epoxysqualene biosynthesis

gomodel:YeastPathways_PWY-5670-1

Epoxysqualene biosynthesis in Saccharomyces cerevisiae S288C converts farnesyl diphosphate to presqualene diphosphate, reduces presqualene diphosphate to squalene, and monooxygenates squalene to form (S)-2,3-epoxysqualene.

Pathway type

lipid biosynthesis

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

23 nodes · 26 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
Other participant
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
diphosphoric acid `CHEBI:29888`	small molecule
squalene `CHEBI:15440`	lipid
NAD(P)(+) `CHEBI:13390`	small molecule
NAD(P)H `CHEBI:13392`	small molecule
ERG9 Scer `SGD:S000001233`	protein
cytosol `GO:0005829`	cellular component
water `CHEBI:15377`	small molecule
dioxygen `CHEBI:15379`	small molecule
chemical entity `gomodel:YeastPathways_PWY-5670-1/654d809000002591`	participant
ERG1 Scer `SGD:S000003407`	protein
(S)-2,3-epoxysqualene `CHEBI:15441`	lipid
presqualene diphosphate(3-) `CHEBI:57310`	small molecule
triterpenoid biosynthetic process `GO:0016104`	biological process
2-trans,6-trans-farnesyl diphosphate(3-) `CHEBI:175763`	small molecule
hydron `CHEBI:15378`	small molecule
chemical entity `gomodel:YeastPathways_PWY-5670-1/654d809000002611`	participant
endoplasmic reticulum membrane `GO:0005789`	cellular component
lipid droplet `GO:0005811`	cellular component
magnesium(2+) `CHEBI:18420`	cofactor
FAD(3-) `CHEBI:57692`	cofactor
squalene synthase [NAD(P)H] activity (presqualene diphosphate-forming) `gomodel:RXN-12263`	molecular activity
squalene monooxygenase activity `gomodel:RXN3O-9816`	molecular activity
squalene synthase [NAD(P)H] activity (squalene-forming) `gomodel:RXN66-281`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
squalene synthase [NAD(P)H] activity (presqualene diphosphate-forming) `gomodel:RXN-12263`	has_output	diphosphoric acid `CHEBI:29888`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN-12263 RO:0002234 gomodel:CHEBI_29888_RXN-12263. Source location `./YeastPathways_PWY-5670-1.json#/facts/0; endpoint types: /individuals/11/type; /individuals/8/type`
squalene synthase [NAD(P)H] activity (squalene-forming) `gomodel:RXN66-281`	has_output	squalene `CHEBI:15440`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN66-281 RO:0002234 gomodel:CHEBI_15440_RXN66-281. Source location `./YeastPathways_PWY-5670-1.json#/facts/1; endpoint types: /individuals/13/type; /individuals/5/type`
squalene synthase [NAD(P)H] activity (squalene-forming) `gomodel:RXN66-281`	has_output	diphosphoric acid `CHEBI:29888`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN66-281 RO:0002234 gomodel:CHEBI_29888_RXN66-281. Source location `./YeastPathways_PWY-5670-1.json#/facts/2; endpoint types: /individuals/13/type; /individuals/9/type`
squalene synthase [NAD(P)H] activity (squalene-forming) `gomodel:RXN66-281`	has_output	NAD(P)(+) `CHEBI:13390`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN66-281 RO:0002234 gomodel:CHEBI_13390_RXN66-281. Source location `./YeastPathways_PWY-5670-1.json#/facts/3; endpoint types: /individuals/13/type; /individuals/0/type`
squalene synthase [NAD(P)H] activity (squalene-forming) `gomodel:RXN66-281`	has_input	NAD(P)H `CHEBI:13392`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN66-281 RO:0002233 gomodel:CHEBI_13392_RXN66-281. Source location `./YeastPathways_PWY-5670-1.json#/facts/4; endpoint types: /individuals/13/type; /individuals/1/type`
ERG9 Scer `SGD:S000001233`	enables	squalene synthase [NAD(P)H] activity (presqualene diphosphate-forming) `gomodel:RXN-12263`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN-12263 RO:0002333 gomodel:YHR190W-MONOMER_RXN-12263_controller. Source location `./YeastPathways_PWY-5670-1.json#/facts/5; endpoint types: /individuals/11/type; /individuals/15/type`
squalene monooxygenase activity `gomodel:RXN3O-9816`	has_output	water `CHEBI:15377`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN3O-9816 RO:0002234 gomodel:CHEBI_15377_RXN3O-9816. Source location `./YeastPathways_PWY-5670-1.json#/facts/7; endpoint types: /individuals/12/type; /individuals/2/type`
squalene monooxygenase activity `gomodel:RXN3O-9816`	has_input	dioxygen `CHEBI:15379`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN3O-9816 RO:0002233 gomodel:CHEBI_15379_RXN3O-9816. Source location `./YeastPathways_PWY-5670-1.json#/facts/8; endpoint types: /individuals/12/type; /individuals/4/type`
squalene monooxygenase activity `gomodel:RXN3O-9816`	has_output	chemical entity `gomodel:YeastPathways_PWY-5670-1/654d809000002591`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN3O-9816 RO:0002234 gomodel:YeastPathways_PWY-5670-1/654d809000002591. Source location `./YeastPathways_PWY-5670-1.json#/facts/9; endpoint types: /individuals/12/type; /individuals/40/type`
ERG1 Scer `SGD:S000003407`	enables	squalene monooxygenase activity `gomodel:RXN3O-9816`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN3O-9816 RO:0002333 gomodel:YGR175C-MONOMER_RXN3O-9816_controller. Source location `./YeastPathways_PWY-5670-1.json#/facts/10; endpoint types: /individuals/12/type; /individuals/14/type`
squalene monooxygenase activity `gomodel:RXN3O-9816`	has_input	squalene `CHEBI:15440`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN3O-9816 RO:0002233 gomodel:CHEBI_15440_RXN66-281. Source location `./YeastPathways_PWY-5670-1.json#/facts/11; endpoint types: /individuals/12/type; /individuals/5/type`
squalene monooxygenase activity `gomodel:RXN3O-9816`	has_output	(S)-2,3-epoxysqualene `CHEBI:15441`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN3O-9816 RO:0002234 gomodel:CHEBI_15441_RXN3O-9816. Source location `./YeastPathways_PWY-5670-1.json#/facts/12; endpoint types: /individuals/12/type; /individuals/6/type`
ERG9 Scer `SGD:S000001233`	enables	squalene synthase [NAD(P)H] activity (squalene-forming) `gomodel:RXN66-281`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN66-281 RO:0002333 gomodel:YHR190W-MONOMER_RXN66-281_controller. Source location `./YeastPathways_PWY-5670-1.json#/facts/13; endpoint types: /individuals/13/type; /individuals/16/type`
squalene synthase [NAD(P)H] activity (presqualene diphosphate-forming) `gomodel:RXN-12263`	has_output	presqualene diphosphate(3-) `CHEBI:57310`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN-12263 RO:0002234 gomodel:CHEBI_57310_RXN-12263. Source location `./YeastPathways_PWY-5670-1.json#/facts/14; endpoint types: /individuals/11/type; /individuals/10/type`
squalene monooxygenase activity `gomodel:RXN3O-9816`	part_of	triterpenoid biosynthetic process `GO:0016104`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN3O-9816 BFO:0000050 gomodel:YeastPathways_PWY-5670-1/YeastPathways_PWY-5670-1. Source location `./YeastPathways_PWY-5670-1.json#/facts/15; endpoint types: /individuals/12/type; /individuals/39/type`
squalene synthase [NAD(P)H] activity (presqualene diphosphate-forming) `gomodel:RXN-12263`	part_of	triterpenoid biosynthetic process `GO:0016104`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN-12263 BFO:0000050 gomodel:YeastPathways_PWY-5670-1/YeastPathways_PWY-5670-1. Source location `./YeastPathways_PWY-5670-1.json#/facts/16; endpoint types: /individuals/11/type; /individuals/39/type`
squalene synthase [NAD(P)H] activity (presqualene diphosphate-forming) `gomodel:RXN-12263`	has_input	2-trans,6-trans-farnesyl diphosphate(3-) `CHEBI:175763`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN-12263 RO:0002233 gomodel:CHEBI_175763_RXN-12263. Source location `./YeastPathways_PWY-5670-1.json#/facts/17; endpoint types: /individuals/11/type; /individuals/7/type`
squalene synthase [NAD(P)H] activity (squalene-forming) `gomodel:RXN66-281`	has_input	presqualene diphosphate(3-) `CHEBI:57310`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN66-281 RO:0002233 gomodel:CHEBI_57310_RXN-12263. Source location `./YeastPathways_PWY-5670-1.json#/facts/18; endpoint types: /individuals/13/type; /individuals/10/type`
squalene synthase [NAD(P)H] activity (squalene-forming) `gomodel:RXN66-281`	has_input	hydron `CHEBI:15378`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN66-281 RO:0002233 gomodel:CHEBI_15378_RXN66-281. Source location `./YeastPathways_PWY-5670-1.json#/facts/19; endpoint types: /individuals/13/type; /individuals/3/type`
squalene synthase [NAD(P)H] activity (squalene-forming) `gomodel:RXN66-281`	part_of	triterpenoid biosynthetic process `GO:0016104`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN66-281 BFO:0000050 gomodel:YeastPathways_PWY-5670-1/YeastPathways_PWY-5670-1. Source location `./YeastPathways_PWY-5670-1.json#/facts/20; endpoint types: /individuals/13/type; /individuals/39/type`
squalene monooxygenase activity `gomodel:RXN3O-9816`	has_input	chemical entity `gomodel:YeastPathways_PWY-5670-1/654d809000002611`	gomodel:YeastPathways_PWY-5670-1 Source assertion: The model asserts gomodel:RXN3O-9816 RO:0002233 gomodel:YeastPathways_PWY-5670-1/654d809000002611. Source location `./YeastPathways_PWY-5670-1.json#/facts/21; endpoint types: /individuals/12/type; /individuals/42/type`
ERG9 Scer `SGD:S000001233`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:14562095); ECO:0000269 (PubMed:1807826) Topology: Single-pass membrane protein.	endoplasmic reticulum membrane `GO:0005789`	UniProtKB:P29704 Source assertion: UniProtKB:P29704 annotates location Endoplasmic reticulum membrane (SL-0097). 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/821/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P29704 Source assertion: UniProtKB:P29704 has the exact SGD cross-reference SGD:S000001233. 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/821/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
ERG1 Scer `SGD:S000003407`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:9450962) Topology: Multi-pass membrane protein.	endoplasmic reticulum membrane `GO:0005789`	UniProtKB:P32476 Source assertion: UniProtKB:P32476 annotates location Endoplasmic reticulum membrane (SL-0097). 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/917/comments/1/subcellularLocations/1; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P32476 Source assertion: UniProtKB:P32476 has the exact SGD cross-reference SGD:S000003407. 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/917/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
ERG1 Scer `SGD:S000003407`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:9450962)	lipid droplet `GO:0005811`	UniProtKB:P32476 Source assertion: UniProtKB:P32476 annotates location Lipid droplet (SL-0154). 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/917/comments/1/subcellularLocations/2; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P32476 Source assertion: UniProtKB:P32476 has the exact SGD cross-reference SGD:S000003407. 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/917/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
ERG9 Scer `SGD:S000001233`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000269 (PubMed:8323279)	magnesium(2+) `CHEBI:18420`	UniProtKB:P29704 Source assertion: UniProtKB:P29704 annotates CHEBI:18420 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/821/comments/0/cofactors/0` UniProtKB:P29704 Source assertion: UniProtKB:P29704 has the exact SGD cross-reference SGD:S000001233. 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/821/uniProtKBCrossReferences/0`
ERG1 Scer `SGD:S000003407`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000250 (UniProtKB:Q14534)	FAD(3-) `CHEBI:57692`	UniProtKB:P32476 Source assertion: UniProtKB:P32476 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/917/comments/0/cofactors/0` UniProtKB:P32476 Source assertion: UniProtKB:P32476 has the exact SGD cross-reference SGD:S000003407. 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/917/uniProtKBCrossReferences/0`

References

gomodel:YeastPathways_PWY-5670-1 GO-CAM epoxysqualene biosynthesis model YeastPathways_PWY-5670-1 (source version: Pinned Noctua JSON archive; model date 2024-09-12; member ./YeastPathways_PWY-5670-1.json)
UniProtKB:P29704 Reviewed UniProtKB P29704 location annotations (source version: UniProt release 2026_03)
UniProtKB:P32476 Reviewed UniProtKB P32476 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 3 activity location assignments and 2 mapped physical proteins against reviewed S288C UniProt release2026_03 location/function/caution batch SHA256 95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d. Added 3 independently supported location edges and quarantined 3 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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