adenosine ribonucleotides de novo biosynthesis

gomodel:YeastPathways_PWY-7219

Adenosine ribonucleotides de novo biosynthesis in Saccharomyces cerevisiae S288C converts IMP to adenylo-succinate through ADE12-catalyzed adenylosuccinate synthase activity, cleaves adenylo-succinate to AMP through ADE13-catalyzed adenylosuccinate lyase activity, and phosphorylates AMP to ADP through ADK2- or ADK1-catalyzed AMP kinase activity.

Pathway type

nucleotide biosynthesis

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

25 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
adenosine biosynthetic process `GO:0046086`	biological process
cytosol `GO:0005829`	cellular component
fumarate(2-) `CHEBI:29806`	small molecule
ADE12 Scer `SGD:S000005164`	protein
adenosine 5'-monophosphate(2-) `CHEBI:456215`	small molecule
ATP(4-) `CHEBI:30616`	small molecule
ADP(3-) `CHEBI:456216`	small molecule
ADK2 Scer `SGD:S000000972`	protein
ADK1 Scer `SGD:S000002634`	protein
hydron `CHEBI:15378`	small molecule
N(6)-(1,2-dicarboxylatoethyl)-AMP(4-) `CHEBI:57567`	small molecule
IMP(2-) `CHEBI:58053`	small molecule
hydrogenphosphate `CHEBI:43474`	small molecule
GDP(3-) `CHEBI:58189`	small molecule
GTP(4-) `CHEBI:37565`	small molecule
L-aspartate(1-) `CHEBI:29991`	small molecule
ADE13 Scer `SGD:S000004351`	protein
cytoplasm `GO:0005737`	cellular component
mitochondrial matrix `GO:0005759`	cellular component
mitochondrial intermembrane space `GO:0005758`	cellular component
magnesium(2+) `CHEBI:18420`	cofactor
AMP kinase activity `gomodel:ADENYL-KIN-RXN`	molecular activity
adenylosuccinate synthase activity `gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN`	molecular activity
N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity `gomodel:AMPSYN-RXN`	molecular activity
GTP:AMP phosphotransferase activity `gomodel:YeastPathways_PWY-7219/6a4c244800000590`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
AMP kinase activity `gomodel:ADENYL-KIN-RXN`	part_of	adenosine biosynthetic process `GO:0046086`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:ADENYL-KIN-RXN BFO:0000050 gomodel:YeastPathways_PWY-7219/YeastPathways_PWY-7219. Source location `./YeastPathways_PWY-7219.json#/facts/0; endpoint types: /individuals/0/type; /individuals/39/type`
AMP kinase activity `gomodel:ADENYL-KIN-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:ADENYL-KIN-RXN BFO:0000066 gomodel:reaction_ADENYL-KIN-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-7219.json#/facts/1; endpoint types: /individuals/0/type; /individuals/36/type`
N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity `gomodel:AMPSYN-RXN`	has_output	fumarate(2-) `CHEBI:29806`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:AMPSYN-RXN RO:0002234 gomodel:CHEBI_29806_AMPSYN-RXN. Source location `./YeastPathways_PWY-7219.json#/facts/2; endpoint types: /individuals/2/type; /individuals/4/type`
ADE12 Scer `SGD:S000005164`	enables	adenylosuccinate synthase activity `gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN RO:0002333 gomodel:YNL220W-MONOMER_ADENYLOSUCCINATE-SYNTHASE-RXN_controller. Source location `./YeastPathways_PWY-7219.json#/facts/3; endpoint types: /individuals/1/type; /individuals/16/type`
AMP kinase activity `gomodel:ADENYL-KIN-RXN`	has_input	adenosine 5'-monophosphate(2-) `CHEBI:456215`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:ADENYL-KIN-RXN RO:0002233 gomodel:CHEBI_456215_AMPSYN-RXN. Source location `./YeastPathways_PWY-7219.json#/facts/5; endpoint types: /individuals/0/type; /individuals/9/type`
AMP kinase activity `gomodel:ADENYL-KIN-RXN`	has_input	ATP(4-) `CHEBI:30616`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:ADENYL-KIN-RXN RO:0002233 gomodel:CHEBI_30616_ADENYL-KIN-RXN. Source location `./YeastPathways_PWY-7219.json#/facts/6; endpoint types: /individuals/0/type; /individuals/6/type`
adenylosuccinate synthase activity `gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN`	part_of	adenosine biosynthetic process `GO:0046086`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN BFO:0000050 gomodel:YeastPathways_PWY-7219/YeastPathways_PWY-7219. Source location `./YeastPathways_PWY-7219.json#/facts/7; endpoint types: /individuals/1/type; /individuals/39/type`
ADK2 Scer `SGD:S000000972`	enables	GTP:AMP phosphotransferase activity `gomodel:YeastPathways_PWY-7219/6a4c244800000590`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:YeastPathways_PWY-7219/6a4c244800000590 RO:0002333 gomodel:YeastPathways_PWY-7219/6a4c244800000593. Source location `./YeastPathways_PWY-7219.json#/facts/9; endpoint types: /individuals/40/type; /individuals/43/type`
N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity `gomodel:AMPSYN-RXN`	part_of	adenosine biosynthetic process `GO:0046086`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:AMPSYN-RXN BFO:0000050 gomodel:YeastPathways_PWY-7219/YeastPathways_PWY-7219. Source location `./YeastPathways_PWY-7219.json#/facts/10; endpoint types: /individuals/2/type; /individuals/39/type`
ADK1 Scer `SGD:S000002634`	enables	AMP kinase activity `gomodel:ADENYL-KIN-RXN`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:ADENYL-KIN-RXN RO:0002333 gomodel:YDR226W-MONOMER_ADENYL-KIN-RXN_controller. Source location `./YeastPathways_PWY-7219.json#/facts/11; endpoint types: /individuals/0/type; /individuals/14/type`
adenylosuccinate synthase activity `gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN RO:0002234 gomodel:CHEBI_15378_ADENYLOSUCCINATE-SYNTHASE-RXN. Source location `./YeastPathways_PWY-7219.json#/facts/12; endpoint types: /individuals/1/type; /individuals/3/type`
N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity `gomodel:AMPSYN-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:AMPSYN-RXN BFO:0000066 gomodel:reaction_AMPSYN-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-7219.json#/facts/14; endpoint types: /individuals/2/type; /individuals/38/type`
adenylosuccinate synthase activity `gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN`	has_output	N(6)-(1,2-dicarboxylatoethyl)-AMP(4-) `CHEBI:57567`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN RO:0002234 gomodel:CHEBI_57567_ADENYLOSUCCINATE-SYNTHASE-RXN. Source location `./YeastPathways_PWY-7219.json#/facts/15; endpoint types: /individuals/1/type; /individuals/11/type`
adenylosuccinate synthase activity `gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN BFO:0000066 gomodel:reaction_ADENYLOSUCCINATE-SYNTHASE-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-7219.json#/facts/16; endpoint types: /individuals/1/type; /individuals/37/type`
adenylosuccinate synthase activity `gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN`	has_input	IMP(2-) `CHEBI:58053`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN RO:0002233 gomodel:CHEBI_58053_ADENYLOSUCCINATE-SYNTHASE-RXN. Source location `./YeastPathways_PWY-7219.json#/facts/17; endpoint types: /individuals/1/type; /individuals/12/type`
N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity `gomodel:AMPSYN-RXN`	has_output	adenosine 5'-monophosphate(2-) `CHEBI:456215`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:AMPSYN-RXN RO:0002234 gomodel:CHEBI_456215_AMPSYN-RXN. Source location `./YeastPathways_PWY-7219.json#/facts/18; endpoint types: /individuals/2/type; /individuals/9/type`
adenylosuccinate synthase activity `gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN`	has_output	hydrogenphosphate `CHEBI:43474`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN RO:0002234 gomodel:CHEBI_43474_ADENYLOSUCCINATE-SYNTHASE-RXN. Source location `./YeastPathways_PWY-7219.json#/facts/19; endpoint types: /individuals/1/type; /individuals/8/type`
adenylosuccinate synthase activity `gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN`	has_output	GDP(3-) `CHEBI:58189`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN RO:0002234 gomodel:CHEBI_58189_ADENYLOSUCCINATE-SYNTHASE-RXN. Source location `./YeastPathways_PWY-7219.json#/facts/20; endpoint types: /individuals/1/type; /individuals/13/type`
AMP kinase activity `gomodel:ADENYL-KIN-RXN`	has_output	ADP(3-) `CHEBI:456216`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:ADENYL-KIN-RXN RO:0002234 gomodel:CHEBI_456216_ADENYL-KIN-RXN. Source location `./YeastPathways_PWY-7219.json#/facts/21; endpoint types: /individuals/0/type; /individuals/10/type`
adenylosuccinate synthase activity `gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN`	has_input	GTP(4-) `CHEBI:37565`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN RO:0002233 gomodel:CHEBI_37565_ADENYLOSUCCINATE-SYNTHASE-RXN. Source location `./YeastPathways_PWY-7219.json#/facts/22; endpoint types: /individuals/1/type; /individuals/7/type`
N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity `gomodel:AMPSYN-RXN`	has_input	N(6)-(1,2-dicarboxylatoethyl)-AMP(4-) `CHEBI:57567`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:AMPSYN-RXN RO:0002233 gomodel:CHEBI_57567_ADENYLOSUCCINATE-SYNTHASE-RXN. Source location `./YeastPathways_PWY-7219.json#/facts/23; endpoint types: /individuals/2/type; /individuals/11/type`
adenylosuccinate synthase activity `gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN`	has_input	L-aspartate(1-) `CHEBI:29991`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:ADENYLOSUCCINATE-SYNTHASE-RXN RO:0002233 gomodel:CHEBI_29991_ADENYLOSUCCINATE-SYNTHASE-RXN. Source location `./YeastPathways_PWY-7219.json#/facts/24; endpoint types: /individuals/1/type; /individuals/5/type`
GTP:AMP phosphotransferase activity `gomodel:YeastPathways_PWY-7219/6a4c244800000590`	part_of	adenosine biosynthetic process `GO:0046086`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:YeastPathways_PWY-7219/6a4c244800000590 BFO:0000050 gomodel:YeastPathways_PWY-7219/YeastPathways_PWY-7219. Source location `./YeastPathways_PWY-7219.json#/facts/25; endpoint types: /individuals/40/type; /individuals/39/type`
ADE13 Scer `SGD:S000004351`	enables	N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity `gomodel:AMPSYN-RXN`	gomodel:YeastPathways_PWY-7219 Source assertion: The model asserts gomodel:AMPSYN-RXN RO:0002333 gomodel:YLR359W-MONOMER_AMPSYN-RXN_controller. Source location `./YeastPathways_PWY-7219.json#/facts/26; endpoint types: /individuals/2/type; /individuals/15/type`
ADE12 Scer `SGD:S000005164`	located_in Physical protein location from reviewed UniProt. ECO:0000255 (HAMAP-Rule:MF_03125); ECO:0000269 (PubMed:14562095)	cytoplasm `GO:0005737`	UniProtKB:P80210 Source assertion: UniProtKB:P80210 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/2353/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P80210 Source assertion: UniProtKB:P80210 has the exact SGD cross-reference SGD:S000005164. 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/2353/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
ADK2 Scer `SGD:S000000972`	located_in Physical protein location from reviewed UniProt. ECO:0000255 (HAMAP-Rule:MF_03169); ECO:0000269 (PubMed:1620094)	mitochondrial matrix `GO:0005759`	UniProtKB:P26364 Source assertion: UniProtKB:P26364 annotates location Mitochondrion matrix (SL-0170). 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/745/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P26364 Source assertion: UniProtKB:P26364 has the exact SGD cross-reference SGD:S000000972. 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/745/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
ADK1 Scer `SGD:S000002634`	located_in Physical protein location from reviewed UniProt. ECO:0000255 (HAMAP-Rule:MF_03168); ECO:0000269 (PubMed:12045196); ECO:0000269 (PubMed:2850178) Source qualification: 90% cytoplasmic, 10% mitochondrial	cytosol `GO:0005829`	UniProtKB:P07170 Source assertion: UniProtKB:P07170 annotates location Cytoplasm, cytosol (SL-0091). 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/157/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P07170 Source assertion: UniProtKB:P07170 has the exact SGD cross-reference SGD:S000002634. 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/157/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
ADK1 Scer `SGD:S000002634`	located_in Physical protein location from reviewed UniProt. ECO:0000255 (HAMAP-Rule:MF_03168); ECO:0000269 (PubMed:12045196); ECO:0000269 (PubMed:16823961); ECO:0000269 (PubMed:22984289); ECO:0000269 (PubMed:2850178) Source qualification: 90% cytoplasmic, 10% mitochondrial	mitochondrial intermembrane space `GO:0005758`	UniProtKB:P07170 Source assertion: UniProtKB:P07170 annotates location Mitochondrion intermembrane space (SL-0169). 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/157/comments/1/subcellularLocations/1; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P07170 Source assertion: UniProtKB:P07170 has the exact SGD cross-reference SGD:S000002634. 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/157/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
GTP:AMP phosphotransferase activity `gomodel:YeastPathways_PWY-7219/6a4c244800000590`	has_input Reviewed ADK2 uses GTP, not ATP, to phosphorylate AMP; native instance retained.	GTP(4-) `CHEBI:37565`	UniProtKB:P26364 Source assertion: a ribonucleoside 5'-triphosphate + AMP = a ribonucleoside 5'-diphosphate + ADP Source location `https://rest.uniprot.org/uniprotkb/P26364.json [sha256:6f63766ee236ebf46d0823f592d7405d0c8fbec5c26ef084abcdbd93762cb44d] #/comments/1/reaction` UniProtKB:P26364 Source assertion: ADK2 has GTP:AMP and ITP:AMP phosphotransferase activity and does not accept ATP as phosphate donor. This branch represents its GTP reaction. Source location `https://rest.uniprot.org/uniprotkb/P26364.json [sha256:6f63766ee236ebf46d0823f592d7405d0c8fbec5c26ef084abcdbd93762cb44d] #/comments/0/texts/0`
GTP:AMP phosphotransferase activity `gomodel:YeastPathways_PWY-7219/6a4c244800000590`	has_input Reviewed ADK2 uses GTP, not ATP, to phosphorylate AMP; native instance retained.	adenosine 5'-monophosphate(2-) `CHEBI:456215`	UniProtKB:P26364 Source assertion: a ribonucleoside 5'-triphosphate + AMP = a ribonucleoside 5'-diphosphate + ADP Source location `https://rest.uniprot.org/uniprotkb/P26364.json [sha256:6f63766ee236ebf46d0823f592d7405d0c8fbec5c26ef084abcdbd93762cb44d] #/comments/1/reaction` UniProtKB:P26364 Source assertion: ADK2 has GTP:AMP and ITP:AMP phosphotransferase activity and does not accept ATP as phosphate donor. This branch represents its GTP reaction. Source location `https://rest.uniprot.org/uniprotkb/P26364.json [sha256:6f63766ee236ebf46d0823f592d7405d0c8fbec5c26ef084abcdbd93762cb44d] #/comments/0/texts/0`
GTP:AMP phosphotransferase activity `gomodel:YeastPathways_PWY-7219/6a4c244800000590`	has_output Reviewed ADK2 uses GTP, not ATP, to phosphorylate AMP; native instance retained.	GDP(3-) `CHEBI:58189`	UniProtKB:P26364 Source assertion: a ribonucleoside 5'-triphosphate + AMP = a ribonucleoside 5'-diphosphate + ADP Source location `https://rest.uniprot.org/uniprotkb/P26364.json [sha256:6f63766ee236ebf46d0823f592d7405d0c8fbec5c26ef084abcdbd93762cb44d] #/comments/1/reaction` UniProtKB:P26364 Source assertion: ADK2 has GTP:AMP and ITP:AMP phosphotransferase activity and does not accept ATP as phosphate donor. This branch represents its GTP reaction. Source location `https://rest.uniprot.org/uniprotkb/P26364.json [sha256:6f63766ee236ebf46d0823f592d7405d0c8fbec5c26ef084abcdbd93762cb44d] #/comments/0/texts/0`
GTP:AMP phosphotransferase activity `gomodel:YeastPathways_PWY-7219/6a4c244800000590`	has_output Reviewed ADK2 uses GTP, not ATP, to phosphorylate AMP; native instance retained.	ADP(3-) `CHEBI:456216`	UniProtKB:P26364 Source assertion: a ribonucleoside 5'-triphosphate + AMP = a ribonucleoside 5'-diphosphate + ADP Source location `https://rest.uniprot.org/uniprotkb/P26364.json [sha256:6f63766ee236ebf46d0823f592d7405d0c8fbec5c26ef084abcdbd93762cb44d] #/comments/1/reaction` UniProtKB:P26364 Source assertion: ADK2 has GTP:AMP and ITP:AMP phosphotransferase activity and does not accept ATP as phosphate donor. This branch represents its GTP reaction. Source location `https://rest.uniprot.org/uniprotkb/P26364.json [sha256:6f63766ee236ebf46d0823f592d7405d0c8fbec5c26ef084abcdbd93762cb44d] #/comments/0/texts/0`
ADE12 Scer `SGD:S000005164`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000255 (HAMAP-Rule:MF_03125) Binds 1 Mg(2+) ion per subunit. UniProt note evidence: ECO:0000255 (HAMAP-Rule:MF_03125)	magnesium(2+) `CHEBI:18420`	UniProtKB:P80210 Source assertion: UniProtKB:P80210 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/2353/comments/0/cofactors/0; /results/2353/comments/0/note` UniProtKB:P80210 Source assertion: UniProtKB:P80210 has the exact SGD cross-reference SGD:S000005164. 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/2353/uniProtKBCrossReferences/0`

References

gomodel:YeastPathways_PWY-7219 GO-CAM adenosine ribonucleotides de novo biosynthesis model YeastPathways_PWY-7219 (source version: Pinned Noctua JSON archive; model date 2026-07-08; member ./YeastPathways_PWY-7219.json)
UniProtKB:P80210 Reviewed UniProtKB P80210 location annotations (source version: UniProt release 2026_03)
UniProtKB:P26364 Reviewed UniProtKB P26364 location annotations (source version: UniProt release 2026_03)
UniProtKB:P07170 Reviewed UniProtKB P07170 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.
2026-10-05T06:53:32Z Codex; review-catalytic-function; Reconciled native GO-CAM chemistry with independently reviewed enzyme specificity, direction, physiological scope and source cautions; superseded facts remain in the function 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 1 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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