dolichyl phosphate D-mannose biosynthesis

gomodel:YeastPathways_PWY3O-123

Dolichyl phosphate D-mannose biosynthesis in Saccharomyces cerevisiae S288C converts beta-D-fructofuranose 6-phosphate to alpha-D-mannose 1-phosphate, forms GDP-alpha-D-mannose, and transfers D-mannose to dolichyl phosphate to produce dolichyl D-mannosyl phosphate.

Pathway type

glycan biosynthesis

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

26 nodes · 35 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
PSA1 Scer `SGD:S000002213`	protein
mannose metabolic process `GO:0006013`	biological process
GDP-alpha-D-mannose(2-) `CHEBI:57527`	small molecule
GDP(3-) `CHEBI:58189`	small molecule
cytosol `GO:0005829`	cellular component
hydron `CHEBI:15378`	small molecule
beta-D-fructofuranose 6-phosphate(2-) `CHEBI:57634`	small molecule
alpha-D-mannose 1-phosphate(2-) `CHEBI:58409`	small molecule
dolichyl phosphate `CHEBI:16214`	lipid
dolichyl D-mannosyl phosphate `CHEBI:15809`	lipid
D-mannopyranose 6-phosphate `CHEBI:48066`	small molecule
DPM1 Scer `SGD:S000006387`	protein
SEC53 Scer `SGD:S000001849`	protein
PMI40 Scer `SGD:S000000805`	protein
cytoplasm `GO:0005737`	cellular component
endoplasmic reticulum membrane `GO:0005789`	cellular component
diphosphate(3-) `CHEBI:33019`	small molecule
GTP(4-) `CHEBI:37565`	small molecule
magnesium(2+) `CHEBI:18420`	cofactor
manganese(2+) `CHEBI:29035`	cofactor
calcium(2+) `CHEBI:29108`	cofactor
zinc(2+) `CHEBI:29105`	cofactor
dolichyl-phosphate beta-D-mannosyltransferase activity `gomodel:2.4.1.83-RXN`	molecular activity
alpha-D-mannose 1-phosphate + GTP + H(+) => GDP-alpha-D-mannose + diphosphate `RHEA:15230`	molecular activity	left to right
mannose-6-phosphate isomerase activity `gomodel:MANNPISOM-RXN`	molecular activity
phosphomannomutase activity `gomodel:PHOSMANMUT-RXN`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
PSA1 Scer `SGD:S000002213`	enables	alpha-D-mannose 1-phosphate + GTP + H(+) => GDP-alpha-D-mannose + diphosphate `RHEA:15230`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:MANNPGUANYLTRANGDP-RXN RO:0002333 gomodel:YDL055C-MONOMER_MANNPGUANYLTRANGDP-RXN_controller. Source location `./YeastPathways_PWY3O-123.json#/facts/0; endpoint types: /individuals/10/type; /individuals/13/type` UniProtKB:P41940 Source assertion: UniProtKB:P41940 annotates alpha-D-mannose 1-phosphate plus GTP yielding GDP-alpha-D-mannose and diphosphate (RHEA:15229), correcting the imported GDP/orthophosphate reaction. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_catalytic_activity%2Ccc_function%2Ccc_caution%2Corganism_id [sha256:9600fe7f1e55a4f51554b244607a706b1604904dc71de8960b2f399bf75b0c7c] #/results/3806/comments/1/reaction`
dolichyl-phosphate beta-D-mannosyltransferase activity `gomodel:2.4.1.83-RXN`	part_of	mannose metabolic process `GO:0006013`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:2.4.1.83-RXN BFO:0000050 gomodel:YeastPathways_PWY3O-123/YeastPathways_PWY3O-123. Source location `./YeastPathways_PWY3O-123.json#/facts/1; endpoint types: /individuals/42/type; /individuals/43/type`
alpha-D-mannose 1-phosphate + GTP + H(+) => GDP-alpha-D-mannose + diphosphate `RHEA:15230`	provides_input_for	dolichyl-phosphate beta-D-mannosyltransferase activity `gomodel:2.4.1.83-RXN`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:MANNPGUANYLTRANGDP-RXN RO:0002413 gomodel:2.4.1.83-RXN. Source location `./YeastPathways_PWY3O-123.json#/facts/2; endpoint types: /individuals/10/type; /individuals/42/type` UniProtKB:P41940 Source assertion: UniProtKB:P41940 annotates alpha-D-mannose 1-phosphate plus GTP yielding GDP-alpha-D-mannose and diphosphate (RHEA:15229), correcting the imported GDP/orthophosphate reaction. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_catalytic_activity%2Ccc_function%2Ccc_caution%2Corganism_id [sha256:9600fe7f1e55a4f51554b244607a706b1604904dc71de8960b2f399bf75b0c7c] #/results/3806/comments/1/reaction`
alpha-D-mannose 1-phosphate + GTP + H(+) => GDP-alpha-D-mannose + diphosphate `RHEA:15230`	has_output	GDP-alpha-D-mannose(2-) `CHEBI:57527`	UniProtKB:P41940 Source assertion: UniProtKB:P41940 annotates alpha-D-mannose 1-phosphate plus GTP yielding GDP-alpha-D-mannose and diphosphate (RHEA:15229), correcting the imported GDP/orthophosphate reaction. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_catalytic_activity%2Ccc_function%2Ccc_caution%2Corganism_id [sha256:9600fe7f1e55a4f51554b244607a706b1604904dc71de8960b2f399bf75b0c7c] #/results/3806/comments/1/reaction`
dolichyl-phosphate beta-D-mannosyltransferase activity `gomodel:2.4.1.83-RXN`	has_input	GDP-alpha-D-mannose(2-) `CHEBI:57527`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:2.4.1.83-RXN RO:0002233 gomodel:CHEBI_57527_MANNPGUANYLTRANGDP-RXN. Source location `./YeastPathways_PWY3O-123.json#/facts/4; endpoint types: /individuals/42/type; /individuals/5/type`
dolichyl-phosphate beta-D-mannosyltransferase activity `gomodel:2.4.1.83-RXN`	has_output	GDP(3-) `CHEBI:58189`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:2.4.1.83-RXN RO:0002234 gomodel:CHEBI_58189_2.4.1.83-RXN. Source location `./YeastPathways_PWY3O-123.json#/facts/5; endpoint types: /individuals/42/type; /individuals/7/type`
alpha-D-mannose 1-phosphate + GTP + H(+) => GDP-alpha-D-mannose + diphosphate `RHEA:15230`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:MANNPGUANYLTRANGDP-RXN BFO:0000066 gomodel:reaction_MANNPGUANYLTRANGDP-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY3O-123.json#/facts/6; endpoint types: /individuals/10/type; /individuals/39/type` UniProtKB:P41940 Source assertion: UniProtKB:P41940 annotates alpha-D-mannose 1-phosphate plus GTP yielding GDP-alpha-D-mannose and diphosphate (RHEA:15229), correcting the imported GDP/orthophosphate reaction. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_catalytic_activity%2Ccc_function%2Ccc_caution%2Corganism_id [sha256:9600fe7f1e55a4f51554b244607a706b1604904dc71de8960b2f399bf75b0c7c] #/results/3806/comments/1/reaction`
mannose-6-phosphate isomerase activity `gomodel:MANNPISOM-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:MANNPISOM-RXN BFO:0000066 gomodel:reaction_MANNPISOM-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY3O-123.json#/facts/7; endpoint types: /individuals/11/type; /individuals/40/type`
alpha-D-mannose 1-phosphate + GTP + H(+) => GDP-alpha-D-mannose + diphosphate `RHEA:15230`	has_input	hydron `CHEBI:15378`	UniProtKB:P41940 Source assertion: UniProtKB:P41940 annotates alpha-D-mannose 1-phosphate plus GTP yielding GDP-alpha-D-mannose and diphosphate (RHEA:15229), correcting the imported GDP/orthophosphate reaction. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_catalytic_activity%2Ccc_function%2Ccc_caution%2Corganism_id [sha256:9600fe7f1e55a4f51554b244607a706b1604904dc71de8960b2f399bf75b0c7c] #/results/3806/comments/1/reaction`
mannose-6-phosphate isomerase activity `gomodel:MANNPISOM-RXN`	provides_input_for	phosphomannomutase activity `gomodel:PHOSMANMUT-RXN`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:MANNPISOM-RXN RO:0002413 gomodel:PHOSMANMUT-RXN. Source location `./YeastPathways_PWY3O-123.json#/facts/9; endpoint types: /individuals/11/type; /individuals/12/type`
mannose-6-phosphate isomerase activity `gomodel:MANNPISOM-RXN`	has_input	beta-D-fructofuranose 6-phosphate(2-) `CHEBI:57634`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:MANNPISOM-RXN RO:0002233 gomodel:CHEBI_57634_MANNPISOM-RXN. Source location `./YeastPathways_PWY3O-123.json#/facts/10; endpoint types: /individuals/11/type; /individuals/6/type`
alpha-D-mannose 1-phosphate + GTP + H(+) => GDP-alpha-D-mannose + diphosphate `RHEA:15230`	has_input	alpha-D-mannose 1-phosphate(2-) `CHEBI:58409`	UniProtKB:P41940 Source assertion: UniProtKB:P41940 annotates alpha-D-mannose 1-phosphate plus GTP yielding GDP-alpha-D-mannose and diphosphate (RHEA:15229), correcting the imported GDP/orthophosphate reaction. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_catalytic_activity%2Ccc_function%2Ccc_caution%2Corganism_id [sha256:9600fe7f1e55a4f51554b244607a706b1604904dc71de8960b2f399bf75b0c7c] #/results/3806/comments/1/reaction`
dolichyl-phosphate beta-D-mannosyltransferase activity `gomodel:2.4.1.83-RXN`	has_input	dolichyl phosphate `CHEBI:16214`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:2.4.1.83-RXN RO:0002233 gomodel:CHEBI_16214_2.4.1.83-RXN. Source location `./YeastPathways_PWY3O-123.json#/facts/12; endpoint types: /individuals/42/type; /individuals/2/type`
dolichyl-phosphate beta-D-mannosyltransferase activity `gomodel:2.4.1.83-RXN`	has_output	dolichyl D-mannosyl phosphate `CHEBI:15809`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:2.4.1.83-RXN RO:0002234 gomodel:CHEBI_15809_2.4.1.83-RXN. Source location `./YeastPathways_PWY3O-123.json#/facts/13; endpoint types: /individuals/42/type; /individuals/1/type`
alpha-D-mannose 1-phosphate + GTP + H(+) => GDP-alpha-D-mannose + diphosphate `RHEA:15230`	has_output	diphosphate(3-) `CHEBI:33019`	UniProtKB:P41940 Source assertion: UniProtKB:P41940 annotates alpha-D-mannose 1-phosphate plus GTP yielding GDP-alpha-D-mannose and diphosphate (RHEA:15229), correcting the imported GDP/orthophosphate reaction. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_catalytic_activity%2Ccc_function%2Ccc_caution%2Corganism_id [sha256:9600fe7f1e55a4f51554b244607a706b1604904dc71de8960b2f399bf75b0c7c] #/results/3806/comments/1/reaction`
phosphomannomutase activity `gomodel:PHOSMANMUT-RXN`	provides_input_for	alpha-D-mannose 1-phosphate + GTP + H(+) => GDP-alpha-D-mannose + diphosphate `RHEA:15230`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:PHOSMANMUT-RXN RO:0002413 gomodel:MANNPGUANYLTRANGDP-RXN. Source location `./YeastPathways_PWY3O-123.json#/facts/15; endpoint types: /individuals/12/type; /individuals/10/type` UniProtKB:P41940 Source assertion: UniProtKB:P41940 annotates alpha-D-mannose 1-phosphate plus GTP yielding GDP-alpha-D-mannose and diphosphate (RHEA:15229), correcting the imported GDP/orthophosphate reaction. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_catalytic_activity%2Ccc_function%2Ccc_caution%2Corganism_id [sha256:9600fe7f1e55a4f51554b244607a706b1604904dc71de8960b2f399bf75b0c7c] #/results/3806/comments/1/reaction`
mannose-6-phosphate isomerase activity `gomodel:MANNPISOM-RXN`	part_of	mannose metabolic process `GO:0006013`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:MANNPISOM-RXN BFO:0000050 gomodel:YeastPathways_PWY3O-123/YeastPathways_PWY3O-123. Source location `./YeastPathways_PWY3O-123.json#/facts/16; endpoint types: /individuals/11/type; /individuals/43/type`
mannose-6-phosphate isomerase activity `gomodel:MANNPISOM-RXN`	has_output	D-mannopyranose 6-phosphate `CHEBI:48066`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:MANNPISOM-RXN RO:0002234 gomodel:CHEBI_48066_MANNPISOM-RXN. Source location `./YeastPathways_PWY3O-123.json#/facts/17; endpoint types: /individuals/11/type; /individuals/4/type`
alpha-D-mannose 1-phosphate + GTP + H(+) => GDP-alpha-D-mannose + diphosphate `RHEA:15230`	has_input	GTP(4-) `CHEBI:37565`	UniProtKB:P41940 Source assertion: UniProtKB:P41940 annotates alpha-D-mannose 1-phosphate plus GTP yielding GDP-alpha-D-mannose and diphosphate (RHEA:15229), correcting the imported GDP/orthophosphate reaction. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_catalytic_activity%2Ccc_function%2Ccc_caution%2Corganism_id [sha256:9600fe7f1e55a4f51554b244607a706b1604904dc71de8960b2f399bf75b0c7c] #/results/3806/comments/1/reaction`
phosphomannomutase activity `gomodel:PHOSMANMUT-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:PHOSMANMUT-RXN BFO:0000066 gomodel:reaction_PHOSMANMUT-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY3O-123.json#/facts/20; endpoint types: /individuals/12/type; /individuals/41/type`
phosphomannomutase activity `gomodel:PHOSMANMUT-RXN`	has_output	alpha-D-mannose 1-phosphate(2-) `CHEBI:58409`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:PHOSMANMUT-RXN RO:0002234 gomodel:CHEBI_58409_PHOSMANMUT-RXN. Source location `./YeastPathways_PWY3O-123.json#/facts/21; endpoint types: /individuals/12/type; /individuals/9/type`
DPM1 Scer `SGD:S000006387`	enables	dolichyl-phosphate beta-D-mannosyltransferase activity `gomodel:2.4.1.83-RXN`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:2.4.1.83-RXN RO:0002333 gomodel:YPR183W-MONOMER_2.4.1.83-RXN_controller. Source location `./YeastPathways_PWY3O-123.json#/facts/22; endpoint types: /individuals/42/type; /individuals/16/type`
phosphomannomutase activity `gomodel:PHOSMANMUT-RXN`	has_input	D-mannopyranose 6-phosphate `CHEBI:48066`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:PHOSMANMUT-RXN RO:0002233 gomodel:CHEBI_48066_MANNPISOM-RXN. Source location `./YeastPathways_PWY3O-123.json#/facts/23; endpoint types: /individuals/12/type; /individuals/4/type`
SEC53 Scer `SGD:S000001849`	enables	phosphomannomutase activity `gomodel:PHOSMANMUT-RXN`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:PHOSMANMUT-RXN RO:0002333 gomodel:YFL045C-MONOMER_PHOSMANMUT-RXN_controller. Source location `./YeastPathways_PWY3O-123.json#/facts/24; endpoint types: /individuals/12/type; /individuals/15/type`
PMI40 Scer `SGD:S000000805`	enables	mannose-6-phosphate isomerase activity `gomodel:MANNPISOM-RXN`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:MANNPISOM-RXN RO:0002333 gomodel:YER003C-MONOMER_MANNPISOM-RXN_controller. Source location `./YeastPathways_PWY3O-123.json#/facts/25; endpoint types: /individuals/11/type; /individuals/14/type`
phosphomannomutase activity `gomodel:PHOSMANMUT-RXN`	part_of	mannose metabolic process `GO:0006013`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:PHOSMANMUT-RXN BFO:0000050 gomodel:YeastPathways_PWY3O-123/YeastPathways_PWY3O-123. Source location `./YeastPathways_PWY3O-123.json#/facts/26; endpoint types: /individuals/12/type; /individuals/43/type`
alpha-D-mannose 1-phosphate + GTP + H(+) => GDP-alpha-D-mannose + diphosphate `RHEA:15230`	part_of	mannose metabolic process `GO:0006013`	gomodel:YeastPathways_PWY3O-123 Source assertion: The model asserts gomodel:MANNPGUANYLTRANGDP-RXN BFO:0000050 gomodel:YeastPathways_PWY3O-123/YeastPathways_PWY3O-123. Source location `./YeastPathways_PWY3O-123.json#/facts/27; endpoint types: /individuals/10/type; /individuals/43/type` UniProtKB:P41940 Source assertion: UniProtKB:P41940 annotates alpha-D-mannose 1-phosphate plus GTP yielding GDP-alpha-D-mannose and diphosphate (RHEA:15229), correcting the imported GDP/orthophosphate reaction. Source location `https://rest.uniprot.org/uniprotkb/stream?query=taxonomy_id%3A559292+AND+reviewed%3Atrue&format=json&fields=accession%2Cprotein_name%2Cxref_sgd%2Ccc_catalytic_activity%2Ccc_function%2Ccc_caution%2Corganism_id [sha256:9600fe7f1e55a4f51554b244607a706b1604904dc71de8960b2f399bf75b0c7c] #/results/3806/comments/1/reaction`
PSA1 Scer `SGD:S000002213`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:9195935)	cytoplasm `GO:0005737`	UniProtKB:P41940 Source assertion: UniProtKB:P41940 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/3806/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P41940 Source assertion: UniProtKB:P41940 has the exact SGD cross-reference SGD:S000002213. 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/3806/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
DPM1 Scer `SGD:S000006387`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:14562095); ECO:0000269 (PubMed:15657391) Topology: Single-pass type IV membrane protein. Orientation: Cytoplasmic side.	endoplasmic reticulum membrane `GO:0005789`	UniProtKB:P14020 Source assertion: UniProtKB:P14020 annotates location Endoplasmic reticulum membrane (SL-0097). 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/376/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P14020 Source assertion: UniProtKB:P14020 has the exact SGD cross-reference SGD:S000006387. 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/376/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
SEC53 Scer `SGD:S000001849`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:3905826)	cytoplasm `GO:0005737`	UniProtKB:P07283 Source assertion: UniProtKB:P07283 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/187/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P07283 Source assertion: UniProtKB:P07283 has the exact SGD cross-reference SGD:S000001849. 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/187/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
PMI40 Scer `SGD:S000000805`	located_in Physical protein location from reviewed UniProt. evidence code not specified by source	cytoplasm `GO:0005737`	UniProtKB:P29952 Source assertion: UniProtKB:P29952 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/822/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P29952 Source assertion: UniProtKB:P29952 has the exact SGD cross-reference SGD:S000000805. 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/822/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
DPM1 Scer `SGD:S000006387`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000250 (UniProtKB:Q8U4M3) Binds 1 divalent metal cation. UniProt note evidence: ECO:0000250 (UniProtKB:Q8U4M3)	magnesium(2+) `CHEBI:18420`	UniProtKB:P14020 Source assertion: UniProtKB:P14020 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/376/comments/0/cofactors/0; /results/376/comments/0/note` UniProtKB:P14020 Source assertion: UniProtKB:P14020 has the exact SGD cross-reference SGD:S000006387. 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/376/uniProtKBCrossReferences/0`
DPM1 Scer `SGD:S000006387`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000250 (UniProtKB:Q8U4M3) Binds 1 divalent metal cation. UniProt note evidence: ECO:0000250 (UniProtKB:Q8U4M3)	manganese(2+) `CHEBI:29035`	UniProtKB:P14020 Source assertion: UniProtKB:P14020 annotates CHEBI:29035 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/376/comments/0/cofactors/1; /results/376/comments/0/note` UniProtKB:P14020 Source assertion: UniProtKB:P14020 has the exact SGD cross-reference SGD:S000006387. 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/376/uniProtKBCrossReferences/0`
DPM1 Scer `SGD:S000006387`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000250 (UniProtKB:Q8U4M3) Binds 1 divalent metal cation. UniProt note evidence: ECO:0000250 (UniProtKB:Q8U4M3)	calcium(2+) `CHEBI:29108`	UniProtKB:P14020 Source assertion: UniProtKB:P14020 annotates CHEBI:29108 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/376/comments/0/cofactors/2; /results/376/comments/0/note` UniProtKB:P14020 Source assertion: UniProtKB:P14020 has the exact SGD cross-reference SGD:S000006387. 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/376/uniProtKBCrossReferences/0`
PMI40 Scer `SGD:S000000805`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: not specified Binds 1 zinc ion per subunit.	zinc(2+) `CHEBI:29105`	UniProtKB:P29952 Source assertion: UniProtKB:P29952 annotates CHEBI:29105 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/822/comments/0/cofactors/0; /results/822/comments/0/note` UniProtKB:P29952 Source assertion: UniProtKB:P29952 has the exact SGD cross-reference SGD:S000000805. 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/822/uniProtKBCrossReferences/0`

References

gomodel:YeastPathways_PWY3O-123 SGD GO-CAM dolichyl phosphate D-mannose biosynthesis pathway PWY3O-123 (source version: Pinned Noctua JSON archive; model date 2026-08-03; member ./YeastPathways_PWY3O-123.json)
UniProtKB:P41940 Reviewed UniProtKB P41940 location annotations (source version: UniProt release 2026_03)
UniProtKB:P14020 Reviewed UniProtKB P14020 location annotations (source version: UniProt release 2026_03)
UniProtKB:P07283 Reviewed UniProtKB P07283 location annotations (source version: UniProt release 2026_03)
UniProtKB:P29952 Reviewed UniProtKB P29952 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.
2026-10-05T07:05:26Z Codex; edited; Correct PSA1 guanylyl donor and leaving group; pathway intermediate GDP-mannose retained.
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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2026-10-05T07:05:26Z Codex
- EDIT — Correct PSA1 guanylyl donor and leaving group; pathway intermediate GDP-mannose retained.
  User-authorized full causal graph curation. Correct PSA1 guanylyl donor and leaving group; pathway intermediate GDP-mannose retained. Independent UniProt release2026_03 annotations, Rhea139 and ChEBI255 were inspected; primary literature was checked for the taxon/function distinctions. Exact source pointers and superseded edge assertions are retained in reports/causal_graph_review/gocam-chemical-corrections.json. Native schema validation and focused biochemical regression tests were run. Shared final rendering and full gates are performed by the coordinating agent.
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