00025	ignore:reanno::pseudo6_N2E2:Pf6N2E2_1963	curated:TCDB::O30831
mtlF	polyol ABC transporter, permease component 1 (MtlF/SmoF)	curated:TCDB::O30492	curated:reanno::WCS417:GFF2492	curated:reanno::pseudo13_GW456_L13:PfGW456L13_3041	curated:reanno::pseudo3_N2E3:AO353_25885	ignore:reanno::pseudo5_N2C3_1:AO356_00020	ignore:reanno::pseudo6_N2E2:Pf6N2E2_1962	curated:TCDB::O30832
mtlG	polyol ABC transporter, permease component 2 (MtlG/SmoG)	curated:TCDB::O30493	curated:reanno::WCS417:GFF2491	curated:reanno::pseudo13_GW456_L13:PfGW456L13_3040	curated:reanno::pseudo3_N2E3:AO353_25890	ignore:reanno::pseudo6_N2E2:Pf6N2E2_1961	ignore:reanno::pseudo5_N2C3_1:AO356_00015	curated:TCDB::O30833
mtlK	polyol ABC transporter, ATP component MtlK/SmoG	curated:TCDB::O30494	curated:reanno::WCS417:GFF2490	curated:reanno::pseudo13_GW456_L13:PfGW456L13_3039	curated:reanno::pseudo3_N2E3:AO353_25895	ignore:reanno::pseudo6_N2E2:Pf6N2E2_1960	ignore:reanno::pseudo5_N2C3_1:AO356_00010	curated:TCDB::P54933

# Transporters and PTS systems were identified using
# query: transporter:mannitol:D-mannitol
mannitol-transport: mtlE mtlF mtlG mtlK

PLT5	polyol transporter PLT5	curated:CharProtDB::CH_091483
mannitol-transport: PLT5

# Ignore erroneous annotation of the TRAP transporter component Q3J1R2 from Rhodobacter sphaeroides as SmoM
# Ignore a porin from Pseudomonas aeruginosa

mtlD	mannitol-1-phosphate 5-dehydrogenase	EC:

# In pathway I, the phosphotransferase system forms mannitol 1-phosphate and
# 5-dehydrogenase (mtlD) forms fructose 6-phosphate.
all: mannitol-PTS mtlD

mt1d	mannitol 1-dehydrogenase	EC:
mak	mannose kinase	EC:
import mannose.steps:manA # mannose 6-phosphate isomerase

# In pathway II, mannitol is oxidized to 
# mannose by mt1d, phosphorylated to mannose 6-phosphate, and isomerized
# to fructose 6-phosphate.
all: mannitol-transport mt1d mak manA

# SwissProt P33216 was shown to have this activity (PMID:2789134; PMID:8254318)
mt2d	mannitol 2-dehydrogenase	EC:	EC:	uniprot:P33216

import fructose.steps:scrK # fructokinase

# Alternatively, mannitol 2-dehydrogenase (mt2d) forms fructose, and fructokinase (scrK)
# forms fructose 6-phosphate.
all: mannitol-transport mt2d scrK



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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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