myo-inositol biosynthesis

gomodel:YeastPathways_PWY-2301

myo-Inositol biosynthesis in Saccharomyces cerevisiae S288C converts D-glucopyranose 6-phosphate to 1D-myo-inositol 3-phosphate and hydrolyzes 1D-myo-inositol 3-phosphate to myo-inositol through INM1 or INM2 inositol monophosphate 1-phosphatase activities.

Pathway type

myo inositol biosynthesis

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

17 nodes · 25 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
1D-myo-inositol 3-phosphate(2-) `CHEBI:58401`	small molecule
inositol biosynthetic process `GO:0006021`	biological process
myo-inositol `CHEBI:17268`	small molecule
cytosol `GO:0005829`	cellular component
INO1 Scer `SGD:S000003689`	protein
hydrogenphosphate `CHEBI:43474`	small molecule
water `CHEBI:15377`	small molecule
D-glucopyranose 6-phosphate `CHEBI:4170`	small molecule
INM2 Scer `SGD:S000002695`	protein
INM1 Scer `SGD:S000001088`	protein
cytoplasm `GO:0005737`	cellular component
nucleus `GO:0005634`	cellular component
NAD(1-) `CHEBI:57540`	cofactor
magnesium(2+) `CHEBI:18420`	cofactor
inositol-3-phosphate synthase activity `gomodel:MYO-INOSITOL-1-PHOSPHATE-SYNTHASE-RXN`	molecular activity
inositol monophosphate 1-phosphatase activity (INM1) `gomodel:MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN`	molecular activity
inositol monophosphate 1-phosphatase activity (INM2) `gomodel:YeastPathways_PWY-2301/6a2b236300005397`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
inositol-3-phosphate synthase activity `gomodel:MYO-INOSITOL-1-PHOSPHATE-SYNTHASE-RXN`	has_output	1D-myo-inositol 3-phosphate(2-) `CHEBI:58401`	gomodel:YeastPathways_PWY-2301 Source assertion: The model asserts gomodel:MYO-INOSITOL-1-PHOSPHATE-SYNTHASE-RXN RO:0002234 gomodel:CHEBI_58401_MYO-INOSITOL-1-PHOSPHATE-SYNTHASE-RXN. Source location `./YeastPathways_PWY-2301.json#/facts/0; endpoint types: /individuals/5/type; /individuals/4/type`
inositol monophosphate 1-phosphatase activity (INM1) `gomodel:MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN`	part_of	inositol biosynthetic process `GO:0006021`	gomodel:YeastPathways_PWY-2301 Source assertion: The model asserts gomodel:MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN BFO:0000050 gomodel:YeastPathways_PWY-2301/YeastPathways_PWY-2301. Source location `./YeastPathways_PWY-2301.json#/facts/1; endpoint types: /individuals/6/type; /individuals/19/type`
inositol monophosphate 1-phosphatase activity (INM1) `gomodel:MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN`	has_output	myo-inositol `CHEBI:17268`	gomodel:YeastPathways_PWY-2301 Source assertion: The model asserts gomodel:MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN RO:0002234 gomodel:CHEBI_17268_MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN. Source location `./YeastPathways_PWY-2301.json#/facts/2; endpoint types: /individuals/6/type; /individuals/1/type`
inositol monophosphate 1-phosphatase activity (INM2) `gomodel:YeastPathways_PWY-2301/6a2b236300005397`	has_input	1D-myo-inositol 3-phosphate(2-) `CHEBI:58401`	gomodel:YeastPathways_PWY-2301 Source assertion: The model asserts gomodel:YeastPathways_PWY-2301/6a2b236300005397 RO:0002233 gomodel:CHEBI_58401_MYO-INOSITOL-1-PHOSPHATE-SYNTHASE-RXN. Source location `./YeastPathways_PWY-2301.json#/facts/3; endpoint types: /individuals/20/type; /individuals/4/type`
inositol monophosphate 1-phosphatase activity (INM2) `gomodel:YeastPathways_PWY-2301/6a2b236300005397`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-2301 Source assertion: The model asserts gomodel:YeastPathways_PWY-2301/6a2b236300005397 BFO:0000066 gomodel:YeastPathways_PWY-2301/6a2b236300005403. Source location `./YeastPathways_PWY-2301.json#/facts/4; endpoint types: /individuals/20/type; /individuals/25/type`
INO1 Scer `SGD:S000003689`	enables	inositol-3-phosphate synthase activity `gomodel:MYO-INOSITOL-1-PHOSPHATE-SYNTHASE-RXN`	gomodel:YeastPathways_PWY-2301 Source assertion: The model asserts gomodel:MYO-INOSITOL-1-PHOSPHATE-SYNTHASE-RXN RO:0002333 gomodel:YeastPathways_PWY-2301/654d809000001026. Source location `./YeastPathways_PWY-2301.json#/facts/5; endpoint types: /individuals/5/type; /individuals/31/type`
inositol monophosphate 1-phosphatase activity (INM1) `gomodel:MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN`	has_input	1D-myo-inositol 3-phosphate(2-) `CHEBI:58401`	gomodel:YeastPathways_PWY-2301 Source assertion: The model asserts gomodel:MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN RO:0002233 gomodel:CHEBI_58401_MYO-INOSITOL-1-PHOSPHATE-SYNTHASE-RXN. Source location `./YeastPathways_PWY-2301.json#/facts/6; endpoint types: /individuals/6/type; /individuals/4/type`
inositol monophosphate 1-phosphatase activity (INM2) `gomodel:YeastPathways_PWY-2301/6a2b236300005397`	has_output	hydrogenphosphate `CHEBI:43474`	gomodel:YeastPathways_PWY-2301 Source assertion: The model asserts gomodel:YeastPathways_PWY-2301/6a2b236300005397 RO:0002234 gomodel:YeastPathways_PWY-2301/6a2b236300005400. Source location `./YeastPathways_PWY-2301.json#/facts/7; endpoint types: /individuals/20/type; /individuals/23/type`
inositol monophosphate 1-phosphatase activity (INM2) `gomodel:YeastPathways_PWY-2301/6a2b236300005397`	has_input	water `CHEBI:15377`	gomodel:YeastPathways_PWY-2301 Source assertion: The model asserts gomodel:YeastPathways_PWY-2301/6a2b236300005397 RO:0002233 gomodel:YeastPathways_PWY-2301/6a2b236300005398. Source location `./YeastPathways_PWY-2301.json#/facts/8; endpoint types: /individuals/20/type; /individuals/21/type`
inositol monophosphate 1-phosphatase activity (INM2) `gomodel:YeastPathways_PWY-2301/6a2b236300005397`	has_output	myo-inositol `CHEBI:17268`	gomodel:YeastPathways_PWY-2301 Source assertion: The model asserts gomodel:YeastPathways_PWY-2301/6a2b236300005397 RO:0002234 gomodel:YeastPathways_PWY-2301/6a2b236300005399. Source location `./YeastPathways_PWY-2301.json#/facts/9; endpoint types: /individuals/20/type; /individuals/22/type`
inositol monophosphate 1-phosphatase activity (INM1) `gomodel:MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN`	has_input	water `CHEBI:15377`	gomodel:YeastPathways_PWY-2301 Source assertion: The model asserts gomodel:MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN RO:0002233 gomodel:CHEBI_15377_MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN. Source location `./YeastPathways_PWY-2301.json#/facts/10; endpoint types: /individuals/6/type; /individuals/0/type`
inositol monophosphate 1-phosphatase activity (INM2) `gomodel:YeastPathways_PWY-2301/6a2b236300005397`	part_of	inositol biosynthetic process `GO:0006021`	gomodel:YeastPathways_PWY-2301 Source assertion: The model asserts gomodel:YeastPathways_PWY-2301/6a2b236300005397 BFO:0000050 gomodel:YeastPathways_PWY-2301/YeastPathways_PWY-2301. Source location `./YeastPathways_PWY-2301.json#/facts/11; endpoint types: /individuals/20/type; /individuals/19/type`
inositol monophosphate 1-phosphatase activity (INM1) `gomodel:MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-2301 Source assertion: The model asserts gomodel:MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN BFO:0000066 gomodel:reaction_MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-2301.json#/facts/12; endpoint types: /individuals/6/type; /individuals/18/type`
inositol monophosphate 1-phosphatase activity (INM1) `gomodel:MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN`	has_output	hydrogenphosphate `CHEBI:43474`	gomodel:YeastPathways_PWY-2301 Source assertion: The model asserts gomodel:MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN RO:0002234 gomodel:CHEBI_43474_MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN. Source location `./YeastPathways_PWY-2301.json#/facts/13; endpoint types: /individuals/6/type; /individuals/3/type`
inositol-3-phosphate synthase activity `gomodel:MYO-INOSITOL-1-PHOSPHATE-SYNTHASE-RXN`	has_input	D-glucopyranose 6-phosphate `CHEBI:4170`	gomodel:YeastPathways_PWY-2301 Source assertion: The model asserts gomodel:MYO-INOSITOL-1-PHOSPHATE-SYNTHASE-RXN RO:0002233 gomodel:CHEBI_4170_MYO-INOSITOL-1-PHOSPHATE-SYNTHASE-RXN. Source location `./YeastPathways_PWY-2301.json#/facts/14; endpoint types: /individuals/5/type; /individuals/2/type`
inositol-3-phosphate synthase activity `gomodel:MYO-INOSITOL-1-PHOSPHATE-SYNTHASE-RXN`	part_of	inositol biosynthetic process `GO:0006021`	gomodel:YeastPathways_PWY-2301 Source assertion: The model asserts gomodel:MYO-INOSITOL-1-PHOSPHATE-SYNTHASE-RXN BFO:0000050 gomodel:YeastPathways_PWY-2301/YeastPathways_PWY-2301. Source location `./YeastPathways_PWY-2301.json#/facts/15; endpoint types: /individuals/5/type; /individuals/19/type`
inositol-3-phosphate synthase activity `gomodel:MYO-INOSITOL-1-PHOSPHATE-SYNTHASE-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-2301 Source assertion: The model asserts gomodel:MYO-INOSITOL-1-PHOSPHATE-SYNTHASE-RXN BFO:0000066 gomodel:reaction_MYO-INOSITOL-1-PHOSPHATE-SYNTHASE-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-2301.json#/facts/16; endpoint types: /individuals/5/type; /individuals/17/type`
INM2 Scer `SGD:S000002695`	enables	inositol monophosphate 1-phosphatase activity (INM2) `gomodel:YeastPathways_PWY-2301/6a2b236300005397`	gomodel:YeastPathways_PWY-2301 Source assertion: The model asserts gomodel:YeastPathways_PWY-2301/6a2b236300005397 RO:0002333 gomodel:YeastPathways_PWY-2301/6a2b236300005401. Source location `./YeastPathways_PWY-2301.json#/facts/17; endpoint types: /individuals/20/type; /individuals/24/type`
INM1 Scer `SGD:S000001088`	enables	inositol monophosphate 1-phosphatase activity (INM1) `gomodel:MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN`	gomodel:YeastPathways_PWY-2301 Source assertion: The model asserts gomodel:MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN RO:0002333 gomodel:YHR046C-MONOMER_MYO-INOSITOL-1OR-4-MONOPHOSPHATASE-RXN_controller. Source location `./YeastPathways_PWY-2301.json#/facts/18; endpoint types: /individuals/6/type; /individuals/7/type`
INO1 Scer `SGD:S000003689`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:14562095)	cytoplasm `GO:0005737`	UniProtKB:P11986 Source assertion: UniProtKB:P11986 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/341/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P11986 Source assertion: UniProtKB:P11986 has the exact SGD cross-reference SGD:S000003689. 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/341/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
INM1 Scer `SGD:S000001088`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:14562095)	cytoplasm `GO:0005737`	UniProtKB:P38710 Source assertion: UniProtKB:P38710 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/1417/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P38710 Source assertion: UniProtKB:P38710 has the exact SGD cross-reference SGD:S000001088. 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/1417/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
INM1 Scer `SGD:S000001088`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:14562095)	nucleus `GO:0005634`	UniProtKB:P38710 Source assertion: UniProtKB:P38710 annotates location Nucleus (SL-0191). 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/1417/comments/1/subcellularLocations/1; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P38710 Source assertion: UniProtKB:P38710 has the exact SGD cross-reference SGD:S000001088. 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/1417/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
INO1 Scer `SGD:S000003689`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000269 (PubMed:11779862); ECO:0000269 (PubMed:12832758); ECO:0000269 (PubMed:12836703); ECO:0000269 (PubMed:14684747); ECO:0000269 (Reference:Ref.6)	NAD(1-) `CHEBI:57540`	UniProtKB:P11986 Source assertion: UniProtKB:P11986 annotates CHEBI:57540 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/341/comments/0/cofactors/0` UniProtKB:P11986 Source assertion: UniProtKB:P11986 has the exact SGD cross-reference SGD:S000003689. 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/341/uniProtKBCrossReferences/0`
INM2 Scer `SGD:S000002695`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: not specified	magnesium(2+) `CHEBI:18420`	UniProtKB:Q05533 Source assertion: UniProtKB:Q05533 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/4150/comments/0/cofactors/0` UniProtKB:Q05533 Source assertion: UniProtKB:Q05533 has the exact SGD cross-reference SGD:S000002695. 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/4150/uniProtKBCrossReferences/0`
INM1 Scer `SGD:S000001088`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: not specified	magnesium(2+) `CHEBI:18420`	UniProtKB:P38710 Source assertion: UniProtKB:P38710 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/1417/comments/0/cofactors/0` UniProtKB:P38710 Source assertion: UniProtKB:P38710 has the exact SGD cross-reference SGD:S000001088. 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/1417/uniProtKBCrossReferences/0`

References

gomodel:YeastPathways_PWY-2301 GO-CAM myo-inositol biosynthesis model YeastPathways_PWY-2301 (source version: Pinned Noctua JSON archive; model date 2026-07-02; member ./YeastPathways_PWY-2301.json)
UniProtKB:P11986 Reviewed UniProtKB P11986 location annotations (source version: UniProt release 2026_03)
UniProtKB:P38710 Reviewed UniProtKB P38710 location annotations (source version: UniProt release 2026_03)
UniProtKB:Q05533 UniProtKB Q05533 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 3 mapped physical proteins against reviewed S288C UniProt release2026_03 location/function/caution batch SHA256 95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d. Added 3 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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