Gluconeogenesis (human) with precursor-entry routes

Extension of the human gluconeogenesis module that makes the choice of non-carbohydrate precursor explicit. The three physiological precursors enter the pathway at different points: lactate (via lactate dehydrogenase) and the glucogenic amino acid alanine (via alanine aminotransferase) are converted to pyruvate and so require the pyruvate carboxylase / phosphoenolpyruvate carboxykinase backbone, whereas glycerol enters lower down — glycerol kinase and cytosolic glycerol-3-phosphate dehydrogenase feed dihydroxyacetone phosphate directly into the triose-phosphate pool, bypassing pyruvate carboxylase and PEPCK entirely. All routes converge on the shared fructose-1,6-bisphosphatase step and the terminal endoplasmic-reticulum glucose-6-phosphatase system (G6PC1 plus the SLC37A4 antiporter). Because glycerol bypasses the carboxylation arm, pyruvate carboxylase is no longer required by every route: the only steps common to all precursor routes are the terminal G6PC1·SLC37A4 system, which is therefore the single universal gate of free-glucose output. The module is built to be evaluated against tissue expression so that, per tissue, one can ask not just whether gluconeogenesis is possible but which precursors a tissue is equipped to use.

MODULE:gluconeogenesis_human_substratesDRAFTMetabolic Pathwaymodules/gluconeogenesis_human_substrates.yaml
gluconeogenesisGO:0006094
GO:0006094
gluconeogenesis
Module grounded in the GO biological-process term for gluconeogenesis.
GTEx:gtex_v8
GTEx v8 median gene expression
Tissue expression of the precursor-entry enzymes (LDHA/LDHB, GPT/GPT2, GK+GPD1) is used to resolve which precursors each gluconeogenic tissue can use.
23Nodes
10Parts
6Variant Sets
12Variants
13Annotons
0Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:gluconeogenesis_human_substrates 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.

Gene-review completeness (0/13 grounded genes reviewed)

0 complete review(s) · 0 with deep research · 13 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
FBP2 (muscle fructose-1,6-bisphosphatase) O00757
SLC37A4 (glucose-6-phosphate transporter) O43826
LDHA (L-lactate dehydrogenase A) P00338
LDHB (L-lactate dehydrogenase B) P07195
FBP1 (liver fructose-1,6-bisphosphatase) P09467
PC (pyruvate carboxylase) P11498
GPD1 (glycerol-3-phosphate dehydrogenase) P21695
GPT (alanine aminotransferase 1) P24298
GK (glycerol kinase) P32189
PCK1 (cytosolic PEPCK) P35558
G6PC1 (glucose-6-phosphatase catalytic subunit 1) P35575
PCK2 (mitochondrial PEPCK) Q16822
GPT2 (alanine aminotransferase 2) Q8TD30

Details

Human gluconeogenesis with precursor routesMetabolic Pathwaygluconeogenesis_human_substrates
gluconeogenesisGO:0006094

Precursor-resolved extension of gluconeogenesis_human.yaml. All UniProt and GO ids verified. Glycerol entry bypasses PC/PEPCK, so the only steps shared by all precursor routes are the terminal G6PC1·SLC37A4 system (the universal gate). See modules/experimental/gluconeogenesis-context/resolve_substrates.py for the per-tissue "which precursors can this tissue use?" resolution against GTEx.

Part 1: precursor entry (lactate / alanine via pyruvate; glycerol via DHAP)
Precursor entry into the triose/PEP poolMetabolic Pathwayprecursor_supply
Variant set: Gluconeogenic precursor by precursor (One Or More)
Pyruvate-derived precursors (lactate, alanine)Metabolic Pathwaypyruvate_derived

Requires the carboxylation backbone (PC then PEPCK).

Part 1: generation of pyruvate from lactate or alanine
Pyruvate generationReactionpyruvate_generation
Variant set: Source of pyruvate by precursor (One Or More)
From lactate (lactate dehydrogenase)Reactionfrom_lactate
Variant set: Lactate dehydrogenase isozymes by isozyme (One Or More)
LDHAReactionldha_variant

Annotons

LDHA: L-lactate dehydrogenase A
LDHA_activity
Participant: Gene: LDHA (L-lactate dehydrogenase A)
Gene:
LDHA (L-lactate dehydrogenase A)UniProtKB:P00338

Function

L-lactate dehydrogenase (NAD+) activityGO:0004459
Substrates: L-lactate
Products: pyruvate

Locations

cytosolGO:0005829
LDHBReactionldhb_variant

Annotons

LDHB: L-lactate dehydrogenase B
LDHB_activity
Participant: Gene: LDHB (L-lactate dehydrogenase B)
Gene:
LDHB (L-lactate dehydrogenase B)UniProtKB:P07195

Function

L-lactate dehydrogenase (NAD+) activityGO:0004459
Substrates: L-lactate
Products: pyruvate

Locations

cytosolGO:0005829
From alanine (alanine aminotransferase)Reactionfrom_alanine
Variant set: Alanine aminotransferase isozymes by isozyme (One Or More)
GPT (ALT1)Reactiongpt_variant

Annotons

GPT: alanine aminotransferase 1
GPT_activity
Participant: Gene: GPT (alanine aminotransferase 1)
Gene:
GPT (alanine aminotransferase 1)UniProtKB:P24298

Function

L-alanine:2-oxoglutarate transaminase activityGO:0004021
Substrates: L-alanine 2-oxoglutarate
Products: pyruvate L-glutamate

Locations

cytosolGO:0005829
GPT2 (ALT2)Reactiongpt2_variant

Annotons

GPT2: alanine aminotransferase 2
GPT2_activity
Participant: Gene: GPT2 (alanine aminotransferase 2)
Gene:
GPT2 (alanine aminotransferase 2)UniProtKB:Q8TD30

Function

L-alanine:2-oxoglutarate transaminase activityGO:0004021
Substrates: L-alanine 2-oxoglutarate
Products: pyruvate L-glutamate
Part 2: anaplerotic carboxylation
Pyruvate to oxaloacetateReactionpc_node

Annotons

PC: pyruvate carboxylase
PC_activity
Participant: Gene: PC (pyruvate carboxylase)
Gene:
PC (pyruvate carboxylase)UniProtKB:P11498

Function

pyruvate carboxylase activityGO:0004736
Substrates: pyruvate
Products: oxaloacetate

Locations

mitochondrial matrixGO:0005759
Part 3: phosphoenolpyruvate formation
Oxaloacetate to phosphoenolpyruvateReactionpepck_node
Variant set: PEPCK compartment isozymes by subcellular compartment (One Or More)
Cytosolic PEPCK (PCK1)Reactionpck1_variant

Annotons

PCK1: cytosolic PEPCK
PCK1_activity
Participant: Gene: PCK1 (cytosolic PEPCK)
Gene:
PCK1 (cytosolic PEPCK)UniProtKB:P35558

Function

phosphoenolpyruvate carboxykinase (GTP) activityGO:0004613
Substrates: oxaloacetate
Products: phosphoenolpyruvate

Locations

cytosolGO:0005829
Mitochondrial PEPCK (PCK2)Reactionpck2_variant

Annotons

PCK2: mitochondrial PEPCK
PCK2_activity
Participant: Gene: PCK2 (mitochondrial PEPCK)
Gene:
PCK2 (mitochondrial PEPCK)UniProtKB:Q16822

Function

phosphoenolpyruvate carboxykinase (GTP) activityGO:0004613
Substrates: oxaloacetate
Products: phosphoenolpyruvate

Locations

mitochondrial matrixGO:0005759
Glycerol (bypasses PC and PEPCK)Metabolic Pathwayglycerol_derived

Glycerol enters at dihydroxyacetone phosphate via glycerol kinase and cytosolic glycerol-3-phosphate dehydrogenase, downstream of the carboxylation arm, so it needs neither PC nor PEPCK.

Part 1: glycerol phosphorylation
Glycerol to glycerol 3-phosphateReactiongk_node

Annotons

GK: glycerol kinase
GK_activity
Participant: Gene: GK (glycerol kinase)
Gene:
GK (glycerol kinase)UniProtKB:P32189

Function

glycerol kinase activityGO:0004370
Substrates: glycerol ATP
Products: sn-glycerol 3-phosphate

Locations

cytosolGO:0005829
Part 2: oxidation to DHAP
Glycerol 3-phosphate to dihydroxyacetone phosphateReactiongpd1_node

Annotons

GPD1: glycerol-3-phosphate dehydrogenase (NAD+)
GPD1_activity
Participant: Gene: GPD1 (glycerol-3-phosphate dehydrogenase)
Gene:
GPD1 (glycerol-3-phosphate dehydrogenase)UniProtKB:P21695

Function

glycerol-3-phosphate dehydrogenase (NAD+) activityGO:0141152
Substrates: sn-glycerol 3-phosphate
Products: dihydroxyacetone phosphate

Locations

cytosolGO:0005829
Part 2: shared fructose-1,6-bisphosphate bypass
Fructose 1,6-bisphosphate to fructose 6-phosphateReactionfbpase_step
Variant set: Fructose-1,6-bisphosphatase isozymes by tissue isozyme (One Or More)
Gluconeogenic FBPase (FBP1)Reactionfbp1_variant

Annotons

FBP1: fructose-1,6-bisphosphatase 1
FBP1_activity
Participant: Gene: FBP1 (liver fructose-1,6-bisphosphatase)
Gene:
FBP1 (liver fructose-1,6-bisphosphatase)UniProtKB:P09467

Function

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

Locations

cytosolGO:0005829
Muscle FBPase (FBP2)Reactionfbp2_variant

Annotons

FBP2: fructose-1,6-bisphosphatase 2
FBP2_activity
Participant: Gene: FBP2 (muscle fructose-1,6-bisphosphatase)
Gene:
FBP2 (muscle fructose-1,6-bisphosphatase)UniProtKB:O00757

Function

fructose 1,6-bisphosphate 1-phosphatase activityGO:0042132
Substrates: fructose 1,6-bisphosphate
Products: fructose 6-phosphate
Part 3: shared terminal glucose release (universal gate)
Glucose 6-phosphate to glucose (ER G6Pase system)Transport Stepglucose_release_step

The two-component ER system required by every precursor route, and hence the single universal gate of free-glucose output.

Part 1: catalytic subunit
Glucose-6-phosphatase catalytic subunitReactiong6pc_catalytic_node

Annotons

G6PC1: glucose-6-phosphatase catalytic subunit 1
G6PC1_activity
Participant: Gene: G6PC1 (glucose-6-phosphatase catalytic subunit 1)
Gene:
G6PC1 (glucose-6-phosphatase catalytic subunit 1)UniProtKB:P35575

Function

glucose-6-phosphatase activityGO:0004346
Substrates: D-glucose 6-phosphate
Products: D-glucose

Locations

endoplasmic reticulum membraneGO:0005789
Part 2: glucose-6-phosphate ER transporter
Glucose-6-phosphate ER antiporterTransport Stepg6p_transport_node

Annotons

SLC37A4: glucose-6-phosphate ER antiporter
SLC37A4_activity
Participant: Gene: SLC37A4 (glucose-6-phosphate transporter)
Gene:
SLC37A4 (glucose-6-phosphate transporter)UniProtKB:O43826

Function

glucose-6-phosphate transmembrane transporter activityGO:0015152
Substrates: D-glucose 6-phosphate
Products: D-glucose 6-phosphate (ER lumen)

Locations

endoplasmic reticulum membraneGO:0005789