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:1.1.1.17

# 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:1.1.1.255
mak	mannose kinase	EC:2.7.1.7
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:1.1.1.67	EC:1.1.1.138	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

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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