Definition of D-mannitol catabolism
As rules and steps, or see full text
Rules
Overview: Mannitol degradation in GapMind is based on MetaCyc pathway mannitol degradation I via a phosphotransferase system (link), pathway II via mannitol 1-dehydrogenase (link), or another oxidative pathway with mannitol 2-dehydrogenase (PMID:8254318).
- all:
- mannitol-PTS and mtlD
- or mannitol-transport, mt1d, mak and manA
- or mannitol-transport, mt2d and scrK
- Comment: In pathway I, the phosphotransferase system forms mannitol 1-phosphate and 5-dehydrogenase (mtlD) forms fructose 6-phosphate. In pathway II, mannitol is oxidized to mannose by mt1d, phosphorylated to mannose 6-phosphate, and isomerized to fructose 6-phosphate. Alternatively, mannitol 2-dehydrogenase (mt2d) forms fructose, and fructokinase (scrK) forms fructose 6-phosphate.
- mannitol-transport:
- mtlE, mtlF, mtlG and mtlK
- or PLT5
- Comment: Transporters and PTS systems were identified using query: transporter:mannitol:D-mannitol
- mannitol-PTS:
Steps
mtlA: mannitol phosphotransferase system, EII-CBA components
- Curated sequence P00550: protein-Npi-phosphohistidine-D-mannitol phosphotransferase (EC 2.7.1.197). PTS system mannitol-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69. PTS system mannitol-specific EIICBA component; EIICBA-Mtl; EII-Mtl; EC 2.7.1.197. Mannitol porter (MtlA) (mannitol-1-P forming), the mannitol IICBA complex. mannitol-specific PTS enzyme IICBA component (EC 2.7.1.197; EC 2.7.1.198). mannitol-specific PTS enzyme IICBA component (EC 2.7.1.197; EC 2.7.1.198)
- Curated sequence Q9KKQ7: The mannitol/glucitol transporter, MtlA (IICBAMtl)
- Ignore hits to P42956 when looking for 'other' hits (PTS system, mannitol-specific IICBA component aka EIICBA-Mtl aka Mannitol-permease IIABC component aka Phosphotransferase enzyme II, CBA component aka EC 2.7.1.69 aka EII-Mtl, component of The mannitol porter (MtlA) (mannitol-1-P forming), MtlAF)
- Ignore hits to P50852 when looking for 'other' hits (PTS system mannitol-specific EIICB component; EIICB-Mtl; EII-Mtl; EC 2.7.1.197)
- Ignore hits to O65989 when looking for 'other' hits (PTS system mannitol-specific EIICB component; EIICB-Mtl; EII-Mtl; EC 2.7.1.197)
- Ignore hits to P69826 when looking for 'other' hits (PTS system mannitol-specific cryptic EIICB component; EIICB-Mtl; EII-Mtl; EC 2.7.1.197. EIICB-Mtl. mannitol-specific PTS enzyme IICB component CmtA (EC 2.7.1.197). mannitol-specific PTS enzyme IICB component CmtA (EC 2.7.1.197))
- Ignore hits to P28008 when looking for 'other' hits (PTS system mannitol-specific EIICB component; EIICB-Mtl; EII-Mtl; EC 2.7.1.197)
- Comment: Unified EII-CBA in Escherichia coli (mtlA) and Vibrio cholerae. Ignore similarity to the II-CB only systems.
- Total: 2 characterized proteins
cmtA: mannitol phosphotransferase system, EII-CB component CmtA/MtlF
- Curated sequence P69826: PTS system mannitol-specific cryptic EIICB component; EIICB-Mtl; EII-Mtl; EC 2.7.1.197. EIICB-Mtl. mannitol-specific PTS enzyme IICB component CmtA (EC 2.7.1.197). mannitol-specific PTS enzyme IICB component CmtA (EC 2.7.1.197)
- Curated sequence P42956: PTS system, mannitol-specific IICBA component aka EIICBA-Mtl aka Mannitol-permease IIABC component aka Phosphotransferase enzyme II, CBA component aka EC 2.7.1.69 aka EII-Mtl, component of The mannitol porter (MtlA) (mannitol-1-P forming), MtlAF
- Curated sequence P28008: PTS system mannitol-specific EIICB component; EIICB-Mtl; EII-Mtl; EC 2.7.1.197
- Curated sequence O65989: PTS system mannitol-specific EIICB component; EIICB-Mtl; EII-Mtl; EC 2.7.1.197
- Curated sequence P50852: PTS system mannitol-specific EIICB component; EIICB-Mtl; EII-Mtl; EC 2.7.1.197
- Ignore hits to P00550 when looking for 'other' hits (protein-Npi-phosphohistidine-D-mannitol phosphotransferase (EC 2.7.1.197). PTS system mannitol-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69. PTS system mannitol-specific EIICBA component; EIICBA-Mtl; EII-Mtl; EC 2.7.1.197. Mannitol porter (MtlA) (mannitol-1-P forming), the mannitol IICBA complex. mannitol-specific PTS enzyme IICBA component (EC 2.7.1.197; EC 2.7.1.198). mannitol-specific PTS enzyme IICBA component (EC 2.7.1.197; EC 2.7.1.198))
- Ignore hits to Q9KKQ7 when looking for 'other' hits (The mannitol/glucitol transporter, MtlA (IICBAMtl))
- Comment: 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.
- Total: 5 characterized proteins
cmtB: mannitol phosphotransferase system, EII-A component CmtB/MtlF
- Curated sequence CMTB-MONOMER: mannitol-specific PTS enzyme IIA component CmtB (EC 2.7.1.197). mannitol-specific PTS enzyme IIA component CmtB (EC 2.7.1.197)
- Curated sequence P17876: Mannitol-specific phosphotransferase enzyme IIA component; EIIA; EIII; PTS system mannitol-specific EIIA component
- Curated sequence C0H3V2: Mannitol-specific phosphotransferase enzyme IIA component, component of The mannitol porter (MtlA) (mannitol-1-P forming), MtlAF
- UniProt sequence O65991: SubName: Full=MtlF {ECO:0000313|EMBL:AAC12850.1};
- UniProt sequence Q45420: RecName: Full=Mannitol-specific phosphotransferase enzyme IIA component {ECO:0000250|UniProtKB:P0A0E0}; AltName: Full=EIIA {ECO:0000250|UniProtKB:P0A0E0}; AltName: Full=EIII {ECO:0000303|PubMed:8824601}; AltName: Full=PTS system mannitol-specific EIIA component {ECO:0000250|UniProtKB:P0A0E0};
- Ignore hits to P0A0E0 when looking for 'other' hits (Mannitol-specific phosphotransferase enzyme IIA component; EIIA; EIII; PTS system mannitol-specific EIIA component)
- Comment: For C. acetobutylicum, the mtlF component is is O65991 (see PMID:11160802); and in Geobacillus it is 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 P0A0E0, but I'm not sure this is the correct accession, so ignore it.
- Total: 5 characterized proteins
gutB: mannitol PTS system, EII-A component GutB
- Curated sequence CH_090883: PTS system, glucitol/sorbitol-specific, IIA component. PTS system glucitol/sorbitol-specific EIIA component; EIIA-Gut; EIII-Gut; Glucitol/sorbitol-specific phosphotransferase enzyme IIA component. PTHA aka SRLB aka GUTB aka B2704, component of Glucitol porter. sorbitol-specific PTS enzyme IIA component (EC 2.7.1.198; EC 2.7.1.197). sorbitol-specific PTS enzyme IIA component (EC 2.7.1.198; EC 2.7.1.197)
- Comment: EII-A, EII-BC1, and EII-C2 -- the sorbitol/glucitol system in E. coli, which also transports mannitol.
- Total: 1 characterized proteins
gutE: mannitol PTS system, EII-BC1 component GutE
- Curated sequence P56580: PTS system glucitol/sorbitol-specific EIIB component; EII-Gut; Enzyme II-Gut; Glucitol/sorbitol-specific phosphotransferase enzyme IIB component; EC 2.7.1.198. PTHB aka SRLE aka GUTE aka B2703, component of Glucitol porter. sorbitol-specific PTS enzyme IIBC1 component (EC 2.7.1.198; EC 2.7.1.197). sorbitol-specific PTS enzyme IIBC1 component (EC 2.7.1.198; EC 2.7.1.197)
- Ignore hits to O32522 when looking for 'other' hits (PTS system glucitol/sorbitol-specific EIIB component; EII-Gut; Enzyme II-Gut; Glucitol/sorbitol-specific phosphotransferase enzyme IIB component; EC 2.7.1.198)
- Comment: Ignore similarity to close homolog in Erwinia, annotated as transporting sorbitol only
- Total: 1 characterized proteins
gutA: mannitol PTS system, EII-C2 component GutA
- Curated sequence P56579: PTS system glucitol/sorbitol-specific EIIC component; EIIC-Gut; Glucitol/sorbitol permease IIC component. PTHC aka SRLA aka GUTA aka SBL aka B2702, component of Glucitol porter. sorbitol-specific PTS enzyme IIC2 component (EC 2.7.1.198; EC 2.7.1.197). sorbitol-specific PTS enzyme IIC2 component (EC 2.7.1.198; EC 2.7.1.197)
- Ignore hits to O32521 when looking for 'other' hits (PTS system glucitol/sorbitol-specific EIIC component; EIIC-Gut; Glucitol/sorbitol permease IIC component)
- Comment: Ignore similarity to close homolog in Erwinia, annotated as transporting sorbitol only
- Total: 1 characterized proteins
mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE
- Curated sequence O30491: MtlE, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK
- Curated sequence GFF2493: ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, periplasmic substrate-binding protein
- Curated sequence PfGW456L13_3042: ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, periplasmic substrate-binding component
- Curated sequence AO353_25880: ABC transporter for D-mannitol and D-mannose, periplasmic substrate-binding component
- Ignore hits to AO356_00025 when looking for 'other' hits (ABC transporter for D-Sorbitol, periplasmic substrate-binding component)
- Ignore hits to Pf6N2E2_1963 when looking for 'other' hits (ABC transporter for D-sorbitol, periplasmic substrate-binding component)
- Curated sequence O30831: SmoE, component of Hexitol (glucitol; mannitol) porter
- Comment: 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.
- Total: 5 characterized proteins
mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF)
- Curated sequence O30492: MtlF, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK
- Curated sequence GFF2492: ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, permease component 2
- Curated sequence PfGW456L13_3041: ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, permease component 2
- Curated sequence AO353_25885: ABC transporter for D-mannitol and D-mannose, permease component 1
- Ignore hits to AO356_00020 when looking for 'other' hits (ABC transporter for D-Sorbitol, permease component 2)
- Ignore hits to Pf6N2E2_1962 when looking for 'other' hits (ABC transporter for D-sorbitol, permease component 1)
- Curated sequence O30832: SmoF, component of Hexitol (glucitol; mannitol) porter
- Total: 5 characterized proteins
mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG)
- Curated sequence O30493: MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK
- Curated sequence GFF2491: ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, permease component 1
- Curated sequence PfGW456L13_3040: ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, permease component 1
- Curated sequence AO353_25890: ABC transporter for D-mannitol and D-mannose, permease component 2
- Ignore hits to Pf6N2E2_1961 when looking for 'other' hits (ABC transporter for D-sorbitol, permease component 2)
- Ignore hits to AO356_00015 when looking for 'other' hits (ABC transporter for D-Sorbitol, permease component 1)
- Curated sequence O30833: SmoG, component of Hexitol (glucitol; mannitol) porter
- Total: 5 characterized proteins
mtlK: polyol ABC transporter, ATP component MtlK/SmoG
- Curated sequence O30494: MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK
- Curated sequence GFF2490: ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component
- Curated sequence PfGW456L13_3039: ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component
- Curated sequence AO353_25895: ABC transporter for D-mannitol and D-mannose, ATPase component
- Ignore hits to Pf6N2E2_1960 when looking for 'other' hits (ABC transporter for D-sorbitol, ATPase component)
- Ignore hits to AO356_00010 when looking for 'other' hits (ABC transporter for D-Sorbitol, ATPase component)
- Curated sequence P54933: SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter
- Total: 5 characterized proteins
PLT5: polyol transporter PLT5
- Curated sequence CH_091483: polyol transporter 5. Polyol transporter 5; Protein POLYOL TRANSPORTER 5; AtPLT5; Sugar-proton symporter PLT5. The broad specificity sugar/sugar alcohol (myo-inositol, glycerol, ribose, sorbitol, mannitol, xylitol, erythritol, etc) H+ symporter, AtPLT5 (transports a wide range of hexoses, pentoses, tetroses, sugar alcohols and a sugar acid, but not disaccharides) (Reinders et al., 2005) (expressed in roots, leaves and floral organs)
- Total: 1 characterized proteins
mtlD: mannitol-1-phosphate 5-dehydrogenase
mt1d: mannitol 1-dehydrogenase
mak: mannose kinase
manA: mannose-6-phosphate isomerase
- Curated proteins or TIGRFams with EC 5.3.1.8
- UniProt sequence P29954: RecName: Full=Mannose-6-phosphate isomerase; EC=5.3.1.8; AltName: Full=Phosphohexomutase; AltName: Full=Phosphomannose isomerase; Short=PMI;
- Comment: SMc03111 (P29954) is specifically important for utilizing mannose, which confirms it is mannose 6-phosphate isomerase
- Total: 1 HMMs and 29 characterized proteins
mt2d: mannitol 2-dehydrogenase
scrK: fructokinase
- Curated proteins or TIGRFams with EC 2.7.1.4
- Ignore hits to Q09123 when looking for 'other' hits (Fructokinase; EC 2.7.1.4)
- Comment: ignore fragmentary sequence of Q09123
- Total: 36 characterized proteins
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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:
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