mannose degradation

gomodel:YeastPathways_PWY3O-1743

Mannose degradation in Saccharomyces cerevisiae S288C phosphorylates D-mannopyranose with ATP through GLK1 glucokinase or HXK1/HXK2 hexokinase activity to produce D-mannopyranose 6-phosphate, ADP, and hydron, and converts D-mannopyranose 6-phosphate through PMI40 mannose-6-phosphate isomerase activity to beta-D-fructofuranose 6-phosphate.

Pathway type

carbohydrate degradation

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

18 nodes · 31 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
ADP(3-) `CHEBI:456216`	small molecule
hydron `CHEBI:15378`	small molecule
ATP(4-) `CHEBI:30616`	small molecule
cytosol `GO:0005829`	cellular component
D-mannopyranose 6-phosphate `CHEBI:48066`	small molecule
beta-D-fructofuranose 6-phosphate(2-) `CHEBI:57634`	small molecule
D-mannopyranose `CHEBI:4208`	small molecule
GLK1 Scer `SGD:S000000545`	protein
mannose catabolic process `GO:0019309`	biological process
PMI40 Scer `SGD:S000000805`	protein
HXK1 Scer `SGD:S000001949`	protein
HXK2 Scer `SGD:S000003222`	protein
cytoplasm `GO:0005737`	cellular component
zinc(2+) `CHEBI:29105`	cofactor
D-mannopyranose 6-phosphate <=> β-D-fructofuranose 6-phosphate `gomodel:MANNPISOM-RXN`	molecular activity
D-mannose + ATP -> D-mannopyranose 6-phosphate + ADP + H⁺ `gomodel:RXN3O-9791`	molecular activity
hexokinase activity `gomodel:YeastPathways_PWY3O-1743/6a4c244800000448`	molecular activity
hexokinase activity `gomodel:YeastPathways_PWY3O-1743/6a4c244800000457`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
hexokinase activity `gomodel:YeastPathways_PWY3O-1743/6a4c244800000448`	has_output	ADP(3-) `CHEBI:456216`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:YeastPathways_PWY3O-1743/6a4c244800000448 RO:0002234 gomodel:YeastPathways_PWY3O-1743/6a4c244800000451. Source location `./YeastPathways_PWY3O-1743.json#/facts/0; endpoint types: /individuals/24/type; /individuals/27/type`
hexokinase activity `gomodel:YeastPathways_PWY3O-1743/6a4c244800000448`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:YeastPathways_PWY3O-1743/6a4c244800000448 RO:0002234 gomodel:YeastPathways_PWY3O-1743/6a4c244800000452. Source location `./YeastPathways_PWY3O-1743.json#/facts/1; endpoint types: /individuals/24/type; /individuals/28/type`
D-mannose + ATP -> D-mannopyranose 6-phosphate + ADP + H⁺ `gomodel:RXN3O-9791`	has_input	ATP(4-) `CHEBI:30616`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:RXN3O-9791 RO:0002233 gomodel:CHEBI_30616_RXN3O-9791. Source location `./YeastPathways_PWY3O-1743.json#/facts/2; endpoint types: /individuals/7/type; /individuals/1/type`
D-mannopyranose 6-phosphate <=> β-D-fructofuranose 6-phosphate `gomodel:MANNPISOM-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:MANNPISOM-RXN BFO:0000066 gomodel:reaction_MANNPISOM-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY3O-1743.json#/facts/3; endpoint types: /individuals/6/type; /individuals/21/type`
hexokinase activity `gomodel:YeastPathways_PWY3O-1743/6a4c244800000457`	has_output	D-mannopyranose 6-phosphate `CHEBI:48066`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:YeastPathways_PWY3O-1743/6a4c244800000457 RO:0002234 gomodel:CHEBI_48066_RXN3O-9791. Source location `./YeastPathways_PWY3O-1743.json#/facts/4; endpoint types: /individuals/31/type; /individuals/4/type`
D-mannopyranose 6-phosphate <=> β-D-fructofuranose 6-phosphate `gomodel:MANNPISOM-RXN`	has_output	beta-D-fructofuranose 6-phosphate(2-) `CHEBI:57634`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:MANNPISOM-RXN RO:0002234 gomodel:CHEBI_57634_MANNPISOM-RXN. Source location `./YeastPathways_PWY3O-1743.json#/facts/5; endpoint types: /individuals/6/type; /individuals/5/type`
D-mannose + ATP -> D-mannopyranose 6-phosphate + ADP + H⁺ `gomodel:RXN3O-9791`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:RXN3O-9791 RO:0002234 gomodel:CHEBI_15378_RXN3O-9791. Source location `./YeastPathways_PWY3O-1743.json#/facts/6; endpoint types: /individuals/7/type; /individuals/0/type`
hexokinase activity `gomodel:YeastPathways_PWY3O-1743/6a4c244800000448`	has_input	D-mannopyranose `CHEBI:4208`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:YeastPathways_PWY3O-1743/6a4c244800000448 RO:0002233 gomodel:YeastPathways_PWY3O-1743/6a4c244800000450. Source location `./YeastPathways_PWY3O-1743.json#/facts/7; endpoint types: /individuals/24/type; /individuals/26/type`
GLK1 Scer `SGD:S000000545`	enables	D-mannose + ATP -> D-mannopyranose 6-phosphate + ADP + H⁺ `gomodel:RXN3O-9791`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:RXN3O-9791 RO:0002333 gomodel:YCL040W-MONOMER_RXN3O-9791_controller. Source location `./YeastPathways_PWY3O-1743.json#/facts/8; endpoint types: /individuals/7/type; /individuals/8/type`
D-mannose + ATP -> D-mannopyranose 6-phosphate + ADP + H⁺ `gomodel:RXN3O-9791`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:RXN3O-9791 BFO:0000066 gomodel:reaction_RXN3O-9791_location_lociGO_0005829. Source location `./YeastPathways_PWY3O-1743.json#/facts/9; endpoint types: /individuals/7/type; /individuals/22/type`
hexokinase activity `gomodel:YeastPathways_PWY3O-1743/6a4c244800000457`	has_input	ATP(4-) `CHEBI:30616`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:YeastPathways_PWY3O-1743/6a4c244800000457 RO:0002233 gomodel:YeastPathways_PWY3O-1743/6a4c244800000459. Source location `./YeastPathways_PWY3O-1743.json#/facts/10; endpoint types: /individuals/31/type; /individuals/33/type`
D-mannopyranose 6-phosphate <=> β-D-fructofuranose 6-phosphate `gomodel:MANNPISOM-RXN`	part_of	mannose catabolic process `GO:0019309`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:MANNPISOM-RXN BFO:0000050 gomodel:YeastPathways_PWY3O-1743/YeastPathways_PWY3O-1743. Source location `./YeastPathways_PWY3O-1743.json#/facts/11; endpoint types: /individuals/6/type; /individuals/23/type`
hexokinase activity `gomodel:YeastPathways_PWY3O-1743/6a4c244800000448`	has_input	ATP(4-) `CHEBI:30616`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:YeastPathways_PWY3O-1743/6a4c244800000448 RO:0002233 gomodel:YeastPathways_PWY3O-1743/6a4c244800000449. Source location `./YeastPathways_PWY3O-1743.json#/facts/12; endpoint types: /individuals/24/type; /individuals/25/type`
D-mannose + ATP -> D-mannopyranose 6-phosphate + ADP + H⁺ `gomodel:RXN3O-9791`	has_input	D-mannopyranose `CHEBI:4208`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:RXN3O-9791 RO:0002233 gomodel:CHEBI_4208_RXN3O-9791. Source location `./YeastPathways_PWY3O-1743.json#/facts/13; endpoint types: /individuals/7/type; /individuals/2/type`
hexokinase activity `gomodel:YeastPathways_PWY3O-1743/6a4c244800000457`	has_input	D-mannopyranose `CHEBI:4208`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:YeastPathways_PWY3O-1743/6a4c244800000457 RO:0002233 gomodel:YeastPathways_PWY3O-1743/6a4c244800000458. Source location `./YeastPathways_PWY3O-1743.json#/facts/14; endpoint types: /individuals/31/type; /individuals/32/type`
hexokinase activity `gomodel:YeastPathways_PWY3O-1743/6a4c244800000457`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:YeastPathways_PWY3O-1743/6a4c244800000457 BFO:0000066 gomodel:YeastPathways_PWY3O-1743/6a4c244800000465. Source location `./YeastPathways_PWY3O-1743.json#/facts/15; endpoint types: /individuals/31/type; /individuals/37/type`
D-mannopyranose 6-phosphate <=> β-D-fructofuranose 6-phosphate `gomodel:MANNPISOM-RXN`	has_input	D-mannopyranose 6-phosphate `CHEBI:48066`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:MANNPISOM-RXN RO:0002233 gomodel:CHEBI_48066_RXN3O-9791. Source location `./YeastPathways_PWY3O-1743.json#/facts/16; endpoint types: /individuals/6/type; /individuals/4/type`
hexokinase activity `gomodel:YeastPathways_PWY3O-1743/6a4c244800000448`	has_output	D-mannopyranose 6-phosphate `CHEBI:48066`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:YeastPathways_PWY3O-1743/6a4c244800000448 RO:0002234 gomodel:CHEBI_48066_RXN3O-9791. Source location `./YeastPathways_PWY3O-1743.json#/facts/17; endpoint types: /individuals/24/type; /individuals/4/type`
hexokinase activity `gomodel:YeastPathways_PWY3O-1743/6a4c244800000457`	has_output	ADP(3-) `CHEBI:456216`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:YeastPathways_PWY3O-1743/6a4c244800000457 RO:0002234 gomodel:YeastPathways_PWY3O-1743/6a4c244800000461. Source location `./YeastPathways_PWY3O-1743.json#/facts/18; endpoint types: /individuals/31/type; /individuals/35/type`
hexokinase activity `gomodel:YeastPathways_PWY3O-1743/6a4c244800000457`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:YeastPathways_PWY3O-1743/6a4c244800000457 RO:0002234 gomodel:YeastPathways_PWY3O-1743/6a4c244800000460. Source location `./YeastPathways_PWY3O-1743.json#/facts/19; endpoint types: /individuals/31/type; /individuals/34/type`
D-mannose + ATP -> D-mannopyranose 6-phosphate + ADP + H⁺ `gomodel:RXN3O-9791`	part_of	mannose catabolic process `GO:0019309`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:RXN3O-9791 BFO:0000050 gomodel:YeastPathways_PWY3O-1743/YeastPathways_PWY3O-1743. Source location `./YeastPathways_PWY3O-1743.json#/facts/20; endpoint types: /individuals/7/type; /individuals/23/type`
PMI40 Scer `SGD:S000000805`	enables	D-mannopyranose 6-phosphate <=> β-D-fructofuranose 6-phosphate `gomodel:MANNPISOM-RXN`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:MANNPISOM-RXN RO:0002333 gomodel:YER003C-MONOMER_MANNPISOM-RXN_controller. Source location `./YeastPathways_PWY3O-1743.json#/facts/21; endpoint types: /individuals/6/type; /individuals/9/type`
HXK1 Scer `SGD:S000001949`	enables	hexokinase activity `gomodel:YeastPathways_PWY3O-1743/6a4c244800000448`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:YeastPathways_PWY3O-1743/6a4c244800000448 RO:0002333 gomodel:YeastPathways_PWY3O-1743/6a4c244800000453. Source location `./YeastPathways_PWY3O-1743.json#/facts/22; endpoint types: /individuals/24/type; /individuals/29/type`
hexokinase activity `gomodel:YeastPathways_PWY3O-1743/6a4c244800000457`	part_of	mannose catabolic process `GO:0019309`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:YeastPathways_PWY3O-1743/6a4c244800000457 BFO:0000050 gomodel:YeastPathways_PWY3O-1743/YeastPathways_PWY3O-1743. Source location `./YeastPathways_PWY3O-1743.json#/facts/23; endpoint types: /individuals/31/type; /individuals/23/type`
D-mannose + ATP -> D-mannopyranose 6-phosphate + ADP + H⁺ `gomodel:RXN3O-9791`	has_output	ADP(3-) `CHEBI:456216`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:RXN3O-9791 RO:0002234 gomodel:CHEBI_456216_RXN3O-9791. Source location `./YeastPathways_PWY3O-1743.json#/facts/24; endpoint types: /individuals/7/type; /individuals/3/type`
D-mannose + ATP -> D-mannopyranose 6-phosphate + ADP + H⁺ `gomodel:RXN3O-9791`	has_output	D-mannopyranose 6-phosphate `CHEBI:48066`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:RXN3O-9791 RO:0002234 gomodel:CHEBI_48066_RXN3O-9791. Source location `./YeastPathways_PWY3O-1743.json#/facts/25; endpoint types: /individuals/7/type; /individuals/4/type`
HXK2 Scer `SGD:S000003222`	enables	hexokinase activity `gomodel:YeastPathways_PWY3O-1743/6a4c244800000457`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:YeastPathways_PWY3O-1743/6a4c244800000457 RO:0002333 gomodel:YeastPathways_PWY3O-1743/6a4c244800000462. Source location `./YeastPathways_PWY3O-1743.json#/facts/26; endpoint types: /individuals/31/type; /individuals/36/type`
hexokinase activity `gomodel:YeastPathways_PWY3O-1743/6a4c244800000448`	part_of	mannose catabolic process `GO:0019309`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:YeastPathways_PWY3O-1743/6a4c244800000448 BFO:0000050 gomodel:YeastPathways_PWY3O-1743/YeastPathways_PWY3O-1743. Source location `./YeastPathways_PWY3O-1743.json#/facts/27; endpoint types: /individuals/24/type; /individuals/23/type`
hexokinase activity `gomodel:YeastPathways_PWY3O-1743/6a4c244800000448`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY3O-1743 Source assertion: The model asserts gomodel:YeastPathways_PWY3O-1743/6a4c244800000448 BFO:0000066 gomodel:YeastPathways_PWY3O-1743/6a4c244800000456. Source location `./YeastPathways_PWY3O-1743.json#/facts/28; endpoint types: /individuals/24/type; /individuals/30/type`
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`
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-1743 SGD GO-CAM mannose degradation - imported from: Saccharomyces Genome Database (source version: Pinned Noctua JSON archive; model date 2026-07-07; member ./YeastPathways_PWY3O-1743.json)
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.
2026-10-05T06:43:56Z 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 1 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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