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:
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