xylose metabolism

gomodel:YeastPathways_PWY3O-8

Xylose metabolism in Saccharomyces cerevisiae S288C uses GRE3 aldose reductase to reduce D-xylopyranose to xylitol with NADPH, and XYL2 xylitol dehydrogenase to oxidize xylitol to D-xylulose with NAD+ in the SGD GO-CAM xylose metabolism pathway.

Pathway type

carbohydrate degradation

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

17 nodes · 19 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
NADPH(4-) `CHEBI:57783`	small molecule
XYL2 Scer `SGD:S000004060`	protein
D-xylopyranose `CHEBI:53455`	small molecule
cytosol `GO:0005829`	cellular component
D-xylose metabolic process `GO:0042732`	biological process
GRE3 Scer `SGD:S000001146`	protein
xylitol `CHEBI:17151`	small molecule
hydron `CHEBI:15378`	small molecule
NADH(2-) `CHEBI:57945`	small molecule
D-xylulose `CHEBI:17140`	small molecule
NAD(1-) `CHEBI:57540`	small molecule
NADP(3-) `CHEBI:58349`	small molecule
cytoplasm `GO:0005737`	cellular component
nucleus `GO:0005634`	cellular component
zinc(2+) `CHEBI:29105`	cofactor
xylitol + NAD⁺ -> D-xylulose + NADH + H⁺ `gomodel:D-XYLULOSE-REDUCTASE-RXN`	molecular activity
xylitol + NADP⁺ <=> D-xylopyranose + NADPH + H⁺ `gomodel:RXN-8773`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
xylitol + NADP⁺ <=> D-xylopyranose + NADPH + H⁺ `gomodel:RXN-8773`	has_input	NADPH(4-) `CHEBI:57783`	gomodel:YeastPathways_PWY3O-8 Source assertion: The model asserts gomodel:RXN-8773 RO:0002233 gomodel:CHEBI_57783_RXN-8773. Source location `./YeastPathways_PWY3O-8.json#/facts/0; endpoint types: /individuals/10/type; /individuals/6/type`
XYL2 Scer `SGD:S000004060`	enables	xylitol + NAD⁺ -> D-xylulose + NADH + H⁺ `gomodel:D-XYLULOSE-REDUCTASE-RXN`	gomodel:YeastPathways_PWY3O-8 Source assertion: The model asserts gomodel:D-XYLULOSE-REDUCTASE-RXN RO:0002333 gomodel:YLR070C-MONOMER_D-XYLULOSE-REDUCTASE-RXN_controller. Source location `./YeastPathways_PWY3O-8.json#/facts/1; endpoint types: /individuals/9/type; /individuals/12/type`
xylitol + NADP⁺ <=> D-xylopyranose + NADPH + H⁺ `gomodel:RXN-8773`	has_input	D-xylopyranose `CHEBI:53455`	gomodel:YeastPathways_PWY3O-8 Source assertion: The model asserts gomodel:RXN-8773 RO:0002233 gomodel:CHEBI_53455_RXN-8773. Source location `./YeastPathways_PWY3O-8.json#/facts/2; endpoint types: /individuals/10/type; /individuals/4/type`
xylitol + NAD⁺ -> D-xylulose + NADH + H⁺ `gomodel:D-XYLULOSE-REDUCTASE-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY3O-8 Source assertion: The model asserts gomodel:D-XYLULOSE-REDUCTASE-RXN BFO:0000066 gomodel:reaction_D-XYLULOSE-REDUCTASE-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY3O-8.json#/facts/3; endpoint types: /individuals/9/type; /individuals/27/type`
xylitol + NAD⁺ -> D-xylulose + NADH + H⁺ `gomodel:D-XYLULOSE-REDUCTASE-RXN`	part_of	D-xylose metabolic process `GO:0042732`	gomodel:YeastPathways_PWY3O-8 Source assertion: The model asserts gomodel:D-XYLULOSE-REDUCTASE-RXN BFO:0000050 gomodel:YeastPathways_PWY3O-8/YeastPathways_PWY3O-8. Source location `./YeastPathways_PWY3O-8.json#/facts/4; endpoint types: /individuals/9/type; /individuals/29/type`
GRE3 Scer `SGD:S000001146`	enables	xylitol + NADP⁺ <=> D-xylopyranose + NADPH + H⁺ `gomodel:RXN-8773`	gomodel:YeastPathways_PWY3O-8 Source assertion: The model asserts gomodel:RXN-8773 RO:0002333 gomodel:YHR104W-MONOMER_RXN-8773_controller. Source location `./YeastPathways_PWY3O-8.json#/facts/5; endpoint types: /individuals/10/type; /individuals/11/type`
xylitol + NAD⁺ -> D-xylulose + NADH + H⁺ `gomodel:D-XYLULOSE-REDUCTASE-RXN`	has_input	xylitol `CHEBI:17151`	gomodel:YeastPathways_PWY3O-8 Source assertion: The model asserts gomodel:D-XYLULOSE-REDUCTASE-RXN RO:0002233 gomodel:CHEBI_17151_RXN-8773. Source location `./YeastPathways_PWY3O-8.json#/facts/6; endpoint types: /individuals/9/type; /individuals/3/type`
xylitol + NADP⁺ <=> D-xylopyranose + NADPH + H⁺ `gomodel:RXN-8773`	has_input	hydron `CHEBI:15378`	gomodel:YeastPathways_PWY3O-8 Source assertion: The model asserts gomodel:RXN-8773 RO:0002233 gomodel:CHEBI_15378_RXN-8773. Source location `./YeastPathways_PWY3O-8.json#/facts/7; endpoint types: /individuals/10/type; /individuals/1/type`
xylitol + NAD⁺ -> D-xylulose + NADH + H⁺ `gomodel:D-XYLULOSE-REDUCTASE-RXN`	has_output	NADH(2-) `CHEBI:57945`	gomodel:YeastPathways_PWY3O-8 Source assertion: The model asserts gomodel:D-XYLULOSE-REDUCTASE-RXN RO:0002234 gomodel:CHEBI_57945_D-XYLULOSE-REDUCTASE-RXN. Source location `./YeastPathways_PWY3O-8.json#/facts/8; endpoint types: /individuals/9/type; /individuals/7/type`
xylitol + NAD⁺ -> D-xylulose + NADH + H⁺ `gomodel:D-XYLULOSE-REDUCTASE-RXN`	has_output	D-xylulose `CHEBI:17140`	gomodel:YeastPathways_PWY3O-8 Source assertion: The model asserts gomodel:D-XYLULOSE-REDUCTASE-RXN RO:0002234 gomodel:CHEBI_17140_D-XYLULOSE-REDUCTASE-RXN. Source location `./YeastPathways_PWY3O-8.json#/facts/9; endpoint types: /individuals/9/type; /individuals/2/type`
xylitol + NAD⁺ -> D-xylulose + NADH + H⁺ `gomodel:D-XYLULOSE-REDUCTASE-RXN`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_PWY3O-8 Source assertion: The model asserts gomodel:D-XYLULOSE-REDUCTASE-RXN RO:0002234 gomodel:CHEBI_15378_D-XYLULOSE-REDUCTASE-RXN. Source location `./YeastPathways_PWY3O-8.json#/facts/10; endpoint types: /individuals/9/type; /individuals/0/type`
xylitol + NADP⁺ <=> D-xylopyranose + NADPH + H⁺ `gomodel:RXN-8773`	part_of	D-xylose metabolic process `GO:0042732`	gomodel:YeastPathways_PWY3O-8 Source assertion: The model asserts gomodel:RXN-8773 BFO:0000050 gomodel:YeastPathways_PWY3O-8/YeastPathways_PWY3O-8. Source location `./YeastPathways_PWY3O-8.json#/facts/11; endpoint types: /individuals/10/type; /individuals/29/type`
xylitol + NADP⁺ <=> D-xylopyranose + NADPH + H⁺ `gomodel:RXN-8773`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY3O-8 Source assertion: The model asserts gomodel:RXN-8773 BFO:0000066 gomodel:reaction_RXN-8773_location_lociGO_0005829. Source location `./YeastPathways_PWY3O-8.json#/facts/12; endpoint types: /individuals/10/type; /individuals/28/type`
xylitol + NADP⁺ <=> D-xylopyranose + NADPH + H⁺ `gomodel:RXN-8773`	has_output	xylitol `CHEBI:17151`	gomodel:YeastPathways_PWY3O-8 Source assertion: The model asserts gomodel:RXN-8773 RO:0002234 gomodel:CHEBI_17151_RXN-8773. Source location `./YeastPathways_PWY3O-8.json#/facts/13; endpoint types: /individuals/10/type; /individuals/3/type`
xylitol + NAD⁺ -> D-xylulose + NADH + H⁺ `gomodel:D-XYLULOSE-REDUCTASE-RXN`	has_input	NAD(1-) `CHEBI:57540`	gomodel:YeastPathways_PWY3O-8 Source assertion: The model asserts gomodel:D-XYLULOSE-REDUCTASE-RXN RO:0002233 gomodel:CHEBI_57540_D-XYLULOSE-REDUCTASE-RXN. Source location `./YeastPathways_PWY3O-8.json#/facts/14; endpoint types: /individuals/9/type; /individuals/5/type`
xylitol + NADP⁺ <=> D-xylopyranose + NADPH + H⁺ `gomodel:RXN-8773`	has_output	NADP(3-) `CHEBI:58349`	gomodel:YeastPathways_PWY3O-8 Source assertion: The model asserts gomodel:RXN-8773 RO:0002234 gomodel:CHEBI_58349_RXN-8773. Source location `./YeastPathways_PWY3O-8.json#/facts/15; endpoint types: /individuals/10/type; /individuals/8/type`
GRE3 Scer `SGD:S000001146`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:14562095)	cytoplasm `GO:0005737`	UniProtKB:P38715 Source assertion: UniProtKB:P38715 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/1421/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P38715 Source assertion: UniProtKB:P38715 has the exact SGD cross-reference SGD:S000001146. 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/1421/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
GRE3 Scer `SGD:S000001146`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:14562095)	nucleus `GO:0005634`	UniProtKB:P38715 Source assertion: UniProtKB:P38715 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/1421/comments/1/subcellularLocations/1; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P38715 Source assertion: UniProtKB:P38715 has the exact SGD cross-reference SGD:S000001146. 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/1421/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
XYL2 Scer `SGD:S000004060`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000250 Binds 1 zinc ion per subunit. UniProt note evidence: ECO:0000250	zinc(2+) `CHEBI:29105`	UniProtKB:Q07993 Source assertion: UniProtKB:Q07993 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/5004/comments/0/cofactors/0; /results/5004/comments/0/note` UniProtKB:Q07993 Source assertion: UniProtKB:Q07993 has the exact SGD cross-reference SGD:S000004060. 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/5004/uniProtKBCrossReferences/0`

References

gomodel:YeastPathways_PWY3O-8 SGD GO-CAM xylose metabolism - imported from: Saccharomyces Genome Database (source version: Pinned Noctua JSON archive; model date 2024-07-15; member ./YeastPathways_PWY3O-8.json)
UniProtKB:P38715 Reviewed UniProtKB P38715 location annotations (source version: UniProt release 2026_03)
UniProtKB:Q07993 UniProtKB Q07993 cofactor annotations (source version: 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 2 activity location assignments and 2 mapped physical proteins against reviewed S288C UniProt release2026_03 location/function/caution batch SHA256 95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d. Added 2 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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