Pseudomonas 2-ketogluconate loop

A reusable Pseudomonas peripheral glucose-catabolism module. A PQQ-dependent inner-membrane Gcd oxidizes periplasmic glucose to D-glucono-1,5-lactone, which hydrolyzes to gluconate; a three-subunit Gad complex oxidizes gluconate to 2-ketogluconate; KguT imports it; KguK phosphorylates it; and KguD reduces the phosphorylated intermediate to 6-phosphogluconate. PQQ biosynthesis, porin-mediated glucose entry, PtxS regulation, the alternative gluconate-kinase route, and the downstream Entner-Doudoroff trunk are outside the boundary.

MODULE:pseudomonad_2_ketogluconate_loopCOMPLETECONCRETEMetabolic Pathwaymodules/pseudomonad_2_ketogluconate_loop.yaml
non-phosphorylated glucose catabolic processGO:0019595 D-gluconate metabolic processGO:0019521
PMID:17483213
Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis.
The cached abstract establishes three convergent KT2440 peripheral glucose routes and their flux context, but does not resolve individual kgu genes.
PMID:29607620
Regulation of carbohydrate degradation pathways in Pseudomonas involves a versatile set of transcriptional regulators.
Full-text pathway synthesis places kguT, kguK, and kguD together in the Pseudomonas 2-ketogluconate operon.
kguT, kguK and kguD that form another operon with ptxS
PMID:9352901
Cloning and expression of a gene cluster encoding three subunits of membrane-bound gluconate dehydrogenase from Erwinia cypripedii ATCC 29267 in Escherichia coli.
Primary biochemical and cloning evidence establishes homologous dehydrogenase, cytochrome c, and third-subunit Gad architecture.
PMID:39770733
Characterization and Transcriptional Regulation of the 2-Ketogluconate Utilization Operon in Pseudomonas plecoglossicida.
Cross-species genetics supports the four-gene kgu locus while leaving KguE chemistry unresolved.
RHEA:22152
Quinoprotein glucose dehydrogenase reaction
Defines oxidation of D-glucose to D-glucono-1,5-lactone.
RHEA:12769
Gluconate 2-dehydrogenase reaction
Defines oxidation of D-gluconate to 2-dehydro-D-gluconate.
RHEA:10788
2-dehydrogluconokinase reaction
Defines ATP-dependent phosphorylation of 2-dehydro-D-gluconate.
UniProtKB:Q88HI1
Pseudomonas putida KT2440 PP_3376
Exact KguD candidate; the legacy ptxD name is not treated as evidence for phosphite oxidation.
UniProtKB:Q88HH6
Pseudomonas putida KT2440 Gad cytochrome c subunit
Exact PSEPK implementation of the membrane-associated electron-transfer subunit.
UniProtKB:Q88HH5
Pseudomonas putida KT2440 Gad flavoprotein subunit
Exact PSEPK implementation of the FAD-containing catalytic subunit.
UniProtKB:Q88HH4
Pseudomonas putida KT2440 Gad gamma subunit
Exact PSEPK implementation of the conserved third subunit.
UniProtKB:O34213
Reviewed Pantoea cypripedii Gad subunit 3
Reviewed exemplar verified as the third subunit of the three-component enzyme.
UniProtKB:O34214
Reviewed Pantoea cypripedii Gad flavoprotein subunit
Reviewed exemplar verified as the FAD-containing dehydrogenase subunit.
UniProtKB:O34215
Reviewed Pantoea cypripedii Gad cytochrome c subunit
Reviewed exemplar verified as the cytochrome c electron-transfer subunit.
file:modules/pseudomonad_2_ketogluconate_loop-exemplar-verification.md
Offline-verifiable UniProt exemplar mapping for the Gad complex
Exact reviewed UniProt ID and DE lines document the O34213/O34214/O34215 subunit assignments.

The reusable boundary is restricted to Pseudomonas because the complete transport-plus-conversion route is well supported there; it is not asserted for all Pseudomonadota. KguE (Q88HH8) is a conserved, module-adjacent accessory candidate whose exact reaction is unknown and is therefore not a required catalytic step. PtxS is regulatory and excluded. PP_3376/Q88HI1 is modeled as KguD from direct KT2440 genetics and conserved locus order; phosphite dehydrogenase activity is not claimed. The O34213/O34214/O34215 assignments were verified against reviewed UniProt records as third, flavoprotein, and cytochrome c subunits, respectively; Q88HH4/Q88HH5/Q88HH6 are the corresponding exact KT2440 implementations.

6Nodes
5Parts
0Variant Sets
0Variants
5Annotons
4Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:pseudomonad_2_ketogluconate_loop deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

0 gene-function check(s) reflected in core functions · 0 conflict(s) · 0 evidence or coverage gap(s) (5 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
gcd_activity ORTHOLOG_OF
Gene 		quinoprotein glucose dehydrogenase activity
GO:0008876 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
gad_activity PROTEIN_COMPLEX
Gene 		gluconate 2-dehydrogenase (acceptor) activity
GO:0033717 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
kgut_activity ORTHOLOG_OF
Gene 		monocarboxylic acid transmembrane transporter activity
GO:0008028 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
kguk_activity ORTHOLOG_OF
Gene 		dehydrogluconokinase activity
GO:0047841 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
kgud_activity ORTHOLOG_OF
Gene 		phosphogluconate 2-dehydrogenase activity
GO:0008114 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.

Gene-review completeness (4/8 grounded genes reviewed)

3 complete review(s) · 1 with deep research · 4 missing review · 3 reviewed but lacking deep research

Gene Review Complete Deep research
kguK Q88HH9 ✓ ✓ ✗
kguT Q88HI0 ✓ ✓ ✗
reviewed Gad third subunit O34213 ✗ — —
reviewed Gad flavoprotein subunit O34214 ✗ — —
reviewed Gad cytochrome subunit O34215 ✗ — —
reviewed bacterial Gcd P15877 ✗ — —
PP_3384 Q88HH4 ✓ ✓ ✗
ptxD Q88HI1 ✓ 6/8 ✓

Details

Context
PseudomonasNCBITaxon:286
Pseudomonas 2-ketogluconate loopMetabolic Pathwaypseudomonad_2_ketogluconate_loop
non-phosphorylated glucose catabolic processGO:0019595 D-gluconate metabolic processGO:0019521
Context
PseudomonasNCBITaxon:286

Connections

Gcd produces a gluconolactone that hydrolyzes to the D-gluconate consumed by Gad.
gad_gluconate_oxidation -> kgut_import Provides Input For
Gad supplies periplasmic 2-ketogluconate to KguT.
kgut_import -> kguk_phosphorylation Provides Input For
KguT supplies cytosolic 2-ketogluconate to KguK.
kguk_phosphorylation -> kgud_reduction Provides Input For
KguK supplies 2-dehydro-6-phospho-D-gluconate to KguD.
Part 1: periplasmic glucose oxidation
Gcd glucose oxidationReactiongcd_glucose_oxidation

Annotons

Quinoprotein glucose dehydrogenase
gcd_activity
Participant: Ortholog Of: reviewed bacterial Gcd
Ortholog Of:
reviewed bacterial GcdUniProtKB:P15877 Retain the membrane-bound PQQ enzyme architecture; Q88MX4 is the exact KT2440 implementation.

Function

quinoprotein glucose dehydrogenase activityGO:0008876
Substrates: D-glucose ubiquinone
Products: D-glucono-1,5-lactone ubiquinol
Part 2: periplasmic gluconate oxidation
Three-subunit Gad reactionReactiongad_gluconate_oxidation

Annotons

Gluconate 2-dehydrogenase complex
gad_activity
Participant: Protein Complex: three-subunit membrane-bound gluconate 2-dehydrogenase
Protein Complex:
three-subunit membrane-bound gluconate 2-dehydrogenase
Active units:
Gad cytochrome c subunit
Participant: Ortholog Of: reviewed Gad cytochrome subunit
Ortholog Of:
reviewed Gad cytochrome subunitUniProtKB:O34215 O34215 is the reviewed role exemplar; Q88HH6 is the exact KT2440 cytochrome c subunit.
Role: Membrane-associated heme electron-transfer subunit.
Gad flavoprotein subunit
Participant: Ortholog Of: reviewed Gad flavoprotein subunit
Ortholog Of:
reviewed Gad flavoprotein subunitUniProtKB:O34214 O34214 is the reviewed role exemplar; Q88HH5 is the exact KT2440 flavoprotein subunit.
Role: FAD-containing gluconate-oxidizing subunit.
Gad gamma subunit
Participant: Family: gluconate 2-dehydrogenase subunit 3 family
Family:
gluconate 2-dehydrogenase subunit 3 familyInterPro:IPR027056
Representative Members: reviewed Gad third subunitUniProtKB:O34213 KT2440 PP_3384UniProtKB:Q88HH4
Role: Conserved third subunit with unresolved assembly/export mechanism.

Function

gluconate 2-dehydrogenase (acceptor) activityGO:0033717
Substrates: D-gluconate oxidized acceptor
Products: 2-dehydro-D-gluconate reduced acceptor
Part 3: 2-ketogluconate import
KguT importTransport Stepkgut_import

Annotons

KguT transporter
kgut_activity
Participant: Ortholog Of: KT2440 KguT
Ortholog Of:
KT2440 KguTUniProtKB:Q88HI0 Orthology must be restricted by conserved kgu-locus context because broad MFS families are not substrate-specific.

Function

monocarboxylic acid transmembrane transporter activityGO:0008028
Substrates: periplasmic 2-dehydro-D-gluconate
Products: cytosolic 2-dehydro-D-gluconate
Part 4: 2-ketogluconate phosphorylation
KguK phosphorylationReactionkguk_phosphorylation

Annotons

2-dehydrogluconokinase
kguk_activity
Participant: Ortholog Of: KT2440 KguK
Ortholog Of:
KT2440 KguKUniProtKB:Q88HH9 Orthology must retain kgu-locus context; the broad PfkB/PANTHER assignment is not an exact selector.

Function

dehydrogluconokinase activityGO:0047841
Substrates: 2-dehydro-D-gluconate ATP
Products: 2-dehydro-6-phospho-D-gluconate ADP
Part 5: reduction to 6-phosphogluconate
KguD reductionReactionkgud_reduction

Annotons

Phosphogluconate 2-dehydrogenase
kgud_activity
Participant: Ortholog Of: KT2440 PP_3376/KguD candidate
Ortholog Of:
KT2440 PP_3376/KguD candidateUniProtKB:Q88HI1 Require conserved kgu-locus context and pathway evidence; do not propagate the legacy phosphite-dehydrogenase name.

Function

phosphogluconate 2-dehydrogenase activityGO:0008114
Substrates: 2-dehydro-6-phospho-D-gluconate NAD(P)H
Products: 6-phospho-D-gluconate NAD(P)+