allantoin degradation to glyoxylate I

gomodel:YeastPathways_PWY-5694

Allantoin degradation to glyoxylate I in Saccharomyces cerevisiae S288C hydrolyzes (S)-(+)-allantoin to allantoate, hydrolyzes allantoate to (-)-ureidoglycolate and urea, and cleaves (-)-ureidoglycolate to glyoxylate and urea.

Pathway type

purine degradation

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

16 nodes · 21 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
water `CHEBI:15377`	small molecule
(S)-(+)-allantoin `CHEBI:15678`	small molecule
allantoin catabolic process `GO:0000256`	biological process
DAL1 Scer `SGD:S000001466`	protein
hydron `CHEBI:15378`	small molecule
urea `CHEBI:16199`	small molecule
cytosol `GO:0005829`	cellular component
(-)-ureidoglycolate `CHEBI:57296`	small molecule
glyoxylate `CHEBI:36655`	small molecule
DAL2 Scer `SGD:S000001468`	protein
DAL3 Scer `SGD:S000001471`	protein
allantoate `CHEBI:17536`	small molecule
zinc(2+) `CHEBI:29105`	cofactor
allantoicase activity `gomodel:ALLANTOICASE-RXN`	molecular activity
allantoinase activity `gomodel:ALLANTOINASE-RXN`	molecular activity
ureidoglycolate lyase activity `gomodel:UREIDOGLYCOLATE-LYASE-RXN`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
allantoicase activity `gomodel:ALLANTOICASE-RXN`	has_input	water `CHEBI:15377`	gomodel:YeastPathways_PWY-5694 Source assertion: The model asserts gomodel:ALLANTOICASE-RXN RO:0002233 gomodel:CHEBI_15377_ALLANTOICASE-RXN. Source location `./YeastPathways_PWY-5694.json#/facts/0; endpoint types: /individuals/0/type; /individuals/2/type`
allantoinase activity `gomodel:ALLANTOINASE-RXN`	has_input	(S)-(+)-allantoin `CHEBI:15678`	gomodel:YeastPathways_PWY-5694 Source assertion: The model asserts gomodel:ALLANTOINASE-RXN RO:0002233 gomodel:CHEBI_15678_ALLANTOINASE-RXN. Source location `./YeastPathways_PWY-5694.json#/facts/1; endpoint types: /individuals/1/type; /individuals/5/type`
ureidoglycolate lyase activity `gomodel:UREIDOGLYCOLATE-LYASE-RXN`	part_of	allantoin catabolic process `GO:0000256`	gomodel:YeastPathways_PWY-5694 Source assertion: The model asserts gomodel:UREIDOGLYCOLATE-LYASE-RXN BFO:0000050 gomodel:YeastPathways_PWY-5694/YeastPathways_PWY-5694. Source location `./YeastPathways_PWY-5694.json#/facts/2; endpoint types: /individuals/11/type; /individuals/35/type`
DAL1 Scer `SGD:S000001466`	enables	allantoinase activity `gomodel:ALLANTOINASE-RXN`	gomodel:YeastPathways_PWY-5694 Source assertion: The model asserts gomodel:ALLANTOINASE-RXN RO:0002333 gomodel:YIR027C-MONOMER_ALLANTOINASE-RXN_controller. Source location `./YeastPathways_PWY-5694.json#/facts/3; endpoint types: /individuals/1/type; /individuals/12/type`
allantoinase activity `gomodel:ALLANTOINASE-RXN`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_PWY-5694 Source assertion: The model asserts gomodel:ALLANTOINASE-RXN RO:0002234 gomodel:CHEBI_15378_ALLANTOINASE-RXN. Source location `./YeastPathways_PWY-5694.json#/facts/4; endpoint types: /individuals/1/type; /individuals/4/type`
allantoicase activity `gomodel:ALLANTOICASE-RXN`	has_output	urea `CHEBI:16199`	gomodel:YeastPathways_PWY-5694 Source assertion: The model asserts gomodel:ALLANTOICASE-RXN RO:0002234 gomodel:CHEBI_16199_ALLANTOICASE-RXN. Source location `./YeastPathways_PWY-5694.json#/facts/5; endpoint types: /individuals/0/type; /individuals/6/type`
allantoinase activity `gomodel:ALLANTOINASE-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-5694 Source assertion: The model asserts gomodel:ALLANTOINASE-RXN BFO:0000066 gomodel:reaction_ALLANTOINASE-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-5694.json#/facts/6; endpoint types: /individuals/1/type; /individuals/33/type`
ureidoglycolate lyase activity `gomodel:UREIDOGLYCOLATE-LYASE-RXN`	has_input	(-)-ureidoglycolate `CHEBI:57296`	gomodel:YeastPathways_PWY-5694 Source assertion: The model asserts gomodel:UREIDOGLYCOLATE-LYASE-RXN RO:0002233 gomodel:CHEBI_57296_ALLANTOICASE-RXN. Source location `./YeastPathways_PWY-5694.json#/facts/7; endpoint types: /individuals/11/type; /individuals/10/type`
ureidoglycolate lyase activity `gomodel:UREIDOGLYCOLATE-LYASE-RXN`	has_output	glyoxylate `CHEBI:36655`	gomodel:YeastPathways_PWY-5694 Source assertion: The model asserts gomodel:UREIDOGLYCOLATE-LYASE-RXN RO:0002234 gomodel:CHEBI_36655_UREIDOGLYCOLATE-LYASE-RXN. Source location `./YeastPathways_PWY-5694.json#/facts/8; endpoint types: /individuals/11/type; /individuals/9/type`
allantoicase activity `gomodel:ALLANTOICASE-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-5694 Source assertion: The model asserts gomodel:ALLANTOICASE-RXN BFO:0000066 gomodel:reaction_ALLANTOICASE-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-5694.json#/facts/9; endpoint types: /individuals/0/type; /individuals/32/type`
DAL2 Scer `SGD:S000001468`	enables	allantoicase activity `gomodel:ALLANTOICASE-RXN`	gomodel:YeastPathways_PWY-5694 Source assertion: The model asserts gomodel:ALLANTOICASE-RXN RO:0002333 gomodel:YIR029W-MONOMER_ALLANTOICASE-RXN_controller. Source location `./YeastPathways_PWY-5694.json#/facts/10; endpoint types: /individuals/0/type; /individuals/13/type`
allantoicase activity `gomodel:ALLANTOICASE-RXN`	part_of	allantoin catabolic process `GO:0000256`	gomodel:YeastPathways_PWY-5694 Source assertion: The model asserts gomodel:ALLANTOICASE-RXN BFO:0000050 gomodel:YeastPathways_PWY-5694/YeastPathways_PWY-5694. Source location `./YeastPathways_PWY-5694.json#/facts/11; endpoint types: /individuals/0/type; /individuals/35/type`
DAL3 Scer `SGD:S000001471`	enables	ureidoglycolate lyase activity `gomodel:UREIDOGLYCOLATE-LYASE-RXN`	gomodel:YeastPathways_PWY-5694 Source assertion: The model asserts gomodel:UREIDOGLYCOLATE-LYASE-RXN RO:0002333 gomodel:YIR032C-MONOMER_UREIDOGLYCOLATE-LYASE-RXN_controller. Source location `./YeastPathways_PWY-5694.json#/facts/12; endpoint types: /individuals/11/type; /individuals/14/type`
ureidoglycolate lyase activity `gomodel:UREIDOGLYCOLATE-LYASE-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-5694 Source assertion: The model asserts gomodel:UREIDOGLYCOLATE-LYASE-RXN BFO:0000066 gomodel:reaction_UREIDOGLYCOLATE-LYASE-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-5694.json#/facts/13; endpoint types: /individuals/11/type; /individuals/34/type`
ureidoglycolate lyase activity `gomodel:UREIDOGLYCOLATE-LYASE-RXN`	has_output	urea `CHEBI:16199`	gomodel:YeastPathways_PWY-5694 Source assertion: The model asserts gomodel:UREIDOGLYCOLATE-LYASE-RXN RO:0002234 gomodel:CHEBI_16199_UREIDOGLYCOLATE-LYASE-RXN. Source location `./YeastPathways_PWY-5694.json#/facts/14; endpoint types: /individuals/11/type; /individuals/7/type`
allantoinase activity `gomodel:ALLANTOINASE-RXN`	has_input	water `CHEBI:15377`	gomodel:YeastPathways_PWY-5694 Source assertion: The model asserts gomodel:ALLANTOINASE-RXN RO:0002233 gomodel:CHEBI_15377_ALLANTOINASE-RXN. Source location `./YeastPathways_PWY-5694.json#/facts/15; endpoint types: /individuals/1/type; /individuals/3/type`
allantoinase activity `gomodel:ALLANTOINASE-RXN`	has_output	allantoate `CHEBI:17536`	gomodel:YeastPathways_PWY-5694 Source assertion: The model asserts gomodel:ALLANTOINASE-RXN RO:0002234 gomodel:CHEBI_17536_ALLANTOINASE-RXN. Source location `./YeastPathways_PWY-5694.json#/facts/16; endpoint types: /individuals/1/type; /individuals/8/type`
allantoicase activity `gomodel:ALLANTOICASE-RXN`	has_output	(-)-ureidoglycolate `CHEBI:57296`	gomodel:YeastPathways_PWY-5694 Source assertion: The model asserts gomodel:ALLANTOICASE-RXN RO:0002234 gomodel:CHEBI_57296_ALLANTOICASE-RXN. Source location `./YeastPathways_PWY-5694.json#/facts/17; endpoint types: /individuals/0/type; /individuals/10/type`
allantoicase activity `gomodel:ALLANTOICASE-RXN`	has_input	allantoate `CHEBI:17536`	gomodel:YeastPathways_PWY-5694 Source assertion: The model asserts gomodel:ALLANTOICASE-RXN RO:0002233 gomodel:CHEBI_17536_ALLANTOINASE-RXN. Source location `./YeastPathways_PWY-5694.json#/facts/18; endpoint types: /individuals/0/type; /individuals/8/type`
allantoinase activity `gomodel:ALLANTOINASE-RXN`	part_of	allantoin catabolic process `GO:0000256`	gomodel:YeastPathways_PWY-5694 Source assertion: The model asserts gomodel:ALLANTOINASE-RXN BFO:0000050 gomodel:YeastPathways_PWY-5694/YeastPathways_PWY-5694. Source location `./YeastPathways_PWY-5694.json#/facts/19; endpoint types: /individuals/1/type; /individuals/35/type`
DAL1 Scer `SGD:S000001466`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000250 Binds 2 Zn(2+) ions per subunit. UniProt note evidence: ECO:0000250	zinc(2+) `CHEBI:29105`	UniProtKB:P32375 Source assertion: UniProtKB:P32375 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/4531/comments/0/cofactors/0; /results/4531/comments/0/note` UniProtKB:P32375 Source assertion: UniProtKB:P32375 has the exact SGD cross-reference SGD:S000001466. 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/4531/uniProtKBCrossReferences/0`

References

gomodel:YeastPathways_PWY-5694 GO-CAM allantoin degradation to glyoxylate I model YeastPathways_PWY-5694 (source version: Pinned Noctua JSON archive; model date 2025-02-19; member ./YeastPathways_PWY-5694.json)
UniProtKB:P32375 UniProtKB P32375 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
- REVIEW — Audit causal activity compartments and preserve scoped protein location evidence
  Reviewed all 3 activity location assignments and 3 mapped physical proteins against reviewed S288C UniProt release2026_03 location/function/caution batch SHA256 95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d. Added 0 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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