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 (6/13 grounded genes reviewed)

6 complete review(s) · 0 with deep research · 7 missing review · 6 reviewed but lacking deep research

Gene Review Complete Deep research
G6PC1 P35575
GPD1 P21695
LDHA P00338
LDHB P07195
FBP2 (muscle fructose-1,6-bisphosphatase) O00757
FBP1 (liver fructose-1,6-bisphosphatase) P09467
GPT (alanine aminotransferase 1) P24298
GK (glycerol kinase) P32189
PCK1 (cytosolic PEPCK) P35558
PC P11498
PCK2 (mitochondrial PEPCK) Q16822
GPT2 (alanine aminotransferase 2) Q8TD30
SLC37A4 O43826

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