phenylalanine biosynthesis

gomodel:YeastPathways_PWY3O-4153

Phenylalanine biosynthesis in Saccharomyces cerevisiae S288C uses chorismate mutase, prephenate dehydratase, and aromatic-amino-acid transaminase activities to convert chorismate through prephenate and 3-phenylpyruvate to L-phenylalanine.

Pathway type

amino acid biosynthesis

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

23 nodes · 33 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
L-phenylalanine biosynthetic process `GO:0009094`	biological process
L-phenylalanine zwitterion `CHEBI:58095`	small molecule
L-alanine zwitterion `CHEBI:57972`	small molecule
(1s,4s)-prephenate(2-) `CHEBI:29934`	small molecule
keto-phenylpyruvate `CHEBI:18005`	small molecule
ARO8 Scer `SGD:S000003170`	protein
2-oxoglutarate(2-) `CHEBI:16810`	small molecule
PHA2 Scer `SGD:S000005260`	protein
cytosol `GO:0005829`	cellular component
carbon dioxide `CHEBI:16526`	small molecule
ARO7 Scer `SGD:S000006264`	protein
hydron `CHEBI:15378`	small molecule
chorismate(2-) `CHEBI:29748`	small molecule
pyruvate `CHEBI:15361`	small molecule
water `CHEBI:15377`	small molecule
L-glutamate(1-) `CHEBI:29985`	small molecule
ARO9 Scer `SGD:S000001179`	protein
cytoplasm `GO:0005737`	cellular component
pyridoxal 5'-phosphate(2-) `CHEBI:597326`	cofactor
L-phenylalanine + pyruvate <=> 3-phenyl-2-oxopropanoate + L-alanine `gomodel:2.6.1.58-RXN`	molecular activity
chorismate <=> prephenate `gomodel:CHORISMATEMUT-RXN`	molecular activity
prephenate + H⁺ <=> 3-phenyl-2-oxopropanoate + CO₂ + H₂O `gomodel:PREPHENATEDEHYDRAT-RXN`	molecular activity
L-phenylalanine + 2-oxoglutarate <=> 3-phenyl-2-oxopropanoate + L-glutamate `gomodel:RXN-10814`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
L-phenylalanine + 2-oxoglutarate <=> 3-phenyl-2-oxopropanoate + L-glutamate `gomodel:RXN-10814`	part_of	L-phenylalanine biosynthetic process `GO:0009094`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:RXN-10814 BFO:0000050 gomodel:YeastPathways_PWY3O-4153/YeastPathways_PWY3O-4153. Source location `./YeastPathways_PWY3O-4153.json#/facts/0; endpoint types: /individuals/15/type; /individuals/45/type`
L-phenylalanine + pyruvate <=> 3-phenyl-2-oxopropanoate + L-alanine `gomodel:2.6.1.58-RXN`	has_output	L-phenylalanine zwitterion `CHEBI:58095`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:2.6.1.58-RXN RO:0002234 gomodel:CHEBI_58095_2.6.1.58-RXN. Source location `./YeastPathways_PWY3O-4153.json#/facts/1; endpoint types: /individuals/44/type; /individuals/10/type`
L-phenylalanine + pyruvate <=> 3-phenyl-2-oxopropanoate + L-alanine `gomodel:2.6.1.58-RXN`	has_input	L-alanine zwitterion `CHEBI:57972`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:2.6.1.58-RXN RO:0002233 gomodel:CHEBI_57972_2.6.1.58-RXN. Source location `./YeastPathways_PWY3O-4153.json#/facts/2; endpoint types: /individuals/44/type; /individuals/9/type`
prephenate + H⁺ <=> 3-phenyl-2-oxopropanoate + CO₂ + H₂O `gomodel:PREPHENATEDEHYDRAT-RXN`	part_of	L-phenylalanine biosynthetic process `GO:0009094`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:PREPHENATEDEHYDRAT-RXN BFO:0000050 gomodel:YeastPathways_PWY3O-4153/YeastPathways_PWY3O-4153. Source location `./YeastPathways_PWY3O-4153.json#/facts/3; endpoint types: /individuals/14/type; /individuals/45/type`
chorismate <=> prephenate `gomodel:CHORISMATEMUT-RXN`	has_output	(1s,4s)-prephenate(2-) `CHEBI:29934`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:CHORISMATEMUT-RXN RO:0002234 gomodel:CHEBI_29934_CHORISMATEMUT-RXN. Source location `./YeastPathways_PWY3O-4153.json#/facts/4; endpoint types: /individuals/12/type; /individuals/7/type`
L-phenylalanine + 2-oxoglutarate <=> 3-phenyl-2-oxopropanoate + L-glutamate `gomodel:RXN-10814`	has_input	keto-phenylpyruvate `CHEBI:18005`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:RXN-10814 RO:0002233 gomodel:CHEBI_18005_PREPHENATEDEHYDRAT-RXN. Source location `./YeastPathways_PWY3O-4153.json#/facts/5; endpoint types: /individuals/15/type; /individuals/5/type`
L-phenylalanine + 2-oxoglutarate <=> 3-phenyl-2-oxopropanoate + L-glutamate `gomodel:RXN-10814`	has_output	L-phenylalanine zwitterion `CHEBI:58095`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:RXN-10814 RO:0002234 gomodel:CHEBI_58095_RXN-10814. Source location `./YeastPathways_PWY3O-4153.json#/facts/6; endpoint types: /individuals/15/type; /individuals/11/type`
ARO8 Scer `SGD:S000003170`	enables	L-phenylalanine + 2-oxoglutarate <=> 3-phenyl-2-oxopropanoate + L-glutamate `gomodel:RXN-10814`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:RXN-10814 RO:0002333 gomodel:YeastPathways_PWY3O-4153/6690711d00000281. Source location `./YeastPathways_PWY3O-4153.json#/facts/7; endpoint types: /individuals/15/type; /individuals/46/type`
L-phenylalanine + 2-oxoglutarate <=> 3-phenyl-2-oxopropanoate + L-glutamate `gomodel:RXN-10814`	has_output	2-oxoglutarate(2-) `CHEBI:16810`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:RXN-10814 RO:0002234 gomodel:CHEBI_16810_RXN-10814. Source location `./YeastPathways_PWY3O-4153.json#/facts/8; endpoint types: /individuals/15/type; /individuals/4/type`
PHA2 Scer `SGD:S000005260`	enables	prephenate + H⁺ <=> 3-phenyl-2-oxopropanoate + CO₂ + H₂O `gomodel:PREPHENATEDEHYDRAT-RXN`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:PREPHENATEDEHYDRAT-RXN RO:0002333 gomodel:MONOMER3O-279_PREPHENATEDEHYDRAT-RXN_controller. Source location `./YeastPathways_PWY3O-4153.json#/facts/9; endpoint types: /individuals/14/type; /individuals/13/type`
chorismate <=> prephenate `gomodel:CHORISMATEMUT-RXN`	part_of	L-phenylalanine biosynthetic process `GO:0009094`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:CHORISMATEMUT-RXN BFO:0000050 gomodel:YeastPathways_PWY3O-4153/YeastPathways_PWY3O-4153. Source location `./YeastPathways_PWY3O-4153.json#/facts/10; endpoint types: /individuals/12/type; /individuals/45/type`
chorismate <=> prephenate `gomodel:CHORISMATEMUT-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:CHORISMATEMUT-RXN BFO:0000066 gomodel:reaction_CHORISMATEMUT-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY3O-4153.json#/facts/11; endpoint types: /individuals/12/type; /individuals/41/type`
prephenate + H⁺ <=> 3-phenyl-2-oxopropanoate + CO₂ + H₂O `gomodel:PREPHENATEDEHYDRAT-RXN`	has_output	carbon dioxide `CHEBI:16526`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:PREPHENATEDEHYDRAT-RXN RO:0002234 gomodel:CHEBI_16526_PREPHENATEDEHYDRAT-RXN. Source location `./YeastPathways_PWY3O-4153.json#/facts/12; endpoint types: /individuals/14/type; /individuals/3/type`
L-phenylalanine + pyruvate <=> 3-phenyl-2-oxopropanoate + L-alanine `gomodel:2.6.1.58-RXN`	has_input	keto-phenylpyruvate `CHEBI:18005`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:2.6.1.58-RXN RO:0002233 gomodel:CHEBI_18005_PREPHENATEDEHYDRAT-RXN. Source location `./YeastPathways_PWY3O-4153.json#/facts/13; endpoint types: /individuals/44/type; /individuals/5/type`
ARO7 Scer `SGD:S000006264`	enables	chorismate <=> prephenate `gomodel:CHORISMATEMUT-RXN`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:CHORISMATEMUT-RXN RO:0002333 gomodel:YPR060C-MONOMER_CHORISMATEMUT-RXN_controller. Source location `./YeastPathways_PWY3O-4153.json#/facts/14; endpoint types: /individuals/12/type; /individuals/17/type`
L-phenylalanine + pyruvate <=> 3-phenyl-2-oxopropanoate + L-alanine `gomodel:2.6.1.58-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:2.6.1.58-RXN BFO:0000066 gomodel:reaction_2.6.1.58-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY3O-4153.json#/facts/15; endpoint types: /individuals/44/type; /individuals/40/type`
prephenate + H⁺ <=> 3-phenyl-2-oxopropanoate + CO₂ + H₂O `gomodel:PREPHENATEDEHYDRAT-RXN`	has_input	hydron `CHEBI:15378`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:PREPHENATEDEHYDRAT-RXN RO:0002233 gomodel:CHEBI_15378_PREPHENATEDEHYDRAT-RXN. Source location `./YeastPathways_PWY3O-4153.json#/facts/16; endpoint types: /individuals/14/type; /individuals/2/type`
chorismate <=> prephenate `gomodel:CHORISMATEMUT-RXN`	has_input	chorismate(2-) `CHEBI:29748`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:CHORISMATEMUT-RXN RO:0002233 gomodel:CHEBI_29748_CHORISMATEMUT-RXN. Source location `./YeastPathways_PWY3O-4153.json#/facts/17; endpoint types: /individuals/12/type; /individuals/6/type`
L-phenylalanine + pyruvate <=> 3-phenyl-2-oxopropanoate + L-alanine `gomodel:2.6.1.58-RXN`	part_of	L-phenylalanine biosynthetic process `GO:0009094`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:2.6.1.58-RXN BFO:0000050 gomodel:YeastPathways_PWY3O-4153/YeastPathways_PWY3O-4153. Source location `./YeastPathways_PWY3O-4153.json#/facts/18; endpoint types: /individuals/44/type; /individuals/45/type`
prephenate + H⁺ <=> 3-phenyl-2-oxopropanoate + CO₂ + H₂O `gomodel:PREPHENATEDEHYDRAT-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:PREPHENATEDEHYDRAT-RXN BFO:0000066 gomodel:reaction_PREPHENATEDEHYDRAT-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY3O-4153.json#/facts/19; endpoint types: /individuals/14/type; /individuals/42/type`
L-phenylalanine + pyruvate <=> 3-phenyl-2-oxopropanoate + L-alanine `gomodel:2.6.1.58-RXN`	has_output	pyruvate `CHEBI:15361`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:2.6.1.58-RXN RO:0002234 gomodel:CHEBI_15361_2.6.1.58-RXN. Source location `./YeastPathways_PWY3O-4153.json#/facts/20; endpoint types: /individuals/44/type; /individuals/0/type`
L-phenylalanine + 2-oxoglutarate <=> 3-phenyl-2-oxopropanoate + L-glutamate `gomodel:RXN-10814`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:RXN-10814 BFO:0000066 gomodel:reaction_RXN-10814_location_lociGO_0005829. Source location `./YeastPathways_PWY3O-4153.json#/facts/21; endpoint types: /individuals/15/type; /individuals/43/type`
prephenate + H⁺ <=> 3-phenyl-2-oxopropanoate + CO₂ + H₂O `gomodel:PREPHENATEDEHYDRAT-RXN`	has_input	(1s,4s)-prephenate(2-) `CHEBI:29934`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:PREPHENATEDEHYDRAT-RXN RO:0002233 gomodel:CHEBI_29934_CHORISMATEMUT-RXN. Source location `./YeastPathways_PWY3O-4153.json#/facts/22; endpoint types: /individuals/14/type; /individuals/7/type`
prephenate + H⁺ <=> 3-phenyl-2-oxopropanoate + CO₂ + H₂O `gomodel:PREPHENATEDEHYDRAT-RXN`	has_output	keto-phenylpyruvate `CHEBI:18005`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:PREPHENATEDEHYDRAT-RXN RO:0002234 gomodel:CHEBI_18005_PREPHENATEDEHYDRAT-RXN. Source location `./YeastPathways_PWY3O-4153.json#/facts/23; endpoint types: /individuals/14/type; /individuals/5/type`
prephenate + H⁺ <=> 3-phenyl-2-oxopropanoate + CO₂ + H₂O `gomodel:PREPHENATEDEHYDRAT-RXN`	has_output	water `CHEBI:15377`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:PREPHENATEDEHYDRAT-RXN RO:0002234 gomodel:CHEBI_15377_PREPHENATEDEHYDRAT-RXN. Source location `./YeastPathways_PWY3O-4153.json#/facts/24; endpoint types: /individuals/14/type; /individuals/1/type`
L-phenylalanine + 2-oxoglutarate <=> 3-phenyl-2-oxopropanoate + L-glutamate `gomodel:RXN-10814`	has_input	L-glutamate(1-) `CHEBI:29985`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:RXN-10814 RO:0002233 gomodel:CHEBI_29985_RXN-10814. Source location `./YeastPathways_PWY3O-4153.json#/facts/25; endpoint types: /individuals/15/type; /individuals/8/type`
ARO9 Scer `SGD:S000001179`	enables	L-phenylalanine + pyruvate <=> 3-phenyl-2-oxopropanoate + L-alanine `gomodel:2.6.1.58-RXN`	gomodel:YeastPathways_PWY3O-4153 Source assertion: The model asserts gomodel:2.6.1.58-RXN RO:0002333 gomodel:YHR137W-MONOMER_2.6.1.58-RXN_controller. Source location `./YeastPathways_PWY3O-4153.json#/facts/26; endpoint types: /individuals/44/type; /individuals/16/type`
ARO8 Scer `SGD:S000003170`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:14562095)	cytoplasm `GO:0005737`	UniProtKB:P53090 Source assertion: UniProtKB:P53090 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/2112/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P53090 Source assertion: UniProtKB:P53090 has the exact SGD cross-reference SGD:S000003170. 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/2112/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
PHA2 Scer `SGD:S000005260`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:14562095)	cytoplasm `GO:0005737`	UniProtKB:P32452 Source assertion: UniProtKB:P32452 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/4536/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P32452 Source assertion: UniProtKB:P32452 has the exact SGD cross-reference SGD:S000005260. 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/4536/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
ARO7 Scer `SGD:S000006264`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:12455686)	cytoplasm `GO:0005737`	UniProtKB:P32178 Source assertion: UniProtKB:P32178 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/855/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P32178 Source assertion: UniProtKB:P32178 has the exact SGD cross-reference SGD:S000006264. 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/855/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
ARO9 Scer `SGD:S000001179`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:14562095)	cytoplasm `GO:0005737`	UniProtKB:P38840 Source assertion: UniProtKB:P38840 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/1469/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P38840 Source assertion: UniProtKB:P38840 has the exact SGD cross-reference SGD:S000001179. 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/1469/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
ARO8 Scer `SGD:S000003170`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000269 (PubMed:23893908)	pyridoxal 5'-phosphate(2-) `CHEBI:597326`	UniProtKB:P53090 Source assertion: UniProtKB:P53090 annotates CHEBI:597326 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/2112/comments/0/cofactors/0` UniProtKB:P53090 Source assertion: UniProtKB:P53090 has the exact SGD cross-reference SGD:S000003170. 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/2112/uniProtKBCrossReferences/0`
ARO9 Scer `SGD:S000001179`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000250 (UniProtKB:O84395)	pyridoxal 5'-phosphate(2-) `CHEBI:597326`	UniProtKB:P38840 Source assertion: UniProtKB:P38840 annotates CHEBI:597326 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/1469/comments/0/cofactors/0` UniProtKB:P38840 Source assertion: UniProtKB:P38840 has the exact SGD cross-reference SGD:S000001179. 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/1469/uniProtKBCrossReferences/0`

References

gomodel:YeastPathways_PWY3O-4153 SGD GO-CAM phenylalanine biosynthesis - imported from: Saccharomyces Genome Database (source version: Pinned Noctua JSON archive; model date 2024-08-08; member ./YeastPathways_PWY3O-4153.json)
UniProtKB:P53090 Reviewed UniProtKB P53090 location annotations (source version: UniProt release 2026_03)
UniProtKB:P32452 Reviewed UniProtKB P32452 location annotations (source version: UniProt release 2026_03)
UniProtKB:P32178 Reviewed UniProtKB P32178 location annotations (source version: UniProt release 2026_03)
UniProtKB:P38840 Reviewed UniProtKB P38840 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 4 activity location assignments and 4 mapped physical proteins against reviewed S288C UniProt release2026_03 location/function/caution batch SHA256 95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d. Added 4 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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