urea degradation I

gomodel:YeastPathways_PWY-5703

Urea degradation I in Saccharomyces cerevisiae S288C uses Dur12p to carboxylate urea to urea-1-carboxylate and then hydrolyze urea-1-carboxylate to ammonium and carbon dioxide.

Pathway type

urea degradation

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

15 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
carbon dioxide `CHEBI:16526`	small molecule
water `CHEBI:15377`	small molecule
urea-1-carboxylate `CHEBI:15832`	small molecule
hydron `CHEBI:15378`	small molecule
ADP `CHEBI:16761`	small molecule
DUR12 Scer `SGD:S000000412`	protein
ATP `CHEBI:15422`	small molecule
cytosol `GO:0005829`	cellular component
urea catabolic process `GO:0043419`	biological process
urea `CHEBI:16199`	small molecule
phosphate `CHEBI:26020`	small molecule
ammonium `CHEBI:28938`	small molecule
biotinate `CHEBI:57586`	cofactor
allophanate hydrolase activity `gomodel:ALLOPHANATE-HYDROLASE-RXN`	molecular activity
urea carboxylase activity `gomodel:UREA-CARBOXYLASE-RXN`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
allophanate hydrolase activity `gomodel:ALLOPHANATE-HYDROLASE-RXN`	has_output	carbon dioxide `CHEBI:16526`	gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:ALLOPHANATE-HYDROLASE-RXN RO:0002234 gomodel:YeastPathways_PWY-5703/654d809000001036. Source location `./YeastPathways_PWY-5703.json#/facts/0; endpoint types: /individuals/0/type; /individuals/45/type` gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:ALLOPHANATE-HYDROLASE-RXN RO:0002234 gomodel:CHEBI_16526_ALLOPHANATE-HYDROLASE-RXN. Source location `./YeastPathways_PWY-5703.json#/facts/10; endpoint types: /individuals/0/type; /individuals/7/type`
urea carboxylase activity `gomodel:UREA-CARBOXYLASE-RXN`	provides_input_for	allophanate hydrolase activity `gomodel:ALLOPHANATE-HYDROLASE-RXN`	gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:UREA-CARBOXYLASE-RXN RO:0002413 gomodel:ALLOPHANATE-HYDROLASE-RXN. Source location `./YeastPathways_PWY-5703.json#/facts/1; endpoint types: /individuals/13/type; /individuals/0/type`
allophanate hydrolase activity `gomodel:ALLOPHANATE-HYDROLASE-RXN`	has_input	water `CHEBI:15377`	gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:ALLOPHANATE-HYDROLASE-RXN RO:0002233 gomodel:CHEBI_15377_ALLOPHANATE-HYDROLASE-RXN. Source location `./YeastPathways_PWY-5703.json#/facts/2; endpoint types: /individuals/0/type; /individuals/1/type`
allophanate hydrolase activity `gomodel:ALLOPHANATE-HYDROLASE-RXN`	has_input	urea-1-carboxylate `CHEBI:15832`	gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:ALLOPHANATE-HYDROLASE-RXN RO:0002233 gomodel:CHEBI_15832_UREA-CARBOXYLASE-RXN. Source location `./YeastPathways_PWY-5703.json#/facts/3; endpoint types: /individuals/0/type; /individuals/5/type`
allophanate hydrolase activity `gomodel:ALLOPHANATE-HYDROLASE-RXN`	has_input	hydron `CHEBI:15378`	gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:ALLOPHANATE-HYDROLASE-RXN RO:0002233 gomodel:CHEBI_15378_ALLOPHANATE-HYDROLASE-RXN. Source location `./YeastPathways_PWY-5703.json#/facts/4; endpoint types: /individuals/0/type; /individuals/3/type` gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:ALLOPHANATE-HYDROLASE-RXN RO:0002233 gomodel:YeastPathways_PWY-5703/654d809000001030. Source location `./YeastPathways_PWY-5703.json#/facts/20; endpoint types: /individuals/0/type; /individuals/39/type` gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:ALLOPHANATE-HYDROLASE-RXN RO:0002233 gomodel:YeastPathways_PWY-5703/654d809000001032. Source location `./YeastPathways_PWY-5703.json#/facts/23; endpoint types: /individuals/0/type; /individuals/41/type`
urea carboxylase activity `gomodel:UREA-CARBOXYLASE-RXN`	has_output	ADP `CHEBI:16761`	gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:UREA-CARBOXYLASE-RXN RO:0002234 gomodel:CHEBI_456216_UREA-CARBOXYLASE-RXN. Source location `./YeastPathways_PWY-5703.json#/facts/5; endpoint types: /individuals/13/type; /individuals/12/type`
DUR12 Scer `SGD:S000000412`	enables	urea carboxylase activity `gomodel:UREA-CARBOXYLASE-RXN`	gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:UREA-CARBOXYLASE-RXN RO:0002333 gomodel:YBR208C-MONOMER_UREA-CARBOXYLASE-RXN_controller. Source location `./YeastPathways_PWY-5703.json#/facts/6; endpoint types: /individuals/13/type; /individuals/15/type`
urea carboxylase activity `gomodel:UREA-CARBOXYLASE-RXN`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:UREA-CARBOXYLASE-RXN RO:0002234 gomodel:YeastPathways_PWY-5703/654d809000001028. Source location `./YeastPathways_PWY-5703.json#/facts/7; endpoint types: /individuals/13/type; /individuals/37/type` gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:UREA-CARBOXYLASE-RXN RO:0002234 gomodel:CHEBI_15378_UREA-CARBOXYLASE-RXN. Source location `./YeastPathways_PWY-5703.json#/facts/8; endpoint types: /individuals/13/type; /individuals/4/type`
DUR12 Scer `SGD:S000000412`	enables	allophanate hydrolase activity `gomodel:ALLOPHANATE-HYDROLASE-RXN`	gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:ALLOPHANATE-HYDROLASE-RXN RO:0002333 gomodel:YBR208C-MONOMER_ALLOPHANATE-HYDROLASE-RXN_controller. Source location `./YeastPathways_PWY-5703.json#/facts/9; endpoint types: /individuals/0/type; /individuals/14/type`
urea carboxylase activity `gomodel:UREA-CARBOXYLASE-RXN`	has_input	ATP `CHEBI:15422`	gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:UREA-CARBOXYLASE-RXN RO:0002233 gomodel:CHEBI_30616_UREA-CARBOXYLASE-RXN. Source location `./YeastPathways_PWY-5703.json#/facts/11; endpoint types: /individuals/13/type; /individuals/10/type`
allophanate hydrolase activity `gomodel:ALLOPHANATE-HYDROLASE-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:ALLOPHANATE-HYDROLASE-RXN BFO:0000066 gomodel:reaction_ALLOPHANATE-HYDROLASE-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-5703.json#/facts/12; endpoint types: /individuals/0/type; /individuals/33/type`
urea carboxylase activity `gomodel:UREA-CARBOXYLASE-RXN`	has_input	water `CHEBI:15377`	gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:UREA-CARBOXYLASE-RXN RO:0002233 gomodel:CHEBI_15377_UREA-CARBOXYLASE-RXN. Source location `./YeastPathways_PWY-5703.json#/facts/13; endpoint types: /individuals/13/type; /individuals/2/type`
urea carboxylase activity `gomodel:UREA-CARBOXYLASE-RXN`	part_of	urea catabolic process `GO:0043419`	gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:UREA-CARBOXYLASE-RXN BFO:0000050 gomodel:YeastPathways_PWY-5703/YeastPathways_PWY-5703. Source location `./YeastPathways_PWY-5703.json#/facts/14; endpoint types: /individuals/13/type; /individuals/35/type`
urea carboxylase activity `gomodel:UREA-CARBOXYLASE-RXN`	has_input	urea `CHEBI:16199`	gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:UREA-CARBOXYLASE-RXN RO:0002233 gomodel:CHEBI_16199_UREA-CARBOXYLASE-RXN. Source location `./YeastPathways_PWY-5703.json#/facts/15; endpoint types: /individuals/13/type; /individuals/6/type`
urea carboxylase activity `gomodel:UREA-CARBOXYLASE-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:UREA-CARBOXYLASE-RXN BFO:0000066 gomodel:reaction_UREA-CARBOXYLASE-RXN_location_lociGO_0005829. Source location `./YeastPathways_PWY-5703.json#/facts/16; endpoint types: /individuals/13/type; /individuals/34/type`
allophanate hydrolase activity `gomodel:ALLOPHANATE-HYDROLASE-RXN`	part_of	urea catabolic process `GO:0043419`	gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:ALLOPHANATE-HYDROLASE-RXN BFO:0000050 gomodel:YeastPathways_PWY-5703/YeastPathways_PWY-5703. Source location `./YeastPathways_PWY-5703.json#/facts/17; endpoint types: /individuals/0/type; /individuals/35/type`
urea carboxylase activity `gomodel:UREA-CARBOXYLASE-RXN`	has_input	carbon dioxide `CHEBI:16526`	gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:UREA-CARBOXYLASE-RXN RO:0002233 gomodel:CHEBI_16526_UREA-CARBOXYLASE-RXN. Source location `./YeastPathways_PWY-5703.json#/facts/18; endpoint types: /individuals/13/type; /individuals/8/type`
urea carboxylase activity `gomodel:UREA-CARBOXYLASE-RXN`	has_output	urea-1-carboxylate `CHEBI:15832`	gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:UREA-CARBOXYLASE-RXN RO:0002234 gomodel:CHEBI_15832_UREA-CARBOXYLASE-RXN. Source location `./YeastPathways_PWY-5703.json#/facts/19; endpoint types: /individuals/13/type; /individuals/5/type`
urea carboxylase activity `gomodel:UREA-CARBOXYLASE-RXN`	has_output	phosphate `CHEBI:26020`	gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:UREA-CARBOXYLASE-RXN RO:0002234 gomodel:CHEBI_43474_UREA-CARBOXYLASE-RXN. Source location `./YeastPathways_PWY-5703.json#/facts/21; endpoint types: /individuals/13/type; /individuals/11/type`
allophanate hydrolase activity `gomodel:ALLOPHANATE-HYDROLASE-RXN`	has_output	ammonium `CHEBI:28938`	gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:ALLOPHANATE-HYDROLASE-RXN RO:0002234 gomodel:CHEBI_28938_ALLOPHANATE-HYDROLASE-RXN. Source location `./YeastPathways_PWY-5703.json#/facts/22; endpoint types: /individuals/0/type; /individuals/9/type` gomodel:YeastPathways_PWY-5703 Source assertion: The model asserts gomodel:ALLOPHANATE-HYDROLASE-RXN RO:0002234 gomodel:YeastPathways_PWY-5703/654d809000001034. Source location `./YeastPathways_PWY-5703.json#/facts/24; endpoint types: /individuals/0/type; /individuals/43/type`
DUR12 Scer `SGD:S000000412`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: not specified	biotinate `CHEBI:57586`	UniProtKB:P32528 Source assertion: UniProtKB:P32528 annotates CHEBI:57586 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/941/comments/0/cofactors/0` UniProtKB:P32528 Source assertion: UniProtKB:P32528 has the exact SGD cross-reference SGD:S000000412. 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/941/uniProtKBCrossReferences/0`

References

gomodel:YeastPathways_PWY-5703 GO-CAM urea degradation I model YeastPathways_PWY-5703 (source version: Pinned Noctua JSON archive; model date 2026-08-03; member ./YeastPathways_PWY-5703.json)
UniProtKB:P32528 UniProtKB P32528 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 2 activity location assignments and 1 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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