trans, trans-farnesyl diphosphate biosynthesis

gomodel:YeastPathways_PWY-5123

trans, trans-farnesyl diphosphate biosynthesis in Saccharomyces cerevisiae S288C isomerizes isopentenyl diphosphate to dimethylallyl diphosphate, condenses dimethylallyl diphosphate with isopentenyl diphosphate to geranyl diphosphate, and condenses geranyl diphosphate with isopentenyl diphosphate to (2E,6E)-farnesyl diphosphate.

Pathway type

lipid biosynthesis

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

14 nodes · 24 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
ERG20 Scer `SGD:S000003703`	protein
prenyl diphosphate(3-) `CHEBI:57623`	small molecule
cytosol `GO:0005829`	cellular component
geranyl diphosphate(3-) `CHEBI:58057`	small molecule
trans, trans-farnesyl diphosphate biosynthetic process `GO:0045337`	biological process
IDI1 Scer `SGD:S000006038`	protein
isopentenyl diphosphate(3-) `CHEBI:128769`	small molecule
diphosphoric acid `CHEBI:29888`	small molecule
2-trans,6-trans-farnesyl diphosphate(3-) `CHEBI:175763`	small molecule
cytoplasm `GO:0005737`	cellular component
magnesium(2+) `CHEBI:18420`	cofactor
geranyl diphosphate + isopentenyl diphosphate -> (2E,6E)-farnesyl diphosphate + diphosphate `gomodel:FPPSYN-RXN`	molecular activity
dimethylallyl diphosphate + isopentenyl diphosphate -> geranyl diphosphate + diphosphate `gomodel:GPPSYN-RXN`	molecular activity
isopentenyl diphosphate <=> dimethylallyl diphosphate `gomodel:IPPISOM-RXN`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
ERG20 Scer `SGD:S000003703`	enables	dimethylallyl diphosphate + isopentenyl diphosphate -> geranyl diphosphate + diphosphate `gomodel:GPPSYN-RXN`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:GPPSYN-RXN RO:0002333 gomodel:YJL167W-MONOMER_GPPSYN-RXN_controller. Source location `./YeastPathways_PWY-5123.json#/facts/0; endpoint types: /individuals/9/type; /individuals/12/type`
dimethylallyl diphosphate + isopentenyl diphosphate -> geranyl diphosphate + diphosphate `gomodel:GPPSYN-RXN`	has_input	prenyl diphosphate(3-) `CHEBI:57623`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:GPPSYN-RXN RO:0002233 gomodel:CHEBI_57623_IPPISOM-RXN. Source location `./YeastPathways_PWY-5123.json#/facts/1; endpoint types: /individuals/9/type; /individuals/6/type`
ERG20 Scer `SGD:S000003703`	enables	geranyl diphosphate + isopentenyl diphosphate -> (2E,6E)-farnesyl diphosphate + diphosphate `gomodel:FPPSYN-RXN`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:FPPSYN-RXN RO:0002333 gomodel:YJL167W-MONOMER_FPPSYN-RXN_controller. Source location `./YeastPathways_PWY-5123.json#/facts/2; endpoint types: /individuals/8/type; /individuals/11/type`
geranyl diphosphate + isopentenyl diphosphate -> (2E,6E)-farnesyl diphosphate + diphosphate `gomodel:FPPSYN-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:FPPSYN-RXN BFO:0000066 gomodel:reaction_FPPSYN-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-5123.json#/facts/3; endpoint types: /individuals/8/type; /individuals/30/type`
geranyl diphosphate + isopentenyl diphosphate -> (2E,6E)-farnesyl diphosphate + diphosphate `gomodel:FPPSYN-RXN`	has_input	geranyl diphosphate(3-) `CHEBI:58057`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:FPPSYN-RXN RO:0002233 gomodel:CHEBI_58057_GPPSYN-RXN. Source location `./YeastPathways_PWY-5123.json#/facts/4; endpoint types: /individuals/8/type; /individuals/7/type`
geranyl diphosphate + isopentenyl diphosphate -> (2E,6E)-farnesyl diphosphate + diphosphate `gomodel:FPPSYN-RXN`	part_of	trans, trans-farnesyl diphosphate biosynthetic process `GO:0045337`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:FPPSYN-RXN BFO:0000050 gomodel:YeastPathways_PWY-5123/YeastPathways_PWY-5123. Source location `./YeastPathways_PWY-5123.json#/facts/5; endpoint types: /individuals/8/type; /individuals/33/type`
isopentenyl diphosphate <=> dimethylallyl diphosphate `gomodel:IPPISOM-RXN`	part_of	trans, trans-farnesyl diphosphate biosynthetic process `GO:0045337`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:IPPISOM-RXN BFO:0000050 gomodel:YeastPathways_PWY-5123/YeastPathways_PWY-5123. Source location `./YeastPathways_PWY-5123.json#/facts/6; endpoint types: /individuals/10/type; /individuals/33/type`
IDI1 Scer `SGD:S000006038`	enables	isopentenyl diphosphate <=> dimethylallyl diphosphate `gomodel:IPPISOM-RXN`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:IPPISOM-RXN RO:0002333 gomodel:YPL117C-MONOMER_IPPISOM-RXN_controller. Source location `./YeastPathways_PWY-5123.json#/facts/7; endpoint types: /individuals/10/type; /individuals/13/type`
geranyl diphosphate + isopentenyl diphosphate -> (2E,6E)-farnesyl diphosphate + diphosphate `gomodel:FPPSYN-RXN`	has_input	isopentenyl diphosphate(3-) `CHEBI:128769`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:FPPSYN-RXN RO:0002233 gomodel:CHEBI_128769_FPPSYN-RXN. Source location `./YeastPathways_PWY-5123.json#/facts/8; endpoint types: /individuals/8/type; /individuals/0/type`
isopentenyl diphosphate <=> dimethylallyl diphosphate `gomodel:IPPISOM-RXN`	provides_input_for	dimethylallyl diphosphate + isopentenyl diphosphate -> geranyl diphosphate + diphosphate `gomodel:GPPSYN-RXN`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:IPPISOM-RXN RO:0002413 gomodel:GPPSYN-RXN. Source location `./YeastPathways_PWY-5123.json#/facts/9; endpoint types: /individuals/10/type; /individuals/9/type`
dimethylallyl diphosphate + isopentenyl diphosphate -> geranyl diphosphate + diphosphate `gomodel:GPPSYN-RXN`	has_input	isopentenyl diphosphate(3-) `CHEBI:128769`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:GPPSYN-RXN RO:0002233 gomodel:CHEBI_128769_GPPSYN-RXN. Source location `./YeastPathways_PWY-5123.json#/facts/10; endpoint types: /individuals/9/type; /individuals/1/type`
dimethylallyl diphosphate + isopentenyl diphosphate -> geranyl diphosphate + diphosphate `gomodel:GPPSYN-RXN`	has_output	diphosphoric acid `CHEBI:29888`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:GPPSYN-RXN RO:0002234 gomodel:CHEBI_29888_GPPSYN-RXN. Source location `./YeastPathways_PWY-5123.json#/facts/11; endpoint types: /individuals/9/type; /individuals/5/type`
dimethylallyl diphosphate + isopentenyl diphosphate -> geranyl diphosphate + diphosphate `gomodel:GPPSYN-RXN`	has_output	geranyl diphosphate(3-) `CHEBI:58057`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:GPPSYN-RXN RO:0002234 gomodel:CHEBI_58057_GPPSYN-RXN. Source location `./YeastPathways_PWY-5123.json#/facts/12; endpoint types: /individuals/9/type; /individuals/7/type`
isopentenyl diphosphate <=> dimethylallyl diphosphate `gomodel:IPPISOM-RXN`	has_input	isopentenyl diphosphate(3-) `CHEBI:128769`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:IPPISOM-RXN RO:0002233 gomodel:CHEBI_128769_IPPISOM-RXN. Source location `./YeastPathways_PWY-5123.json#/facts/13; endpoint types: /individuals/10/type; /individuals/2/type`
dimethylallyl diphosphate + isopentenyl diphosphate -> geranyl diphosphate + diphosphate `gomodel:GPPSYN-RXN`	part_of	trans, trans-farnesyl diphosphate biosynthetic process `GO:0045337`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:GPPSYN-RXN BFO:0000050 gomodel:YeastPathways_PWY-5123/YeastPathways_PWY-5123. Source location `./YeastPathways_PWY-5123.json#/facts/14; endpoint types: /individuals/9/type; /individuals/33/type`
geranyl diphosphate + isopentenyl diphosphate -> (2E,6E)-farnesyl diphosphate + diphosphate `gomodel:FPPSYN-RXN`	has_output	diphosphoric acid `CHEBI:29888`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:FPPSYN-RXN RO:0002234 gomodel:CHEBI_29888_FPPSYN-RXN. Source location `./YeastPathways_PWY-5123.json#/facts/15; endpoint types: /individuals/8/type; /individuals/4/type`
isopentenyl diphosphate <=> dimethylallyl diphosphate `gomodel:IPPISOM-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:IPPISOM-RXN BFO:0000066 gomodel:reaction_IPPISOM-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-5123.json#/facts/16; endpoint types: /individuals/10/type; /individuals/32/type`
isopentenyl diphosphate <=> dimethylallyl diphosphate `gomodel:IPPISOM-RXN`	has_output	prenyl diphosphate(3-) `CHEBI:57623`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:IPPISOM-RXN RO:0002234 gomodel:CHEBI_57623_IPPISOM-RXN. Source location `./YeastPathways_PWY-5123.json#/facts/17; endpoint types: /individuals/10/type; /individuals/6/type`
dimethylallyl diphosphate + isopentenyl diphosphate -> geranyl diphosphate + diphosphate `gomodel:GPPSYN-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:GPPSYN-RXN BFO:0000066 gomodel:reaction_GPPSYN-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-5123.json#/facts/18; endpoint types: /individuals/9/type; /individuals/31/type`
dimethylallyl diphosphate + isopentenyl diphosphate -> geranyl diphosphate + diphosphate `gomodel:GPPSYN-RXN`	provides_input_for	geranyl diphosphate + isopentenyl diphosphate -> (2E,6E)-farnesyl diphosphate + diphosphate `gomodel:FPPSYN-RXN`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:GPPSYN-RXN RO:0002413 gomodel:FPPSYN-RXN. Source location `./YeastPathways_PWY-5123.json#/facts/19; endpoint types: /individuals/9/type; /individuals/8/type`
geranyl diphosphate + isopentenyl diphosphate -> (2E,6E)-farnesyl diphosphate + diphosphate `gomodel:FPPSYN-RXN`	has_output	2-trans,6-trans-farnesyl diphosphate(3-) `CHEBI:175763`	gomodel:YeastPathways_PWY-5123 Source assertion: The model asserts gomodel:FPPSYN-RXN RO:0002234 gomodel:CHEBI_175763_FPPSYN-RXN. Source location `./YeastPathways_PWY-5123.json#/facts/20; endpoint types: /individuals/8/type; /individuals/3/type`
IDI1 Scer `SGD:S000006038`	located_in Physical protein location from reviewed UniProt. ECO:0000305	cytoplasm `GO:0005737`	UniProtKB:P15496 Source assertion: UniProtKB:P15496 annotates location Cytoplasm (SL-0086). 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/417/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P15496 Source assertion: UniProtKB:P15496 has the exact SGD cross-reference SGD:S000006038. 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/417/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
ERG20 Scer `SGD:S000003703`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000250 (UniProtKB:Q12051) Binds 2 Mg(2+) ions per subunit. UniProt note evidence: ECO:0000250 (UniProtKB:Q12051)	magnesium(2+) `CHEBI:18420`	UniProtKB:P08524 Source assertion: UniProtKB:P08524 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/209/comments/0/cofactors/0; /results/209/comments/0/note` UniProtKB:P08524 Source assertion: UniProtKB:P08524 has the exact SGD cross-reference SGD:S000003703. 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/209/uniProtKBCrossReferences/0`
IDI1 Scer `SGD:S000006038`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000250 (UniProtKB:Q46822) Binds 1 Mg(2+) ion per subunit. UniProt note evidence: ECO:0000250 (UniProtKB:Q46822)	magnesium(2+) `CHEBI:18420`	UniProtKB:P15496 Source assertion: UniProtKB:P15496 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/417/comments/0/cofactors/0; /results/417/comments/0/note` UniProtKB:P15496 Source assertion: UniProtKB:P15496 has the exact SGD cross-reference SGD:S000006038. 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/417/uniProtKBCrossReferences/0`

References

gomodel:YeastPathways_PWY-5123 SGD GO-CAM trans, trans-farnesyl diphosphate biosynthesis pathway PWY-5123 (source version: Pinned Noctua JSON archive; model date 2026-08-03; member ./YeastPathways_PWY-5123.json)
UniProtKB:P15496 Reviewed UniProtKB P15496 location annotations (source version: UniProt release 2026_03)
UniProtKB:P08524 UniProtKB P08524 cofactor annotations (source version: 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 1 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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