Generic gluconeogenesis module

A generic, taxon-neutral decomposition of gluconeogenesis as a module. The module is intentionally phrased as a set of functions and pathway segments rather than as a fixed list of genes, so it can represent bacterial, fungal, plant, and animal implementations.

MODULE:generic_gluconeogenesisDRAFTMetabolic Pathwaymodules/gluconeogenesis.yaml
gluconeogenesisGO:0006094
MetaCyc:GLUCONEO-PWY
gluconeogenesis pathway
MetaCyc represents gluconeogenesis as a conserved pathway with organism-specific enzyme variants.
GO:0006094
gluconeogenesis
The module is grounded in the GO biological process term for gluconeogenesis.
11Nodes
5Parts
2Variant Sets
5Variants
6Annotons
4Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

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

Leaf nodes lacking representative members

8 leaf node(s) with no concrete protein grounding:

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Gene-review completeness (0/0 grounded genes reviewed)

No concrete UniProt-grounded genes in this module.

Details

Generic gluconeogenesisMetabolic Pathwaygeneric_gluconeogenesis
gluconeogenesisGO:0006094

A species-specific module can specialize the abstract participants with genes, complexes, cell types, compartments, and transport edges. The schema permits those specializations without requiring the generic module to name every enzyme family.

Connections

Oxaloacetate produced by the entry step feeds the phosphoenolpyruvate-forming step.
Part 1: carboxylation entry step
Pyruvate to oxaloacetateReactionpyruvate_to_oxaloacetate
pyruvate carboxylase reaction

Annotons

Pyruvate carboxylase function
pyruvate_carboxylase_activity
Participant: Any With Function: pyruvate carboxylase activity
Required Function:
pyruvate carboxylase activityGO:0004736
Substrates: pyruvate bicarbonate
Products: oxaloacetate

Function

pyruvate carboxylase activityGO:0004736
Substrates: pyruvate bicarbonate
Products: oxaloacetate

Locations

mitochondrial matrixGO:0005759

Generates oxaloacetate from pyruvate. In concrete organism modules, the compartment and transport coupling may need to be made explicit.

Part 2: phosphoenolpyruvate-forming step
Oxaloacetate to phosphoenolpyruvateReactionoxaloacetate_to_phosphoenolpyruvate

This variant set illustrates abstract function selectors: a realized module can enumerate possible paths without grounding to extant genes.

Variant set: PEP carboxykinase energy donor variants by enzyme chemistry (Exactly One)
GTP-dependent PEP carboxykinase routeReactiongtp_pepck_variant

Annotons

GTP-dependent phosphoenolpyruvate carboxykinase
gtp_pepck_activity
Participant: Any With Function: phosphoenolpyruvate carboxykinase (GTP) activity
Required Function:
phosphoenolpyruvate carboxykinase (GTP) activityGO:0004613

Function

phosphoenolpyruvate carboxykinase (GTP) activityGO:0004613
Substrates: oxaloacetate GTP
Products: phosphoenolpyruvate GDP
ATP-dependent PEP carboxykinase routeReactionatp_pepck_variant

Annotons

ATP-dependent phosphoenolpyruvate carboxykinase
atp_pepck_activity
Participant: Any With Function: phosphoenolpyruvate carboxykinase (ATP) activity
Required Function:
phosphoenolpyruvate carboxykinase (ATP) activityGO:0004612

Function

phosphoenolpyruvate carboxykinase (ATP) activityGO:0004612
Substrates: oxaloacetate ATP
Products: phosphoenolpyruvate ADP
Diphosphate-dependent PEP carboxykinase routeReactiondiphosphate_pepck_variant

Annotons

Diphosphate-dependent phosphoenolpyruvate carboxykinase
diphosphate_pepck_activity
Participant: Any With Function: phosphoenolpyruvate carboxykinase (diphosphate) activity
Required Function:
phosphoenolpyruvate carboxykinase (diphosphate) activityGO:0030585

Function

phosphoenolpyruvate carboxykinase (diphosphate) activityGO:0030585
Substrates: oxaloacetate diphosphate
Products: phosphoenolpyruvate phosphate
Part 3: reversible glycolytic trunk
Reversible glycolytic trunkMetabolic Pathwayreversible_glycolytic_trunk

Reversible reactions connecting phosphoenolpyruvate-derived intermediates to fructose 1,6-bisphosphate. This is left coarse here because the module sketch focuses on bypass and terminal variants.

reversible glycolysis segment
Part 4: fructose 1,6-bisphosphate bypass
Fructose 1,6-bisphosphate to fructose 6-phosphateReactionfructose_bisphosphatase_step

Annotons

Fructose 1,6-bisphosphatase function
fructose_bisphosphatase_activity
Participant: Any With Function: fructose 1,6-bisphosphate 1-phosphatase activity
Required Function:
fructose 1,6-bisphosphate 1-phosphatase activityGO:0042132

Function

fructose 1,6-bisphosphate 1-phosphatase activityGO:0042132
Substrates: fructose 1,6-bisphosphate
Products: fructose 6-phosphate

Locations

cytosolGO:0005829
Part 5: terminal glucose or glucose-6-phosphate endpoint
Terminal hexose endpointReactionterminal_hexose_endpoint
Variant set: Terminal product variants by physiological endpoint (Exactly One)
Glucose release endpointReactionglucose_release_variant

Annotons

Glucose-6-phosphatase function
glucose_6_phosphatase_activity
Participant: Any With Function: glucose-6-phosphatase activity
Required Function:
glucose-6-phosphatase activityGO:0004346

Function

glucose-6-phosphatase activityGO:0004346
Substrates: glucose 6-phosphate
Products: glucose
Glucose 6-phosphate endpointMetabolic Pathwayglucose_6_phosphate_endpoint_variant

Some realizations may stop at glucose 6-phosphate as a local biosynthetic or storage precursor rather than releasing free glucose.

glucose 6-phosphate as terminal gluconeogenic product