Definition of D-sorbitol (glucitol) catabolism
As rules and steps, or see full text
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.
Steps
mtlE: ABC transporter for polyols MtlEFGK, substrate-binding component MtlE
- Curated sequence O30491: MtlE, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK
- Curated sequence BPHYT_RS16115: ABC transporter for D-Sorbitol, periplasmic substrate-binding component
- Curated sequence GFF1305: ABC transporter for D-Sorbitol, periplasmic substrate-binding component
- Curated sequence GFF2493: ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, periplasmic substrate-binding protein
- Curated sequence Ac3H11_2944: ABC transporter for D-Sorbitol, periplasmic substrate-binding component
- Curated sequence AO356_00025: ABC transporter for D-Sorbitol, periplasmic substrate-binding component
- Curated sequence Pf6N2E2_1963: ABC transporter for D-sorbitol, periplasmic substrate-binding component
- Curated sequence O30831: SmoE, component of Hexitol (glucitol; mannitol) porter
- Ignore hits to AO353_25880 when looking for 'other' hits (ABC transporter for D-mannitol and D-mannose, periplasmic substrate-binding component)
- Ignore hits to PfGW456L13_3042 when looking for 'other' hits (ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, periplasmic substrate-binding component)
- Total: 8 characterized proteins
mtlF: ABC transporter for polyols MtlEFGK, permease component MtlF
- Curated sequence O30492: MtlF, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK
- Curated sequence BPHYT_RS16110: ABC transporter for D-Sorbitol, permease component 2
- Curated sequence GFF1304: ABC transporter for D-Sorbitol, permease component 2
- Curated sequence GFF2492: ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, permease component 2
- Curated sequence Ac3H11_2943: ABC transporter for D-Sorbitol, permease component 2
- Curated sequence AO356_00020: ABC transporter for D-Sorbitol, permease component 2
- Curated sequence Pf6N2E2_1962: ABC transporter for D-sorbitol, permease component 1
- Curated sequence O30832: SmoF, component of Hexitol (glucitol; mannitol) porter
- Ignore hits to AO353_25885 when looking for 'other' hits (ABC transporter for D-mannitol and D-mannose, permease component 1)
- Ignore hits to PfGW456L13_3041 when looking for 'other' hits (ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, permease component 2)
- Total: 8 characterized proteins
mtlG: ABC transporter for polyols MtlEFGK, permease component MtlG
- Curated sequence O30493: MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK
- Curated sequence BPHYT_RS16105: ABC transporter for D-Sorbitol, permease component 1
- Curated sequence GFF1303: ABC transporter for D-Sorbitol, permease component 1
- Curated sequence GFF2491: ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, permease component 1
- Curated sequence Ac3H11_2942: ABC transporter for D-Sorbitol, permease component 1
- Curated sequence AO356_00015: ABC transporter for D-Sorbitol, permease component 1
- Curated sequence Pf6N2E2_1961: ABC transporter for D-sorbitol, permease component 2
- Ignore hits to AO353_25890 when looking for 'other' hits (ABC transporter for D-mannitol and D-mannose, permease component 2)
- Ignore hits to PfGW456L13_3040 when looking for 'other' hits (ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, permease component 1)
- Ignore hits to O30833 when looking for 'other' hits (SmoG, component of Hexitol (glucitol; mannitol) porter)
- Total: 7 characterized proteins
mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK
- Curated sequence O30494: MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK
- Curated sequence BPHYT_RS16095: ABC transporter for D-Sorbitol, ATPase component
- Curated sequence GFF1302: ABC transporter for D-Sorbitol, ATPase component
- Curated sequence GFF2490: ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component
- Curated sequence Ac3H11_2941: ABC transporter for D-Sorbitol, ATPase component
- Curated sequence AO356_00010: ABC transporter for D-Sorbitol, ATPase component
- Curated sequence Pf6N2E2_1960: ABC transporter for D-sorbitol, ATPase component
- Ignore hits to AO353_25895 when looking for 'other' hits (ABC transporter for D-mannitol and D-mannose, ATPase component)
- Ignore hits to PfGW456L13_3039 when looking for 'other' hits (ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component)
- Ignore hits to P54933 when looking for 'other' hits (SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter)
- Total: 7 characterized proteins
srlA: PTS system for sorbitol SrlABE, EII-C2 component SrlA
- Curated sequence O32332: PTS system glucitol/sorbitol-specific EIIC component; EIIC-Gut; Glucitol/sorbitol permease IIC component. Glucitol/sorbitol permease IIC component, component of The Glucitol Enzyme II complex, IICBC (GutA1A2) IIA (GutB)
- Curated sequence O32521: PTS system glucitol/sorbitol-specific EIIC component; EIIC-Gut; Glucitol/sorbitol permease IIC component
- 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)
- Total: 3 characterized proteins
srlB: PTS system for sorbitol SrlABE, EII-A component SrlB
- 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)
- Curated sequence O32334: GutB, component of The Glucitol Enzyme II complex, IICBC (GutA1A2) IIA (GutB)
- UniProt sequence O32523: SubName: Full=Sorbitol phosphotransferase enzyme II {ECO:0000313|EMBL:CAA74943.1};
- Comment: 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.
- Total: 3 characterized proteins
srlE: PTS system for sorbitol SrlABE, EII-BC1 component SrlE
- Curated sequence O32333: PTS system glucitol/sorbitol-specific EIIB component; EII-Gut; Enzyme II-Gut; Glucitol/sorbitol-specific phosphotransferase enzyme IIB component; EC 2.7.1.198. PTS system, glucitol/sorbitol-specific, IIBC component. Glucitol/sorbitol-specific phosphotransferase enzyme IIB component, component of The Glucitol Enzyme II complex, IICBC (GutA1A2) IIA (GutB)
- Curated sequence O32522: PTS system glucitol/sorbitol-specific EIIB component; EII-Gut; Enzyme II-Gut; Glucitol/sorbitol-specific phosphotransferase enzyme IIB component; EC 2.7.1.198
- 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)
- Total: 3 characterized proteins
mtlA: PTS system for polyols, 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)
- Comment: 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
- Total: 2 characterized proteins
SOT: sorbitol:H+ co-transporter SOT1 or SOT2
- 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)
- Curated sequence AGG19156.1: Sorbitol (glucitol):H+ co-transporter, SOT2 (Km for sorbitol of 0.81 mM) of 491 aas and 12 TMSs (Gao et al. 2003). SOT2 of Prunus cerasus is mainly expressed only early in fruit development and not in leaves
- Curated sequence AIU41385.1: Sorbitol (D-Glucitol):H+ co-transporter, SOT1 (Km for sorbitol of 0.64 mM) of 509 aas and 12 TMSs (Gao et al. 2003). SOT1 of P. cerasus is expressed throughout fruit development, but especially when growth and sorbitol accumulation rates are highest. In leaves, PcSOT1 expression is highest in young, expanding tissues, but substantially less in mature leaves
- Comment: Various monomeric transporters related to SOT1 or SOT2
- Total: 3 characterized proteins
sdh: sorbitol 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
srlD: sorbitol 6-phosphate 2-dehydrogenase
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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