UTP and CTP de novo biosynthesis

gomodel:YeastPathways_PWY-7176

UTP and CTP de novo biosynthesis in Saccharomyces cerevisiae S288C converts UMP to UDP via URA6-catalyzed UMP kinase activity, phosphorylates UDP to UTP through YNK1-catalyzed nucleoside diphosphate kinase activity, and aminates UTP to CTP through URA8- or URA7-catalyzed CTP synthase activity.

Pathway type

nucleotide biosynthesis

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

25 nodes · 46 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
UTP(4-) `CHEBI:46398`	small molecule
L-glutamine zwitterion `CHEBI:58359`	small molecule
L-glutamate(1-) `CHEBI:29985`	small molecule
ATP(4-) `CHEBI:30616`	small molecule
'de novo' pyrimidine nucleobase biosynthetic process `GO:0006207`	biological process
cytosol `GO:0005829`	cellular component
UDP(3-) `CHEBI:58223`	small molecule
hydron `CHEBI:15378`	small molecule
CTP(4-) `CHEBI:37563`	small molecule
ADP(3-) `CHEBI:456216`	small molecule
YNK1 Scer `SGD:S000001550`	protein
URA8 Scer `SGD:S000003864`	protein
hydrogenphosphate `CHEBI:43474`	small molecule
water `CHEBI:15377`	small molecule
uridine 5'-monophosphate(2-) `CHEBI:57865`	small molecule
URA7 Scer `SGD:S000000135`	protein
URA6 Scer `SGD:S000001507`	protein
cytoplasm `GO:0005737`	cellular component
mitochondrial intermembrane space `GO:0005758`	cellular component
nucleus `GO:0005634`	cellular component
magnesium(2+) `CHEBI:18420`	cofactor
CTP synthase activity `gomodel:CTPSYN-RXN`	molecular activity
ATP + UMP -> ADP + UDP `gomodel:RXN-12002`	molecular activity
nucleoside diphosphate kinase activity `gomodel:UDPKIN-RXN`	molecular activity
CTP synthase activity `gomodel:YeastPathways_PWY-7176/6a4c244800000283`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
CTP synthase activity `gomodel:YeastPathways_PWY-7176/6a4c244800000283`	has_input	UTP(4-) `CHEBI:46398`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:YeastPathways_PWY-7176/6a4c244800000283 RO:0002233 gomodel:CHEBI_46398_UDPKIN-RXN. Source location `./YeastPathways_PWY-7176.json#/facts/0; endpoint types: /individuals/46/type; /individuals/11/type`
CTP synthase activity `gomodel:CTPSYN-RXN`	has_input	L-glutamine zwitterion `CHEBI:58359`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:CTPSYN-RXN RO:0002233 gomodel:CHEBI_58359_CTPSYN-RXN. Source location `./YeastPathways_PWY-7176.json#/facts/1; endpoint types: /individuals/15/type; /individuals/14/type`
CTP synthase activity `gomodel:CTPSYN-RXN`	has_output	L-glutamate(1-) `CHEBI:29985`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:CTPSYN-RXN RO:0002234 gomodel:CHEBI_29985_CTPSYN-RXN. Source location `./YeastPathways_PWY-7176.json#/facts/2; endpoint types: /individuals/15/type; /individuals/2/type`
CTP synthase activity `gomodel:CTPSYN-RXN`	has_input	ATP(4-) `CHEBI:30616`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:CTPSYN-RXN RO:0002233 gomodel:CHEBI_30616_CTPSYN-RXN. Source location `./YeastPathways_PWY-7176.json#/facts/3; endpoint types: /individuals/15/type; /individuals/3/type`
CTP synthase activity `gomodel:YeastPathways_PWY-7176/6a4c244800000283`	part_of	'de novo' pyrimidine nucleobase biosynthetic process `GO:0006207`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:YeastPathways_PWY-7176/6a4c244800000283 BFO:0000050 gomodel:YeastPathways_PWY-7176/YeastPathways_PWY-7176. Source location `./YeastPathways_PWY-7176.json#/facts/4; endpoint types: /individuals/46/type; /individuals/45/type`
nucleoside diphosphate kinase activity `gomodel:UDPKIN-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:UDPKIN-RXN BFO:0000066 gomodel:reaction_UDPKIN-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-7176.json#/facts/5; endpoint types: /individuals/17/type; /individuals/44/type`
nucleoside diphosphate kinase activity `gomodel:UDPKIN-RXN`	has_input	UDP(3-) `CHEBI:58223`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:UDPKIN-RXN RO:0002233 gomodel:CHEBI_58223_RXN-12002. Source location `./YeastPathways_PWY-7176.json#/facts/6; endpoint types: /individuals/17/type; /individuals/13/type`
CTP synthase activity `gomodel:YeastPathways_PWY-7176/6a4c244800000283`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:YeastPathways_PWY-7176/6a4c244800000283 RO:0002234 gomodel:YeastPathways_PWY-7176/6a4c244800000288. Source location `./YeastPathways_PWY-7176.json#/facts/7; endpoint types: /individuals/46/type; /individuals/51/type`
CTP synthase activity `gomodel:YeastPathways_PWY-7176/6a4c244800000283`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:YeastPathways_PWY-7176/6a4c244800000283 BFO:0000066 gomodel:YeastPathways_PWY-7176/6a4c244800000294. Source location `./YeastPathways_PWY-7176.json#/facts/8; endpoint types: /individuals/46/type; /individuals/56/type`
CTP synthase activity `gomodel:CTPSYN-RXN`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:CTPSYN-RXN RO:0002234 gomodel:CHEBI_15378_CTPSYN-RXN. Source location `./YeastPathways_PWY-7176.json#/facts/9; endpoint types: /individuals/15/type; /individuals/1/type`
ATP + UMP -> ADP + UDP `gomodel:RXN-12002`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:RXN-12002 BFO:0000066 gomodel:reaction_RXN-12002_location_lociGO_0005829. Source location `./YeastPathways_PWY-7176.json#/facts/10; endpoint types: /individuals/16/type; /individuals/43/type`
nucleoside diphosphate kinase activity `gomodel:UDPKIN-RXN`	part_of	'de novo' pyrimidine nucleobase biosynthetic process `GO:0006207`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:UDPKIN-RXN BFO:0000050 gomodel:YeastPathways_PWY-7176/YeastPathways_PWY-7176. Source location `./YeastPathways_PWY-7176.json#/facts/11; endpoint types: /individuals/17/type; /individuals/45/type`
CTP synthase activity `gomodel:YeastPathways_PWY-7176/6a4c244800000283`	has_input	L-glutamine zwitterion `CHEBI:58359`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:YeastPathways_PWY-7176/6a4c244800000283 RO:0002233 gomodel:YeastPathways_PWY-7176/6a4c244800000284. Source location `./YeastPathways_PWY-7176.json#/facts/12; endpoint types: /individuals/46/type; /individuals/47/type`
ATP + UMP -> ADP + UDP `gomodel:RXN-12002`	part_of	'de novo' pyrimidine nucleobase biosynthetic process `GO:0006207`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:RXN-12002 BFO:0000050 gomodel:YeastPathways_PWY-7176/YeastPathways_PWY-7176. Source location `./YeastPathways_PWY-7176.json#/facts/13; endpoint types: /individuals/16/type; /individuals/45/type`
CTP synthase activity `gomodel:CTPSYN-RXN`	part_of	'de novo' pyrimidine nucleobase biosynthetic process `GO:0006207`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:CTPSYN-RXN BFO:0000050 gomodel:YeastPathways_PWY-7176/YeastPathways_PWY-7176. Source location `./YeastPathways_PWY-7176.json#/facts/14; endpoint types: /individuals/15/type; /individuals/45/type`
nucleoside diphosphate kinase activity `gomodel:UDPKIN-RXN`	has_output	UTP(4-) `CHEBI:46398`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:UDPKIN-RXN RO:0002234 gomodel:CHEBI_46398_UDPKIN-RXN. Source location `./YeastPathways_PWY-7176.json#/facts/15; endpoint types: /individuals/17/type; /individuals/11/type`
CTP synthase activity `gomodel:YeastPathways_PWY-7176/6a4c244800000283`	has_output	CTP(4-) `CHEBI:37563`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:YeastPathways_PWY-7176/6a4c244800000283 RO:0002234 gomodel:YeastPathways_PWY-7176/6a4c244800000291. Source location `./YeastPathways_PWY-7176.json#/facts/16; endpoint types: /individuals/46/type; /individuals/54/type`
nucleoside diphosphate kinase activity `gomodel:UDPKIN-RXN`	has_output	ADP(3-) `CHEBI:456216`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:UDPKIN-RXN RO:0002234 gomodel:CHEBI_456216_UDPKIN-RXN. Source location `./YeastPathways_PWY-7176.json#/facts/17; endpoint types: /individuals/17/type; /individuals/10/type`
nucleoside diphosphate kinase activity `gomodel:UDPKIN-RXN`	has_input	ATP(4-) `CHEBI:30616`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:UDPKIN-RXN RO:0002233 gomodel:CHEBI_30616_UDPKIN-RXN. Source location `./YeastPathways_PWY-7176.json#/facts/18; endpoint types: /individuals/17/type; /individuals/5/type`
YNK1 Scer `SGD:S000001550`	enables	nucleoside diphosphate kinase activity `gomodel:UDPKIN-RXN`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:UDPKIN-RXN RO:0002333 gomodel:YeastPathways_PWY-7176/6690711d00000620. Source location `./YeastPathways_PWY-7176.json#/facts/19; endpoint types: /individuals/17/type; /individuals/69/type`
URA8 Scer `SGD:S000003864`	enables	CTP synthase activity `gomodel:CTPSYN-RXN`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:CTPSYN-RXN RO:0002333 gomodel:YJR103W-MONOMER_CTPSYN-RXN_controller. Source location `./YeastPathways_PWY-7176.json#/facts/20; endpoint types: /individuals/15/type; /individuals/18/type`
ATP + UMP -> ADP + UDP `gomodel:RXN-12002`	has_output	UDP(3-) `CHEBI:58223`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:RXN-12002 RO:0002234 gomodel:CHEBI_58223_RXN-12002. Source location `./YeastPathways_PWY-7176.json#/facts/21; endpoint types: /individuals/16/type; /individuals/13/type`
CTP synthase activity `gomodel:YeastPathways_PWY-7176/6a4c244800000283`	has_output	ADP(3-) `CHEBI:456216`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:YeastPathways_PWY-7176/6a4c244800000283 RO:0002234 gomodel:YeastPathways_PWY-7176/6a4c244800000290. Source location `./YeastPathways_PWY-7176.json#/facts/22; endpoint types: /individuals/46/type; /individuals/53/type`
CTP synthase activity `gomodel:CTPSYN-RXN`	has_input	UTP(4-) `CHEBI:46398`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:CTPSYN-RXN RO:0002233 gomodel:CHEBI_46398_UDPKIN-RXN. Source location `./YeastPathways_PWY-7176.json#/facts/23; endpoint types: /individuals/15/type; /individuals/11/type`
ATP + UMP -> ADP + UDP `gomodel:RXN-12002`	has_output	ADP(3-) `CHEBI:456216`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:RXN-12002 RO:0002234 gomodel:CHEBI_456216_RXN-12002. Source location `./YeastPathways_PWY-7176.json#/facts/24; endpoint types: /individuals/16/type; /individuals/9/type`
CTP synthase activity `gomodel:YeastPathways_PWY-7176/6a4c244800000283`	has_input	ATP(4-) `CHEBI:30616`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:YeastPathways_PWY-7176/6a4c244800000283 RO:0002233 gomodel:YeastPathways_PWY-7176/6a4c244800000285. Source location `./YeastPathways_PWY-7176.json#/facts/25; endpoint types: /individuals/46/type; /individuals/48/type`
CTP synthase activity `gomodel:CTPSYN-RXN`	has_output	hydrogenphosphate `CHEBI:43474`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:CTPSYN-RXN RO:0002234 gomodel:CHEBI_43474_CTPSYN-RXN. Source location `./YeastPathways_PWY-7176.json#/facts/26; endpoint types: /individuals/15/type; /individuals/7/type`
CTP synthase activity `gomodel:YeastPathways_PWY-7176/6a4c244800000283`	has_input	water `CHEBI:15377`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:YeastPathways_PWY-7176/6a4c244800000283 RO:0002233 gomodel:YeastPathways_PWY-7176/6a4c244800000286. Source location `./YeastPathways_PWY-7176.json#/facts/27; endpoint types: /individuals/46/type; /individuals/49/type`
CTP synthase activity `gomodel:YeastPathways_PWY-7176/6a4c244800000283`	has_output	L-glutamate(1-) `CHEBI:29985`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:YeastPathways_PWY-7176/6a4c244800000283 RO:0002234 gomodel:YeastPathways_PWY-7176/6a4c244800000287. Source location `./YeastPathways_PWY-7176.json#/facts/28; endpoint types: /individuals/46/type; /individuals/50/type`
ATP + UMP -> ADP + UDP `gomodel:RXN-12002`	has_input	ATP(4-) `CHEBI:30616`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:RXN-12002 RO:0002233 gomodel:CHEBI_30616_RXN-12002. Source location `./YeastPathways_PWY-7176.json#/facts/29; endpoint types: /individuals/16/type; /individuals/4/type`
ATP + UMP -> ADP + UDP `gomodel:RXN-12002`	has_input	uridine 5'-monophosphate(2-) `CHEBI:57865`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:RXN-12002 RO:0002233 gomodel:CHEBI_57865_RXN-12002. Source location `./YeastPathways_PWY-7176.json#/facts/30; endpoint types: /individuals/16/type; /individuals/12/type`
URA7 Scer `SGD:S000000135`	enables	CTP synthase activity `gomodel:YeastPathways_PWY-7176/6a4c244800000283`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:YeastPathways_PWY-7176/6a4c244800000283 RO:0002333 gomodel:YeastPathways_PWY-7176/6a4c244800000292. Source location `./YeastPathways_PWY-7176.json#/facts/31; endpoint types: /individuals/46/type; /individuals/55/type`
CTP synthase activity `gomodel:CTPSYN-RXN`	has_output	ADP(3-) `CHEBI:456216`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:CTPSYN-RXN RO:0002234 gomodel:CHEBI_456216_CTPSYN-RXN. Source location `./YeastPathways_PWY-7176.json#/facts/32; endpoint types: /individuals/15/type; /individuals/8/type`
URA6 Scer `SGD:S000001507`	enables	ATP + UMP -> ADP + UDP `gomodel:RXN-12002`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:RXN-12002 RO:0002333 gomodel:YKL024C-MONOMER_RXN-12002_controller. Source location `./YeastPathways_PWY-7176.json#/facts/33; endpoint types: /individuals/16/type; /individuals/19/type`
CTP synthase activity `gomodel:CTPSYN-RXN`	has_input	water `CHEBI:15377`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:CTPSYN-RXN RO:0002233 gomodel:CHEBI_15377_CTPSYN-RXN. Source location `./YeastPathways_PWY-7176.json#/facts/34; endpoint types: /individuals/15/type; /individuals/0/type`
CTP synthase activity `gomodel:CTPSYN-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:CTPSYN-RXN BFO:0000066 gomodel:reaction_CTPSYN-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-7176.json#/facts/35; endpoint types: /individuals/15/type; /individuals/42/type`
CTP synthase activity `gomodel:CTPSYN-RXN`	has_output	CTP(4-) `CHEBI:37563`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:CTPSYN-RXN RO:0002234 gomodel:CHEBI_37563_CTPSYN-RXN. Source location `./YeastPathways_PWY-7176.json#/facts/36; endpoint types: /individuals/15/type; /individuals/6/type`
CTP synthase activity `gomodel:YeastPathways_PWY-7176/6a4c244800000283`	has_output	hydrogenphosphate `CHEBI:43474`	gomodel:YeastPathways_PWY-7176 Source assertion: The model asserts gomodel:YeastPathways_PWY-7176/6a4c244800000283 RO:0002234 gomodel:YeastPathways_PWY-7176/6a4c244800000289. Source location `./YeastPathways_PWY-7176.json#/facts/37; endpoint types: /individuals/46/type; /individuals/52/type`
YNK1 Scer `SGD:S000001550`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:12472466) Source qualification: Localizes predominantly to the cytoplasm. A small fraction is present in the mitochondrial intermembrane space	cytoplasm `GO:0005737`	UniProtKB:P36010 Source assertion: UniProtKB:P36010 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/1183/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P36010 Source assertion: UniProtKB:P36010 has the exact SGD cross-reference SGD:S000001550. 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/1183/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
YNK1 Scer `SGD:S000001550`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:12472466); ECO:0000269 (PubMed:16823961); ECO:0000269 (PubMed:22984289) Source qualification: Localizes predominantly to the cytoplasm. A small fraction is present in the mitochondrial intermembrane space	mitochondrial intermembrane space `GO:0005758`	UniProtKB:P36010 Source assertion: UniProtKB:P36010 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/1183/comments/1/subcellularLocations/1; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P36010 Source assertion: UniProtKB:P36010 has the exact SGD cross-reference SGD:S000001550. 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/1183/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
URA8 Scer `SGD:S000003864`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:14562095)	cytoplasm `GO:0005737`	UniProtKB:P38627 Source assertion: UniProtKB:P38627 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/1397/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P38627 Source assertion: UniProtKB:P38627 has the exact SGD cross-reference SGD:S000003864. 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/1397/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
URA6 Scer `SGD:S000001507`	located_in Physical protein location from reviewed UniProt. ECO:0000255 (HAMAP-Rule:MF_03172); ECO:0000269 (PubMed:1333436); ECO:0000269 (PubMed:8391780) Source qualification: Predominantly cytoplasmic	cytoplasm `GO:0005737`	UniProtKB:P15700 Source assertion: UniProtKB:P15700 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/422/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P15700 Source assertion: UniProtKB:P15700 has the exact SGD cross-reference SGD:S000001507. 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/422/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
URA6 Scer `SGD:S000001507`	located_in Physical protein location from reviewed UniProt. ECO:0000255 (HAMAP-Rule:MF_03172); ECO:0000269 (PubMed:1333436); ECO:0000269 (PubMed:8391780) Source qualification: Predominantly cytoplasmic	nucleus `GO:0005634`	UniProtKB:P15700 Source assertion: UniProtKB:P15700 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/422/comments/1/subcellularLocations/1; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P15700 Source assertion: UniProtKB:P15700 has the exact SGD cross-reference SGD:S000001507. 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/422/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
YNK1 Scer `SGD:S000001550`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000269 (PubMed:5793714)	magnesium(2+) `CHEBI:18420`	UniProtKB:P36010 Source assertion: UniProtKB:P36010 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/1183/comments/0/cofactors/0` UniProtKB:P36010 Source assertion: UniProtKB:P36010 has the exact SGD cross-reference SGD:S000001550. 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/1183/uniProtKBCrossReferences/0`
URA8 Scer `SGD:S000003864`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: not specified	magnesium(2+) `CHEBI:18420`	UniProtKB:P38627 Source assertion: UniProtKB:P38627 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/1397/comments/0/cofactors/0` UniProtKB:P38627 Source assertion: UniProtKB:P38627 has the exact SGD cross-reference SGD:S000003864. 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/1397/uniProtKBCrossReferences/0`
URA6 Scer `SGD:S000001507`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. Reviewed source qualification: The dispute concerns nucleoside substrate specificity, not magnesium dependence; keep the metal assertion without expanding substrate scope. UniProt evidence: ECO:0000255 (HAMAP-Rule:MF_03172); ECO:0000269 (PubMed:16240436); ECO:0000269 (PubMed:8391780) Binds 1 Mg(2+) ion per monomer. UniProt note evidence: ECO:0000255 (HAMAP-Rule:MF_03172); ECO:0000269 (PubMed:16240436); ECO:0000269 (PubMed:8391780)	magnesium(2+) `CHEBI:18420`	UniProtKB:P15700 Source assertion: UniProtKB:P15700 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/422/comments/0/cofactors/0; /results/422/comments/0/note` UniProtKB:P15700 Source assertion: UniProtKB:P15700 has the exact SGD cross-reference SGD:S000001507. 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/422/uniProtKBCrossReferences/0`

References

gomodel:YeastPathways_PWY-7176 GO-CAM UTP and CTP de novo biosynthesis model YeastPathways_PWY-7176 (source version: Pinned Noctua JSON archive; model date 2026-07-07; member ./YeastPathways_PWY-7176.json)
UniProtKB:P36010 Reviewed UniProtKB P36010 location annotations (source version: UniProt release 2026_03)
UniProtKB:P38627 Reviewed UniProtKB P38627 location annotations (source version: UniProt release 2026_03)
UniProtKB:P15700 Reviewed UniProtKB P15700 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 5 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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