aerobic glycerol degradation

gomodel:YeastPathways_AERO-GLYCEROL-CAT-PWY

Aerobic glycerol degradation phosphorylates glycerol to sn-glycerol 3-phosphate and then oxidizes it to glycerone phosphate with ubiquinone-6 in Saccharomyces cerevisiae S288C.

Pathway type

carbohydrate degradation

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

18 nodes · 19 asserted directed edges

Arrows show recorded subject → object relationships, not necessarily metabolic flow. Select a node for details or an arrow for evidence. Scroll, zoom or find a node to explore.

Reaction / activity
Chemical / cofactor
Protein / complex
Cell / process context
Solid arrow: mechanistic relation
Dashed arrow: membership, location or cofactor relation

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Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Saccharomyces cerevisiae S288C `NCBITaxon:559292`	taxon
sn-glycerol 3-phosphate(2-) `CHEBI:57597`	small molecule
GUT2 Scer `SGD:S000001417`	protein
ubiquinone-6 `CHEBI:52971`	small molecule
ADP(3-) `CHEBI:456216`	small molecule
mitochondrion `GO:0005739`	cellular component
ubiquinol-6 `CHEBI:52970`	small molecule
glycerol `CHEBI:17754`	small molecule
GUT1 Scer `SGD:S000001024`	protein
ATP(4-) `CHEBI:30616`	small molecule
cytosol `GO:0005829`	cellular component
glycerol catabolic process `GO:0019563`	biological process
hydron `CHEBI:15378`	small molecule
glycerone phosphate(2-) `CHEBI:57642`	small molecule
mitochondrial inner membrane `GO:0005743`	cellular component
mitochondrial intermembrane space `GO:0005758`	cellular component
FAD(3-) `CHEBI:57692`	cofactor
glycerol kinase activity `gomodel:GLYCEROL-KIN-RXN`	molecular activity
glycerol-3-phosphate dehydrogenase (quinone) activity `gomodel:RXN3O-9815`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
glycerol kinase activity `gomodel:GLYCEROL-KIN-RXN`	has_output	sn-glycerol 3-phosphate(2-) `CHEBI:57597`	gomodel:YeastPathways_AERO-GLYCEROL-CAT-PWY Source assertion: The model asserts gomodel:GLYCEROL-KIN-RXN RO:0002234 gomodel:CHEBI_57597_GLYCEROL-KIN-RXN. Source location `./YeastPathways_AERO-GLYCEROL-CAT-PWY.json#/facts/0; endpoint types: /individuals/8/type; /individuals/6/type`
GUT2 Scer `SGD:S000001417`	enables	glycerol-3-phosphate dehydrogenase (quinone) activity `gomodel:RXN3O-9815`	gomodel:YeastPathways_AERO-GLYCEROL-CAT-PWY Source assertion: The model asserts gomodel:RXN3O-9815 RO:0002333 gomodel:YIL155C-MONOMER_RXN3O-9815_controller. Source location `./YeastPathways_AERO-GLYCEROL-CAT-PWY.json#/facts/1; endpoint types: /individuals/9/type; /individuals/11/type`
glycerol-3-phosphate dehydrogenase (quinone) activity `gomodel:RXN3O-9815`	has_input	ubiquinone-6 `CHEBI:52971`	gomodel:YeastPathways_AERO-GLYCEROL-CAT-PWY Source assertion: The model asserts gomodel:RXN3O-9815 RO:0002233 gomodel:CHEBI_52971_RXN3O-9815. Source location `./YeastPathways_AERO-GLYCEROL-CAT-PWY.json#/facts/2; endpoint types: /individuals/9/type; /individuals/5/type`
glycerol kinase activity `gomodel:GLYCEROL-KIN-RXN`	has_output	ADP(3-) `CHEBI:456216`	gomodel:YeastPathways_AERO-GLYCEROL-CAT-PWY Source assertion: The model asserts gomodel:GLYCEROL-KIN-RXN RO:0002234 gomodel:CHEBI_456216_GLYCEROL-KIN-RXN. Source location `./YeastPathways_AERO-GLYCEROL-CAT-PWY.json#/facts/3; endpoint types: /individuals/8/type; /individuals/3/type`
glycerol-3-phosphate dehydrogenase (quinone) activity `gomodel:RXN3O-9815`	occurs_in	mitochondrion `GO:0005739`	gomodel:YeastPathways_AERO-GLYCEROL-CAT-PWY Source assertion: The model asserts gomodel:RXN3O-9815 BFO:0000066 gomodel:reaction_RXN3O-9815_location_lociGO_0005829. Source location `./YeastPathways_AERO-GLYCEROL-CAT-PWY.json#/facts/4; endpoint types: /individuals/9/type; /individuals/26/type`
glycerol-3-phosphate dehydrogenase (quinone) activity `gomodel:RXN3O-9815`	has_output	ubiquinol-6 `CHEBI:52970`	gomodel:YeastPathways_AERO-GLYCEROL-CAT-PWY Source assertion: The model asserts gomodel:RXN3O-9815 RO:0002234 gomodel:CHEBI_52970_RXN3O-9815. Source location `./YeastPathways_AERO-GLYCEROL-CAT-PWY.json#/facts/5; endpoint types: /individuals/9/type; /individuals/4/type`
glycerol kinase activity `gomodel:GLYCEROL-KIN-RXN`	has_input	glycerol `CHEBI:17754`	gomodel:YeastPathways_AERO-GLYCEROL-CAT-PWY Source assertion: The model asserts gomodel:GLYCEROL-KIN-RXN RO:0002233 gomodel:CHEBI_17754_GLYCEROL-KIN-RXN. Source location `./YeastPathways_AERO-GLYCEROL-CAT-PWY.json#/facts/6; endpoint types: /individuals/8/type; /individuals/1/type`
GUT1 Scer `SGD:S000001024`	enables	glycerol kinase activity `gomodel:GLYCEROL-KIN-RXN`	gomodel:YeastPathways_AERO-GLYCEROL-CAT-PWY Source assertion: The model asserts gomodel:GLYCEROL-KIN-RXN RO:0002333 gomodel:YHL032C-MONOMER_GLYCEROL-KIN-RXN_controller. Source location `./YeastPathways_AERO-GLYCEROL-CAT-PWY.json#/facts/7; endpoint types: /individuals/8/type; /individuals/10/type`
glycerol kinase activity `gomodel:GLYCEROL-KIN-RXN`	has_input	ATP(4-) `CHEBI:30616`	gomodel:YeastPathways_AERO-GLYCEROL-CAT-PWY Source assertion: The model asserts gomodel:GLYCEROL-KIN-RXN RO:0002233 gomodel:CHEBI_30616_GLYCEROL-KIN-RXN. Source location `./YeastPathways_AERO-GLYCEROL-CAT-PWY.json#/facts/8; endpoint types: /individuals/8/type; /individuals/2/type`
glycerol kinase activity `gomodel:GLYCEROL-KIN-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_AERO-GLYCEROL-CAT-PWY Source assertion: The model asserts gomodel:GLYCEROL-KIN-RXN BFO:0000066 gomodel:reaction_GLYCEROL-KIN-RXN_location_lociGO_0005829. Source location `./YeastPathways_AERO-GLYCEROL-CAT-PWY.json#/facts/9; endpoint types: /individuals/8/type; /individuals/25/type`
glycerol-3-phosphate dehydrogenase (quinone) activity `gomodel:RXN3O-9815`	part_of	glycerol catabolic process `GO:0019563`	gomodel:YeastPathways_AERO-GLYCEROL-CAT-PWY Source assertion: The model asserts gomodel:RXN3O-9815 BFO:0000050 gomodel:YeastPathways_AERO-GLYCEROL-CAT-PWY/YeastPathways_AERO-GLYCEROL-CAT-PWY. Source location `./YeastPathways_AERO-GLYCEROL-CAT-PWY.json#/facts/10; endpoint types: /individuals/9/type; /individuals/27/type`
glycerol kinase activity `gomodel:GLYCEROL-KIN-RXN`	provides_input_for	glycerol-3-phosphate dehydrogenase (quinone) activity `gomodel:RXN3O-9815`	gomodel:YeastPathways_AERO-GLYCEROL-CAT-PWY Source assertion: The model asserts gomodel:GLYCEROL-KIN-RXN RO:0002413 gomodel:RXN3O-9815. Source location `./YeastPathways_AERO-GLYCEROL-CAT-PWY.json#/facts/11; endpoint types: /individuals/8/type; /individuals/9/type`
glycerol kinase activity `gomodel:GLYCEROL-KIN-RXN`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_AERO-GLYCEROL-CAT-PWY Source assertion: The model asserts gomodel:GLYCEROL-KIN-RXN RO:0002234 gomodel:CHEBI_15378_GLYCEROL-KIN-RXN. Source location `./YeastPathways_AERO-GLYCEROL-CAT-PWY.json#/facts/12; endpoint types: /individuals/8/type; /individuals/0/type`
glycerol-3-phosphate dehydrogenase (quinone) activity `gomodel:RXN3O-9815`	has_input	sn-glycerol 3-phosphate(2-) `CHEBI:57597`	gomodel:YeastPathways_AERO-GLYCEROL-CAT-PWY Source assertion: The model asserts gomodel:RXN3O-9815 RO:0002233 gomodel:CHEBI_57597_GLYCEROL-KIN-RXN. Source location `./YeastPathways_AERO-GLYCEROL-CAT-PWY.json#/facts/13; endpoint types: /individuals/9/type; /individuals/6/type`
glycerol kinase activity `gomodel:GLYCEROL-KIN-RXN`	part_of	glycerol catabolic process `GO:0019563`	gomodel:YeastPathways_AERO-GLYCEROL-CAT-PWY Source assertion: The model asserts gomodel:GLYCEROL-KIN-RXN BFO:0000050 gomodel:YeastPathways_AERO-GLYCEROL-CAT-PWY/YeastPathways_AERO-GLYCEROL-CAT-PWY. Source location `./YeastPathways_AERO-GLYCEROL-CAT-PWY.json#/facts/14; endpoint types: /individuals/8/type; /individuals/27/type`
glycerol-3-phosphate dehydrogenase (quinone) activity `gomodel:RXN3O-9815`	has_output	glycerone phosphate(2-) `CHEBI:57642`	gomodel:YeastPathways_AERO-GLYCEROL-CAT-PWY Source assertion: The model asserts gomodel:RXN3O-9815 RO:0002234 gomodel:CHEBI_57642_RXN3O-9815. Source location `./YeastPathways_AERO-GLYCEROL-CAT-PWY.json#/facts/15; endpoint types: /individuals/9/type; /individuals/7/type`
GUT2 Scer `SGD:S000001417`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:11502169)	mitochondrial inner membrane `GO:0005743`	UniProtKB:P32191 Source assertion: UniProtKB:P32191 annotates location Mitochondrion inner membrane (SL-0168). Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_subcellular_location%2Ccc_function%2Ccc_caution%2Corganism_id#/results/3406/comments/0/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P32191 Source assertion: UniProtKB:P32191 has the exact SGD cross-reference SGD:S000001417. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_subcellular_location%2Ccc_function%2Ccc_caution%2Corganism_id#/results/3406/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
GUT2 Scer `SGD:S000001417`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:22984289)	mitochondrial intermembrane space `GO:0005758`	UniProtKB:P32191 Source assertion: UniProtKB:P32191 annotates location Mitochondrion intermembrane space (SL-0169). Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_subcellular_location%2Ccc_function%2Ccc_caution%2Corganism_id#/results/3406/comments/0/subcellularLocations/1; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P32191 Source assertion: UniProtKB:P32191 has the exact SGD cross-reference SGD:S000001417. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_subcellular_location%2Ccc_function%2Ccc_caution%2Corganism_id#/results/3406/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
GUT2 Scer `SGD:S000001417`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: not specified	FAD(3-) `CHEBI:57692`	UniProtKB:P32191 Source assertion: UniProtKB:P32191 annotates CHEBI:57692 as a cofactor of this protein. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_cofactor%2Corganism_id%2Ccc_caution [sha256:1378282d22c5518215707964664b55946f468ba74a227a6ea1bbf27db69ddbc4] #/results/3406/comments/0/cofactors/0` UniProtKB:P32191 Source assertion: UniProtKB:P32191 has the exact SGD cross-reference SGD:S000001417. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_cofactor%2Corganism_id%2Ccc_caution [sha256:1378282d22c5518215707964664b55946f468ba74a227a6ea1bbf27db69ddbc4] #/results/3406/uniProtKBCrossReferences/0`

References

gomodel:YeastPathways_AERO-GLYCEROL-CAT-PWY GO-CAM aerobic glycerol degradation model YeastPathways_AERO-GLYCEROL-CAT-PWY (source version: Pinned Noctua JSON archive; model date 2026-08-04; member ./YeastPathways_AERO-GLYCEROL-CAT-PWY.json)
UniProtKB:P32191 Reviewed UniProtKB P32191 location annotations (source version: UniProt release 2026_03)

Curation history

2026-10-05T06:05:08Z Codex; review-causal-graph; Reviewed every native GO-CAM fact; preserved precise input/output, causal, location, membership and complex-part relations with traceable structured source evidence. Kept distinct generic physical instances and recorded source-scope exclusions in the cohort review ledger.
2026-10-05T06:43:56Z Codex
- EDIT — Audit causal activity compartments and preserve scoped protein location evidence
  Reviewed all 2 activity location assignments and 2 mapped physical proteins against reviewed S288C UniProt release2026_03 location/function/caution batch SHA256 95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d. Added 2 independently supported location edges and quarantined 0 generic cytosol source assertions. Mapped physical protein locations via exact SGD cross-references; retained source ECO grades, molecular form and conditional notes. Physical protein location alone never generates activity location. Explicitly inspected functional assertions support bounded activity projections. Every original activity location and exclusion is recorded in reports/causal_graph_review/gocam-location-review.json. No independent location annotation is treated as an evidence gap, not a negative result. Cytoplasm is not narrowed to cytosol. Microsome fractions are not projected as in-vivo organelles. Semantic validation passed all85 records;4 independent source-role acceptance tests passed.
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