Definition of D-gluconate catabolism
As rules and steps, or see full text
Rules
Overview: In most bacteria, gluconate degradation proceeds via D-gluconate 6-phosphate and either the Entner-Doudoroff pathway or the oxidative pentose phosphate pathway (link). Alternatively, gluconate can be oxidized in the periplasm to 2-ketogluconate before uptake (link).
- all:
- to-gluconate-6-phosphate, edd and eda
- or to-gluconate-6-phosphate and gnd
- or gadh1, gadh2, gadh3, kguT, kguK, kguD, edd and eda
- Comment: Gluconate 6-phosphate can be consumed by the Entner-Doudoroff pathway (edd and eda) or by oxidative decarboxylation (by gnd) to ribulose 5-phosphate, an intermediate in the pentose phosphate pathway. Alternatively, if gluconate is oxidized to 2-ketogluconate in the periplasm (by gadh123), it can be taken up by kguT, phosphorylated, reduced to gluconate 6-phosphate, and consumed by the Entner-Doudoroff pathway.
- to-gluconate-6-phosphate:
- gluconate-PTS
- or gluconate-transport and gntK
- Comment: Cytoplasmic gluconate 6-phosphate can be formed by PTS systems or by the kinase gntK.
- gluconate-PTS: gntEIIA, gntEIIB, gntEIIC and gntEIID
- Comment: PTS systems (forming 6-phosphogluconate)
- gluconate-transport:
- gntA, gntB and gntC
- or gntT
- or ght3
- Comment: Transporters and PTS systems were identified using query: transporter:gluconate:D-gluconate
Steps
gntA: gluconate TRAP transporter, small permease component
- UniProt sequence Q930R3: SubName: Full=TRAP-type small permease component {ECO:0000313|EMBL:AAK64790.1};
- UniProt sequence G8AR26: SubName: Full=TRAP dicarboxylate transport system, small permease component (DctQ-like) {ECO:0000313|EMBL:CCC99887.1};
- Curated sequence GFF2080: fusion of gluconokinase and the small permease component of the D-gluconate TRAP transporter
- UniProt sequence A0A165IVI0: SubName: Full=C4-dicarboxylate ABC transporter permease {ECO:0000313|EMBL:KZT13591.1};
- Comment: A TRAP type transporter for gluconate is described in Sinorhizobium meliloti (PMID:19060150). SMa0249 (gntA, Q930R3) is the small permease component. SMa0250 (gntB, Q930R2) is the large permease component. SMa0252 (gntC, Q930R1) is the periplasmic solute-binding component. Fitness data identified related systems in Azospirillum brasilense Sp245, Pseudomona stutzeri RCH2, Acidovorax sp. GW101-3H11. AZOBR_RS15925 = AZOBR_p130075 = G8AR26 is the small permease component; it was originally annotated as a pseudogene. AZOBR_RS15920 is the large permease component. AZOBR_RS15915 = G8AR24 is the solute receptor (DctP-like) . In psRCH2, these are Psest_2123, Psest_2124, Psest_2125 (GFF2080:GFF2082); the small permease component is fused to gluconokinase. In Acidovorax, these are Ac3H11_3228 (A0A165IVI0), Ac3H11_3227 (A0A165IWV9), Ac3H11_3226 (A0A165IVH1).
- Total: 4 characterized proteins
gntB: gluconate TRAP transporter, large permease component
- UniProt sequence Q930R2: SubName: Full=TRAP-type large permease component {ECO:0000313|EMBL:AAK64791.1};
- Curated sequence AZOBR_RS15920: Large component of TRAP-type D-gluconate transporter
- Curated sequence GFF2081: D-gluconate TRAP transporter, large permease component
- UniProt sequence A0A165IWV9: SubName: Full=L-dehydroascorbate transporter large permease subunit {ECO:0000313|EMBL:KZT13641.1};
- Total: 4 characterized proteins
gntC: gluconate TRAP transporter, periplasmic solute-binding component
- UniProt sequence Q930R1: SubName: Full=TRAP-type periplasmic solute-binding protein {ECO:0000313|EMBL:AAK64792.1};
- UniProt sequence G8AR24: SubName: Full=TRAP dicarboxylate transport system, periplasmic component (DctP-like) {ECO:0000313|EMBL:CCC99885.1};
- Curated sequence GFF2082: D-gluconate TRAP transporter, periplasmic component
- UniProt sequence A0A165IVH1: SubName: Full=ABC transporter substrate-binding protein {ECO:0000313|EMBL:KZT13590.1};
- Total: 4 characterized proteins
gntEIIA: gluconate PTS system, IIA component
- Curated sequence Q82ZC8: PTS system, IIA component, component of The gluconate PTS uptake system. IIAGnt and IIBGnt form a high affinity 2:2 heterotetrameric complex
- Total: 1 characterized proteins
gntEIIB: gluconate PTS system, IIB component
- Curated sequence Q82ZC7: PTS system, IIB component, component of The gluconate PTS uptake system. IIAGnt and IIBGnt form a high affinity 2:2 heterotetrameric complex
- Total: 1 characterized proteins
gntEIIC: gluconate PTS system, IIC component
- Curated sequence Q82ZC5: PTS system, IIC component, component of The gluconate PTS uptake system. IIAGnt and IIBGnt form a high affinity 2:2 heterotetrameric complex
- Total: 1 characterized proteins
gntEIID: gluconate PTS system, IID component
- Curated sequence Q82ZC6: PTS system, IID component, component of The gluconate PTS uptake system. IIAGnt and IIBGnt form a high affinity 2:2 heterotetrameric complex
- Total: 1 characterized proteins
gntT: gluconate:H+ symporter GntT
- Curated sequence P39344: Gnt-II system L-idonate transporter; L-Ido transporter; 5-keto-D-gluconate transporter. L-Idonate/D-Gluconate:H+ symporter, IdnT, GntW, YjgT. L-idonate/5-ketogluconate/gluconate transporter
- Curated sequence P39835: High-affinity gluconate transporter; Gluconate permease; Gnt-I system. D-Gluconate:H+ symporter, GntT. high-affinity gluconate transporter. high-affinity gluconate transporter
- Curated sequence P0AC94: D-Fructuronate/D-gluconate:H+ symporter, GntP. fructuronate transporter. fructuronate transporter
- Curated sequence P0AC96: Low-affinity (212. low-affinity gluconate transporter. low-affinity gluconate transporter
- Curated sequence P12012: D-Gluconate:H+ symporter of 448 aas and 11 TMSs
- Curated sequence BPHYT_RS16725: gluconate:H+ symporter (gntT)
- Curated sequence RR42_RS28835: gluconate:H+ symporter (gntT)
- Total: 7 characterized proteins
ght3: gluconate transporter Ght3
gntK: D-gluconate kinase
- Curated proteins or TIGRFams with EC 2.7.1.12
- Curated sequence GFF2080: fusion of gluconokinase and the small permease component of the D-gluconate TRAP transporter
- Ignore hits to Q61036 when looking for 'other' hits (Serine/threonine-protein kinase PAK 3; Beta-PAK; CDC42/RAC effector kinase PAK-B; p21-activated kinase 3; PAK-3; EC 2.7.11.1. gluconokinase (EC 2.7.1.12); non-specific serine/threonine protein kinase (EC 2.7.11.1))
- Ignore hits to Q29502 when looking for 'other' hits (gluconokinase (EC 2.7.1.12))
- Curated sequence CH_125646: gluconokinase
- Comment: Psest_2123 (GFF2080) is a fusion of the TRAP component and gluconate kinase (but was not given the EC number) CH_125646 is annotated as gluconokinase but was not given the EC number
- Total: 1 HMMs and 10 characterized proteins
gnd: 6-phosphogluconate dehydrogenase, decarboxylating
edd: phosphogluconate dehydratase
eda: 2-keto-3-deoxygluconate 6-phosphate aldolase
gadh1: gluconate 2-dehydrogenase flavoprotein subunit
- Curated sequence O34214: Gluconate 2-dehydrogenase flavoprotein; GA 2-DH dehydrogenase subunit; GADH dehydrogenase subunit; EC 1.1.99.3. gluconate 2-dehydrogenase dehydrogenase subunit (EC 1.1.99.3)
- Curated sequence MONOMER-12745: D-gluconate dehydrogenase dehydrogenase subunit (EC 1.1.99.3)
- Curated sequence A4PIB0: gluconate 2-dehydrogenase (EC 1.1.1.215)
- UniProt sequence G5EBD9: SubName: Full=Gluconate 2-dehydrogenase alpha chain {ECO:0000313|EMBL:AAW60992.1}; EC=1.1.99.3 {ECO:0000313|EMBL:AAW60992.1};
- Curated sequence C0LE03: gluconate 2-dehydrogenase (EC 1.1.1.215)
- Comment: gluconate 2-dehydrogenase has three subunits; known in Pseudomonas fluorescens and Pantoea/Pectobacterium cypripedii. There's also papers about two different enzymes in Gluconobacter. PMID:17720837 describes A4PIA9 = gndS = gadh3; A4PIB0 = gndL = gadh1; A4PIB1 = gndC = gadh2; BRENDA includes only A4PIB0. PMID:27392695 shows that overexpressing GOX1232 to GOX1230 (Q5FRK3 G5EBD9 Q5FRK5), paralogs of gndSLC, leads to increased production of 2-ketogluconate; BRENDA includes only Q5FRK5. Finally, C0LE03 is listed by BRENDA as a gluconate 2-dehydrogenase and is nearly identical to Q4KKM7 = link, so include that as well. Some papers also mention GOX0147 = 5FTU6 but that is the cytoplasmic 2-ketogluconate reductase.
- Total: 5 characterized proteins
gadh2: gluconate 2-dehydrogenase cytochrome c subunit
- Curated sequence O34215: Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3. gluconate 2-dehydrogenase cytochrome c subunit (EC 1.1.99.3)
- Curated sequence MONOMER-12746: D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3)
- UniProt sequence A4PIB1: SubName: Full=Gluconate 2-dehydrogenase cytochrome c {ECO:0000313|EMBL:BAF52628.1};
- Curated sequence Q5FRK5: gluconate 2-dehydrogenase (EC 1.1.1.215)
- Total: 4 characterized proteins
gadh3: gluconate 2-dehydrogenase subunit 3
- Curated sequence O34213: Gluconate 2-dehydrogenase subunit 3; GA 2-DH subunit 3; GADH subunit 3; EC 1.1.99.3. gluconate 2-dehydrogenase subunit 3 (EC 1.1.99.3)
- Curated sequence MONOMER-12747: D-gluconate dehydrogenase 21.7 kD subunit (EC 1.1.99.3)
- UniProt sequence A4PIA9: SubName: Full=Gluconate 2-dehydrogenase small subunit {ECO:0000313|EMBL:BAF52626.1};
- UniProt sequence Q5FRK3: SubName: Full=Gluconate 2-dehydrogenase gamma chain {ECO:0000313|EMBL:AAW60993.1}; EC=1.1.99.3 {ECO:0000313|EMBL:AAW60993.1};
- Total: 4 characterized proteins
kguT: 2-ketogluconate transporter
kguK: 2-ketogluconokinase
kguD: 2-keto-6-phosphogluconate reductase
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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