Definition of D-galacturonate catabolism
As rules and steps, or see full text
Rules
Overview: Galacturonate utilization in GapMind is based on MetaCyc pathways D-galacturonate degradation I via tagaturonate (link), pathway II via oxidation to 5-dehydro-4-deoxy-glucarate (link), and another oxidative pathway (PMID:30249705). Pathway III via galactonate (link) is reported only in fungi and is not included in GapMind.
- all:
- galacturonate-transport, uxaC, uxaB, uxaA, kdgK and eda
- or galacturonate-transport, udh, gli, gci, kdgD and dopDH
- or galacturonate-transport, udh, uxuL, garD, kdgD and dopDH
- Comment: Pathway I begins with isomerization to tagaturonate (a keto sugar) by uxaC. Pathway II begins with oxidation to galactaro-1,5-lactone by udh, isomerization to the 1,4-lactone by gli, and isomerization to 5-keto-4-deoxyglucarate by gci. In another oxidative pathway, the 1,5-lactone is hydrolyzed by uxuL or uxuF giving meso-galactorate, and then a dehydratase (garD) forms 5-keto-4-deoxyglucarate. In both oxidative pathways, this is decarboxylated/dehydrated to 2,5-dioxopentanonate and oxidized to 2-oxoglutarate.
- galacturonate-transport:
- exuT
- or gatA
- or PS417_04205
- Comment: Transporters were identified using query: transporter:galacturonate:D-galacturonate:galaturonate:D-galaturonate:D-galactopyranuronate:CPD-12523:CPD-12524:CPD-15633
Steps
exuT: D-galacturonate transporter ExuT
- Curated sequence P0AA78: Hexuronate transporter. hexuronate transporter. hexuronate transporter
- Curated sequence P0AA78: Hexuronate (glucuronate; galacturonate) porter, ExuT (Nemoz et al. 1976). It also transports D-glucose (HJ Kim et al., Front. Microbiol., 23 January 2020)
- Curated sequence P94774: The Aldohexuronate (glucuronate, galacturonate) uptake porter
- UniProt sequence Q8A0B6: SubName: Full=Hexuronate transporter {ECO:0000313|EMBL:AAO79210.1};
- UniProt sequence A0A1X9Z948: SubName: Full=MFS transporter {ECO:0000313|EMBL:ARS41786.1};
- UniProt sequence A0A166QG26: SubName: Full=MFS transporter {ECO:0000313|EMBL:KZN20203.1};
- UniProt sequence D8IX31: SubName: Full=Phthalate permease of the major facilitator superfamily protein {ECO:0000313|EMBL:ADJ66068.1};
- Comment: BT4105 (Q8A0B6), CA265_RS19855 (A0A1X9Z948), Pf1N1B4_5129 (A0A166QG26), and HSERO_RS23010 (D8IX31) are related proteins with specific phenotypes on D-galacturonate
- Total: 7 characterized proteins
gatA: D-galacturonate transporter gatA
PS417_04205: D-galacturonate transporter
uxaC: D-galacturonate isomerase
uxaB: tagaturonate reductase
uxaA: D-altronate dehydratase
kdgK: 2-keto-3-deoxygluconate kinase
- Curated proteins or TIGRFams with EC 2.7.1.45
- Curated proteins or TIGRFams with EC 2.7.1.178
- Ignore hits to Q9ZU29 when looking for 'other' hits (2-dehydro-3-deoxyglucono/galactono-kinase (EC 2.7.1.178))
- Ignore hits to DEHYDDEOXGALACTKIN-MONOMER when looking for 'other' hits (2-dehydro-3-deoxygalactonokinase (EC 2.7.1.178; EC 2.7.1.58). 2-dehydro-3-deoxygalactonokinase (EC 2.7.1.178))
- Comment: The entry for Q9ZU29 is erroneous (the correct accession is Q97U29). EcoCyc 2-dehydro-3-deoxygalactonokinase (dgoK) is given this EC number as well but I could not determine why. It doesn't link to the ketodeoxygluconate kinase reaction.
- Total: 14 characterized proteins
eda: 2-keto-3-deoxygluconate 6-phosphate aldolase
udh: D-galacturonate dehydrogenase
gli: D-galactarolactone isomerase
gci: D-galactarolactone cycloisomerase
- Curated proteins or TIGRFams with EC 5.5.1.27
- Ignore hits to A9CEQ7 when looking for 'other' hits (D-galactarolactone cycloisomerase (EC 5.5.1.27). D-galactarolactone isomerase; GLI; Galactaro delta-lactone isomerase; EC 5.4.1.4. D-galactarolactone isomerase (EC 5.4.1.4))
- Comment: BRENDA misannotates gli as gci
- Total: 1 characterized proteins
kdgD: 5-dehydro-4-deoxyglucarate dehydratase
dopDH: 2,5-dioxopentanonate dehydrogenase
uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF)
- UniProt sequence B2UIY8: SubName: Full=SMP-30/Gluconolaconase/LRE domain protein {ECO:0000313|EMBL:ACD29539.1};
- UniProt sequence Q888H2: SubName: Full=Senescence marker protein-30 family protein {ECO:0000313|EMBL:AAO54583.1};
- UniProt sequence A4JG52: SubName: Full=3-carboxymuconate cyclase-like protein {ECO:0000313|EMBL:ABO55255.1};
- UniProt sequence A0A0H3KPX2: SubName: Full=6-phosphogluconolactonase {ECO:0000313|EMBL:BAG44069.1}; EC=3.1.1.31 {ECO:0000313|EMBL:BAG44069.1};
- UniProt sequence Q39EM3: SubName: Full=3-carboxymuconate cyclase-like protein {ECO:0000313|EMBL:ABB09093.1};
- UniProt sequence Q881W7: SubName: Full=Uncharacterized protein {ECO:0000313|EMBL:AAO56265.1};
- Curated sequence GFF3393: galactaro-1,5-lactonase
- Curated sequence HSERO_RS15795: galactaro-1,5-lactonase
- Comment: Two families of D-galactaro-1,5-lactonase were described, uxuL and uxuF. All of these proteins are active on D-glucaro-1,5-lactone as well, although PSPTO_2765 is much more active on galactaro,1-5-lactone. UxuL = Rpic_4446 PSPTO_1052 UxuF = Bcep1808_2255 BMULJ_02167 Bcep18194_A5499 PSPTO_2765 PS417_17365 (GFF3393) and HSERO_RS15795 were inferred from mutant phenotype
- Total: 8 characterized proteins
garD: meso-galactarate dehydratase (L-threo-forming) GarD
- Curated proteins or TIGRFams with EC 4.2.1.42
- Ignore hits to Q8EMJ9 when looking for 'other' hits (Galactarate dehydratase (D-threo-forming); GalrD; GalrD-II; EC 4.2.1.158. galactarate dehydratase (D-threo-forming) (EC 4.2.1.158); galactarate dehydratase (EC 4.2.1.42). galactarate dehydratase (D-threo-forming) (EC 4.2.1.158))
- Comment: Q8EMJ9 is the D-threo-forming enzyme, and is misannotated in BRENDA
- Total: 1 HMMs and 4 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 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