threonine degradation

gomodel:YeastPathways_THREOCAT2-PWY

Threonine degradation in Saccharomyces cerevisiae S288C includes CHA1-enabled threonine deamination to 2-oxobutanoate and the GLY1 threonine aldolase route to glycine and acetaldehyde. The broader native outline contains unassigned or neighbouring reactions; KBL is absent and threonine dehydrogenase is uncertain in yeast. An unsupported reverse cystathionine-condensation branch is excluded.

Pathway type

amino acid degradation

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

Read the source YAML

Pathway network

14 nodes · 16 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

Show at full size (scroll to explore)

Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Saccharomyces cerevisiae S288C `NCBITaxon:559292`	taxon
L-threonine zwitterion `CHEBI:57926`	small molecule
cytosol `GO:0005829`	cellular component
L-threonine catabolic process `GO:0006567`	biological process
2-oxobutanoate `CHEBI:16763`	lipid
ammonia `CHEBI:16134`	small molecule
CHA1 Scer `SGD:S000000569`	protein
water `CHEBI:15377`	small molecule
Low specificity L-threonine aldolase `UniProtKB:P37303`	protein
acetaldehyde `CHEBI:15343`	small molecule
glycine zwitterion `CHEBI:57305`	small molecule
mitochondrion `GO:0005739`	cellular component
pyridoxal 5'-phosphate(2-) `CHEBI:597326`	cofactor
threonine deaminase activity `gomodel:THREDEHYD2-RXN`	molecular activity
threonine aldolase activity `GO:0004793`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
threonine deaminase activity `gomodel:THREDEHYD2-RXN`	has_input	L-threonine zwitterion `CHEBI:57926`	gomodel:YeastPathways_THREOCAT2-PWY Source assertion: The model asserts gomodel:THREDEHYD2-RXN RO:0002233 gomodel:CHEBI_57926_THREDEHYD2-RXN. Source location `./YeastPathways_THREOCAT2-PWY.json#/facts/7; endpoint types: /individuals/52/type; /individuals/38/type`
threonine deaminase activity `gomodel:THREDEHYD2-RXN`	part_of	L-threonine catabolic process `GO:0006567`	gomodel:YeastPathways_THREOCAT2-PWY Source assertion: The model asserts gomodel:THREDEHYD2-RXN BFO:0000050 gomodel:YeastPathways_THREOCAT2-PWY/YeastPathways_THREOCAT2-PWY. Source location `./YeastPathways_THREOCAT2-PWY.json#/facts/18; endpoint types: /individuals/52/type; /individuals/138/type`
threonine deaminase activity `gomodel:THREDEHYD2-RXN`	has_output	ammonia `CHEBI:16134`	gomodel:YeastPathways_THREOCAT2-PWY Source assertion: The model asserts gomodel:THREDEHYD2-RXN RO:0002234 gomodel:CHEBI_16134_THREDEHYD2-RXN. Source location `./YeastPathways_THREOCAT2-PWY.json#/facts/42; endpoint types: /individuals/52/type; /individuals/13/type`
CHA1 Scer `SGD:S000000569`	enables	threonine deaminase activity `gomodel:THREDEHYD2-RXN`	gomodel:YeastPathways_THREOCAT2-PWY Source assertion: The model asserts gomodel:THREDEHYD2-RXN RO:0002333 gomodel:YCL064C-MONOMER_THREDEHYD2-RXN_controller. Source location `./YeastPathways_THREOCAT2-PWY.json#/facts/45; endpoint types: /individuals/52/type; /individuals/56/type`
threonine deaminase activity `gomodel:THREDEHYD2-RXN`	has_output	water `CHEBI:15377`	gomodel:YeastPathways_THREOCAT2-PWY Source assertion: The model asserts gomodel:THREDEHYD2-RXN RO:0002234 gomodel:CHEBI_15377_THREDEHYD2-RXN. Source location `./YeastPathways_THREOCAT2-PWY.json#/facts/49; endpoint types: /individuals/52/type; /individuals/6/type`
threonine deaminase activity `gomodel:THREDEHYD2-RXN`	has_output	2-oxobutanoate `CHEBI:16763`	gomodel:YeastPathways_THREOCAT2-PWY Source assertion: The model asserts gomodel:THREDEHYD2-RXN RO:0002234 gomodel:CHEBI_16763_THREDEHYD2-RXN. Source location `./YeastPathways_THREOCAT2-PWY.json#/facts/60; endpoint types: /individuals/52/type; /individuals/16/type`
threonine deaminase activity `gomodel:THREDEHYD2-RXN`	has_input	water `CHEBI:15377`	gomodel:YeastPathways_THREOCAT2-PWY Source assertion: The model asserts gomodel:THREDEHYD2-RXN RO:0002233 gomodel:CHEBI_15377_THREDEHYD2-RXN. Source location `./YeastPathways_THREOCAT2-PWY.json#/facts/77; endpoint types: /individuals/52/type; /individuals/6/type`
Low specificity L-threonine aldolase `UniProtKB:P37303`	enables	threonine aldolase activity `GO:0004793`	UniProtKB:P37303 Source assertion: Reviewed GLY1 is annotated to threonine aldolase activity and catalyzes L-threonine cleavage to acetaldehyde and glycine; the catalytic annotation cites experimental evidence from PMID:9151955. Source location `UniProt JSON #/results/0/comments/1/reaction; /results/0/uniProtKBCrossReferences/38`
threonine aldolase activity `GO:0004793`	has_input	L-threonine zwitterion `CHEBI:57926`	UniProtKB:P37303 Source assertion: The reviewed GLY1 catalytic reaction is L-threonine = acetaldehyde + glycine; its ChEBI cross-references identify L-threonine as CHEBI:57926. Source location `UniProt JSON #/results/0/comments/1/reaction`
threonine aldolase activity `GO:0004793`	has_output	acetaldehyde `CHEBI:15343`	UniProtKB:P37303 Source assertion: The reviewed GLY1 catalytic reaction produces acetaldehyde, cross-referenced as CHEBI:15343, from L-threonine. Source location `UniProt JSON #/results/0/comments/1/reaction`
threonine aldolase activity `GO:0004793`	has_output	glycine zwitterion `CHEBI:57305`	UniProtKB:P37303 Source assertion: The reviewed GLY1 catalytic reaction produces glycine, cross-referenced as CHEBI:57305, from L-threonine. Source location `UniProt JSON #/results/0/comments/1/reaction`
Low specificity L-threonine aldolase `UniProtKB:P37303`	located_in	cytosol `GO:0005829`	UniProtKB:P37303 Source assertion: The reviewed GLY1 entry records a cytosol annotation (GO:0005829) with IDA:SGD evidence. Source location `UniProt JSON #/results/0/uniProtKBCrossReferences/36`
threonine aldolase activity `GO:0004793`	part_of	L-threonine catabolic process `GO:0006567`	UniProtKB:P37303 Source assertion: UniProt assigns GLY1 to the single-step L-threonine degradation via the aldolase pathway and records L-threonine catabolic process (GO:0006567). Source location `UniProt JSON #/results/0/comments/5; /results/0/uniProtKBCrossReferences/40`
CHA1 Scer `SGD:S000000569`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:14562095); ECO:0000269 (PubMed:16823961)	mitochondrion `GO:0005739`	UniProtKB:P25379 Source assertion: UniProtKB:P25379 annotates location Mitochondrion (SL-0173). 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/3364/comments/0/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P25379 Source assertion: UniProtKB:P25379 has the exact SGD cross-reference SGD:S000000569. 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/3364/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
CHA1 Scer `SGD:S000000569`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000250	pyridoxal 5'-phosphate(2-) `CHEBI:597326`	UniProtKB:P25379 Source assertion: UniProtKB:P25379 annotates CHEBI:597326 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/3364/comments/0/cofactors/0` UniProtKB:P25379 Source assertion: UniProtKB:P25379 has the exact SGD cross-reference SGD:S000000569. 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/3364/uniProtKBCrossReferences/0`
Low specificity L-threonine aldolase `UniProtKB:P37303`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: not specified	pyridoxal 5'-phosphate(2-) `CHEBI:597326`	UniProtKB:P37303 Source assertion: UniProtKB:P37303 annotates CHEBI:597326 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/1258/comments/0/cofactors/0`

References

gomodel:YeastPathways_THREOCAT2-PWY GO-CAM threonine degradation model YeastPathways_THREOCAT2-PWY (source version: Pinned Noctua JSON archive; model date 2024-07-30; member ./YeastPathways_THREOCAT2-PWY.json)
UniProtKB:P37303 UniProt reviewed GLY1 (P37303), Saccharomyces cerevisiae S288C (source version: Entry 198; annotation update 2026-06-10)
UniProtKB:P25379 Reviewed UniProtKB P25379 location annotations (source version: UniProt release 2026_03)
UniProtKB:P31373 Reviewed UniProtKB P31373 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.
2026-10-05T06:53:32Z Codex; review-catalytic-function; Reconciled native GO-CAM chemistry with independently reviewed enzyme specificity, direction, physiological scope and source cautions; superseded facts remain in the function review ledger.
2026-10-05T06:43:56Z Codex
- EDIT — 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 2 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.
Read this curation session