spermidine biosynthesis I

gomodel:YeastPathways_BSUBPOLYAMSYN-PWY

Spermidine biosynthesis I decarboxylates S-adenosyl-L-methionine through SPE2 and transfers its aminopropyl group to 1,4-butanediammonium through SPE3 to form spermidine in Saccharomyces cerevisiae S288C.

Pathway type

polyamine biosynthesis

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

14 nodes · 17 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
S-adenosylmethioninaminium `CHEBI:57443`	small molecule
spermidine biosynthetic process `GO:0008295`	biological process
cytosol `GO:0005829`	cellular component
S-adenosyl-L-methionine zwitterion `CHEBI:59789`	small molecule
carbon dioxide `CHEBI:16526`	small molecule
5'-S-methyl-5'-thioadenosine `CHEBI:17509`	small molecule
spermidine(3+) `CHEBI:57834`	small molecule
hydron `CHEBI:15378`	small molecule
1,4-butanediammonium `CHEBI:326268`	small molecule
SPE3 Scer `SGD:S000006273`	protein
SPE2 Scer `SGD:S000005412`	protein
pyruvoyl group `CHEBI:45360`	cofactor
adenosylmethionine decarboxylase activity `gomodel:SAMDECARB-RXN`	molecular activity
spermidine synthase activity `gomodel:SPERMIDINESYN-RXN`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
spermidine synthase activity `gomodel:SPERMIDINESYN-RXN`	has_input	S-adenosylmethioninaminium `CHEBI:57443`	gomodel:YeastPathways_BSUBPOLYAMSYN-PWY Source assertion: The model asserts gomodel:SPERMIDINESYN-RXN RO:0002233 gomodel:CHEBI_57443_SAMDECARB-RXN. Source location `./YeastPathways_BSUBPOLYAMSYN-PWY.json#/facts/0; endpoint types: /individuals/9/type; /individuals/5/type`
adenosylmethionine decarboxylase activity `gomodel:SAMDECARB-RXN`	part_of	spermidine biosynthetic process `GO:0008295`	gomodel:YeastPathways_BSUBPOLYAMSYN-PWY Source assertion: The model asserts gomodel:SAMDECARB-RXN BFO:0000050 gomodel:YeastPathways_BSUBPOLYAMSYN-PWY/YeastPathways_BSUBPOLYAMSYN-PWY. Source location `./YeastPathways_BSUBPOLYAMSYN-PWY.json#/facts/1; endpoint types: /individuals/8/type; /individuals/27/type`
adenosylmethionine decarboxylase activity `gomodel:SAMDECARB-RXN`	has_output	S-adenosylmethioninaminium `CHEBI:57443`	gomodel:YeastPathways_BSUBPOLYAMSYN-PWY Source assertion: The model asserts gomodel:SAMDECARB-RXN RO:0002234 gomodel:CHEBI_57443_SAMDECARB-RXN. Source location `./YeastPathways_BSUBPOLYAMSYN-PWY.json#/facts/2; endpoint types: /individuals/8/type; /individuals/5/type`
spermidine synthase activity `gomodel:SPERMIDINESYN-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_BSUBPOLYAMSYN-PWY Source assertion: The model asserts gomodel:SPERMIDINESYN-RXN BFO:0000066 gomodel:reaction_SPERMIDINESYN-RXN_location_lociGO_0005829. Source location `./YeastPathways_BSUBPOLYAMSYN-PWY.json#/facts/3; endpoint types: /individuals/9/type; /individuals/26/type`
adenosylmethionine decarboxylase activity `gomodel:SAMDECARB-RXN`	has_input	S-adenosyl-L-methionine zwitterion `CHEBI:59789`	gomodel:YeastPathways_BSUBPOLYAMSYN-PWY Source assertion: The model asserts gomodel:SAMDECARB-RXN RO:0002233 gomodel:CHEBI_59789_SAMDECARB-RXN. Source location `./YeastPathways_BSUBPOLYAMSYN-PWY.json#/facts/4; endpoint types: /individuals/8/type; /individuals/7/type`
adenosylmethionine decarboxylase activity `gomodel:SAMDECARB-RXN`	provides_input_for	spermidine synthase activity `gomodel:SPERMIDINESYN-RXN`	gomodel:YeastPathways_BSUBPOLYAMSYN-PWY Source assertion: The model asserts gomodel:SAMDECARB-RXN RO:0002413 gomodel:SPERMIDINESYN-RXN. Source location `./YeastPathways_BSUBPOLYAMSYN-PWY.json#/facts/5; endpoint types: /individuals/8/type; /individuals/9/type`
adenosylmethionine decarboxylase activity `gomodel:SAMDECARB-RXN`	has_output	carbon dioxide `CHEBI:16526`	gomodel:YeastPathways_BSUBPOLYAMSYN-PWY Source assertion: The model asserts gomodel:SAMDECARB-RXN RO:0002234 gomodel:CHEBI_16526_SAMDECARB-RXN. Source location `./YeastPathways_BSUBPOLYAMSYN-PWY.json#/facts/6; endpoint types: /individuals/8/type; /individuals/2/type`
spermidine synthase activity `gomodel:SPERMIDINESYN-RXN`	has_output	5'-S-methyl-5'-thioadenosine `CHEBI:17509`	gomodel:YeastPathways_BSUBPOLYAMSYN-PWY Source assertion: The model asserts gomodel:SPERMIDINESYN-RXN RO:0002234 gomodel:CHEBI_17509_SPERMIDINESYN-RXN. Source location `./YeastPathways_BSUBPOLYAMSYN-PWY.json#/facts/7; endpoint types: /individuals/9/type; /individuals/3/type`
spermidine synthase activity `gomodel:SPERMIDINESYN-RXN`	has_output	spermidine(3+) `CHEBI:57834`	gomodel:YeastPathways_BSUBPOLYAMSYN-PWY Source assertion: The model asserts gomodel:SPERMIDINESYN-RXN RO:0002234 gomodel:CHEBI_57834_SPERMIDINESYN-RXN. Source location `./YeastPathways_BSUBPOLYAMSYN-PWY.json#/facts/8; endpoint types: /individuals/9/type; /individuals/6/type`
adenosylmethionine decarboxylase activity `gomodel:SAMDECARB-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_BSUBPOLYAMSYN-PWY Source assertion: The model asserts gomodel:SAMDECARB-RXN BFO:0000066 gomodel:reaction_SAMDECARB-RXN_location_lociGO_0005829. Source location `./YeastPathways_BSUBPOLYAMSYN-PWY.json#/facts/9; endpoint types: /individuals/8/type; /individuals/25/type`
adenosylmethionine decarboxylase activity `gomodel:SAMDECARB-RXN`	has_input	hydron `CHEBI:15378`	gomodel:YeastPathways_BSUBPOLYAMSYN-PWY Source assertion: The model asserts gomodel:SAMDECARB-RXN RO:0002233 gomodel:CHEBI_15378_SAMDECARB-RXN. Source location `./YeastPathways_BSUBPOLYAMSYN-PWY.json#/facts/10; endpoint types: /individuals/8/type; /individuals/0/type`
spermidine synthase activity `gomodel:SPERMIDINESYN-RXN`	has_input	1,4-butanediammonium `CHEBI:326268`	gomodel:YeastPathways_BSUBPOLYAMSYN-PWY Source assertion: The model asserts gomodel:SPERMIDINESYN-RXN RO:0002233 gomodel:CHEBI_326268_SPERMIDINESYN-RXN. Source location `./YeastPathways_BSUBPOLYAMSYN-PWY.json#/facts/11; endpoint types: /individuals/9/type; /individuals/4/type`
SPE3 Scer `SGD:S000006273`	enables	spermidine synthase activity `gomodel:SPERMIDINESYN-RXN`	gomodel:YeastPathways_BSUBPOLYAMSYN-PWY Source assertion: The model asserts gomodel:SPERMIDINESYN-RXN RO:0002333 gomodel:YPR069C-MONOMER_SPERMIDINESYN-RXN_controller. Source location `./YeastPathways_BSUBPOLYAMSYN-PWY.json#/facts/12; endpoint types: /individuals/9/type; /individuals/11/type`
spermidine synthase activity `gomodel:SPERMIDINESYN-RXN`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_BSUBPOLYAMSYN-PWY Source assertion: The model asserts gomodel:SPERMIDINESYN-RXN RO:0002234 gomodel:CHEBI_15378_SPERMIDINESYN-RXN. Source location `./YeastPathways_BSUBPOLYAMSYN-PWY.json#/facts/13; endpoint types: /individuals/9/type; /individuals/1/type`
SPE2 Scer `SGD:S000005412`	enables	adenosylmethionine decarboxylase activity `gomodel:SAMDECARB-RXN`	gomodel:YeastPathways_BSUBPOLYAMSYN-PWY Source assertion: The model asserts gomodel:SAMDECARB-RXN RO:0002333 gomodel:YOL052C-MONOMER_SAMDECARB-RXN_controller. Source location `./YeastPathways_BSUBPOLYAMSYN-PWY.json#/facts/14; endpoint types: /individuals/8/type; /individuals/10/type`
spermidine synthase activity `gomodel:SPERMIDINESYN-RXN`	part_of	spermidine biosynthetic process `GO:0008295`	gomodel:YeastPathways_BSUBPOLYAMSYN-PWY Source assertion: The model asserts gomodel:SPERMIDINESYN-RXN BFO:0000050 gomodel:YeastPathways_BSUBPOLYAMSYN-PWY/YeastPathways_BSUBPOLYAMSYN-PWY. Source location `./YeastPathways_BSUBPOLYAMSYN-PWY.json#/facts/15; endpoint types: /individuals/9/type; /individuals/27/type`
SPE2 Scer `SGD:S000005412`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. Reviewed source qualification: The cofactor note explicitly describes a covalently bound pyruvoyl group; use the exact group class rather than free pyruvate. UniProt evidence: not specified Binds 1 pyruvoyl group covalently per subunit. UniProt note evidence: ECO:0000269 (PubMed:2266128)	pyruvoyl group `CHEBI:45360`	CHEBI:45360 Source assertion: ChEBI labels CHEBI:45360 as pyruvoyl group. Source location `chebi.obo [Term] id: CHEBI:45360; name: pyruvoyl group` UniProtKB:P21182 Source assertion: UniProtKB:P21182 cross-references CHEBI:15361, but its note specifies a covalently bound pyruvoyl group; that group is projected to CHEBI:45360. 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/540/comments/0/cofactors/0; /results/540/comments/0/note` UniProtKB:P21182 Source assertion: UniProtKB:P21182 has the exact SGD cross-reference SGD:S000005412. 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/540/uniProtKBCrossReferences/0`

References

gomodel:YeastPathways_BSUBPOLYAMSYN-PWY GO-CAM spermidine biosynthesis I model YeastPathways_BSUBPOLYAMSYN-PWY (source version: Pinned Noctua JSON archive; model date 2026-08-03; member ./YeastPathways_BSUBPOLYAMSYN-PWY.json)
UniProtKB:P21182 UniProtKB P21182 cofactor annotations (source version: 2026_03)
CHEBI:45360 ChEBI CHEBI:45360: pyruvoyl group (source version: ChEBI release 255)

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
- REVIEW — 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 0 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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