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:
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