glycine cleavage

gomodel:YeastPathways_GLYCLEAV-PWY

Glycine cleavage in Saccharomyces cerevisiae S288C uses GCV2 to decarboxylate glycine with lipoylprotein, GCV1 to transfer the aminomethyl group to tetrahydrofolate, and LPD1 to reoxidize dihydrolipoylprotein with NAD.

Pathway type

amino acid degradation

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

23 nodes · 26 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
5,10-methylenetetrahydrofolic acid `CHEBI:20502`	small molecule
LPD1 Scer `SGD:S000001876`	protein
hydron `CHEBI:15378`	small molecule
glycine decarboxylation via glycine cleavage system `GO:0019464`	biological process
cytosol `GO:0005829`	cellular component
dihydrolipoylprotein `CHEBI:16194`	protein
S(8)-aminomethyldihydrolipoylprotein `CHEBI:16882`	protein
lipoylprotein `CHEBI:15804`	protein
NAD(1-) `CHEBI:57540`	small molecule
ammonium `CHEBI:28938`	small molecule
NADH(2-) `CHEBI:57945`	small molecule
GCV1 Scer `SGD:S000002426`	protein
glycine zwitterion `CHEBI:57305`	small molecule
tetrahydrofolate `CHEBI:67016`	small molecule
carbon dioxide `CHEBI:16526`	small molecule
GCV2 Scer `SGD:S000004801`	protein
mitochondrial matrix `GO:0005759`	cellular component
mitochondrion `GO:0005739`	cellular component
FAD(3-) `CHEBI:57692`	cofactor
pyridoxal 5'-phosphate(2-) `CHEBI:597326`	cofactor
glycine dehydrogenase (decarboxylating) activity `gomodel:GCVP-RXN`	molecular activity
aminomethyltransferase activity `gomodel:GCVT-RXN`	molecular activity
dihydrolipoyl dehydrogenase (NADH) activity `gomodel:RXN-8629`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
aminomethyltransferase activity `gomodel:GCVT-RXN`	has_output	5,10-methylenetetrahydrofolic acid `CHEBI:20502`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:GCVT-RXN RO:0002234 gomodel:CHEBI_20502_GCVT-RXN. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/0; endpoint types: /individuals/12/type; /individuals/6/type`
LPD1 Scer `SGD:S000001876`	enables	dihydrolipoyl dehydrogenase (NADH) activity `gomodel:RXN-8629`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:RXN-8629 RO:0002333 gomodel:YFL018C-MONOMER_RXN-8629_controller. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/1; endpoint types: /individuals/13/type; /individuals/15/type`
glycine dehydrogenase (decarboxylating) activity `gomodel:GCVP-RXN`	has_input	hydron `CHEBI:15378`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:GCVP-RXN RO:0002233 gomodel:CHEBI_15378_GCVP-RXN. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/2; endpoint types: /individuals/11/type; /individuals/0/type`
glycine dehydrogenase (decarboxylating) activity `gomodel:GCVP-RXN`	part_of	glycine decarboxylation via glycine cleavage system `GO:0019464`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:GCVP-RXN BFO:0000050 gomodel:YeastPathways_GLYCLEAV-PWY/YeastPathways_GLYCLEAV-PWY. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/3; endpoint types: /individuals/11/type; /individuals/40/type`
dihydrolipoyl dehydrogenase (NADH) activity `gomodel:RXN-8629`	has_input	dihydrolipoylprotein `CHEBI:16194`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:RXN-8629 RO:0002233 gomodel:CHEBI_16194_GCVT-RXN. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/5; endpoint types: /individuals/13/type; /individuals/3/type`
glycine dehydrogenase (decarboxylating) activity `gomodel:GCVP-RXN`	has_output	S(8)-aminomethyldihydrolipoylprotein `CHEBI:16882`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:GCVP-RXN RO:0002234 gomodel:CHEBI_16882_GCVP-RXN. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/6; endpoint types: /individuals/11/type; /individuals/5/type`
dihydrolipoyl dehydrogenase (NADH) activity `gomodel:RXN-8629`	part_of	glycine decarboxylation via glycine cleavage system `GO:0019464`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:RXN-8629 BFO:0000050 gomodel:YeastPathways_GLYCLEAV-PWY/YeastPathways_GLYCLEAV-PWY. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/7; endpoint types: /individuals/13/type; /individuals/40/type`
dihydrolipoyl dehydrogenase (NADH) activity `gomodel:RXN-8629`	has_output	lipoylprotein `CHEBI:15804`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:RXN-8629 RO:0002234 gomodel:CHEBI_15804_RXN-8629. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/8; endpoint types: /individuals/13/type; /individuals/2/type`
dihydrolipoyl dehydrogenase (NADH) activity `gomodel:RXN-8629`	has_input	NAD(1-) `CHEBI:57540`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:RXN-8629 RO:0002233 gomodel:CHEBI_57540_RXN-8629. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/9; endpoint types: /individuals/13/type; /individuals/9/type`
aminomethyltransferase activity `gomodel:GCVT-RXN`	has_output	ammonium `CHEBI:28938`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:GCVT-RXN RO:0002234 gomodel:CHEBI_28938_GCVT-RXN. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/10; endpoint types: /individuals/12/type; /individuals/7/type`
aminomethyltransferase activity `gomodel:GCVT-RXN`	part_of	glycine decarboxylation via glycine cleavage system `GO:0019464`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:GCVT-RXN BFO:0000050 gomodel:YeastPathways_GLYCLEAV-PWY/YeastPathways_GLYCLEAV-PWY. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/11; endpoint types: /individuals/12/type; /individuals/40/type`
dihydrolipoyl dehydrogenase (NADH) activity `gomodel:RXN-8629`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:RXN-8629 RO:0002234 gomodel:CHEBI_15378_RXN-8629. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/13; endpoint types: /individuals/13/type; /individuals/1/type`
glycine dehydrogenase (decarboxylating) activity `gomodel:GCVP-RXN`	has_input	lipoylprotein `CHEBI:15804`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:GCVP-RXN RO:0002233 gomodel:CHEBI_15804_RXN-8629. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/14; endpoint types: /individuals/11/type; /individuals/2/type`
aminomethyltransferase activity `gomodel:GCVT-RXN`	has_input	S(8)-aminomethyldihydrolipoylprotein `CHEBI:16882`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:GCVT-RXN RO:0002233 gomodel:CHEBI_16882_GCVP-RXN. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/15; endpoint types: /individuals/12/type; /individuals/5/type`
aminomethyltransferase activity `gomodel:GCVT-RXN`	has_output	dihydrolipoylprotein `CHEBI:16194`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:GCVT-RXN RO:0002234 gomodel:CHEBI_16194_GCVT-RXN. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/16; endpoint types: /individuals/12/type; /individuals/3/type`
dihydrolipoyl dehydrogenase (NADH) activity `gomodel:RXN-8629`	has_output	NADH(2-) `CHEBI:57945`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:RXN-8629 RO:0002234 gomodel:CHEBI_57945_RXN-8629. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/17; endpoint types: /individuals/13/type; /individuals/10/type`
GCV1 Scer `SGD:S000002426`	enables	aminomethyltransferase activity `gomodel:GCVT-RXN`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:GCVT-RXN RO:0002333 gomodel:YDR019C-MONOMER_GCVT-RXN_controller. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/18; endpoint types: /individuals/12/type; /individuals/14/type`
glycine dehydrogenase (decarboxylating) activity `gomodel:GCVP-RXN`	has_input	glycine zwitterion `CHEBI:57305`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:GCVP-RXN RO:0002233 gomodel:CHEBI_57305_GCVP-RXN. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/20; endpoint types: /individuals/11/type; /individuals/8/type`
aminomethyltransferase activity `gomodel:GCVT-RXN`	has_input	tetrahydrofolate `CHEBI:67016`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:GCVT-RXN RO:0002233 gomodel:YeastPathways_GLYCLEAV-PWY/65692e7e00001185. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/21; endpoint types: /individuals/12/type; /individuals/41/type`
glycine dehydrogenase (decarboxylating) activity `gomodel:GCVP-RXN`	has_output	carbon dioxide `CHEBI:16526`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:GCVP-RXN RO:0002234 gomodel:CHEBI_16526_GCVP-RXN. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/22; endpoint types: /individuals/11/type; /individuals/4/type`
GCV2 Scer `SGD:S000004801`	enables	glycine dehydrogenase (decarboxylating) activity `gomodel:GCVP-RXN`	gomodel:YeastPathways_GLYCLEAV-PWY Source assertion: The model asserts gomodel:GCVP-RXN RO:0002333 gomodel:YMR189W-MONOMER_GCVP-RXN_controller. Source location `./YeastPathways_GLYCLEAV-PWY.json#/facts/23; endpoint types: /individuals/11/type; /individuals/16/type`
LPD1 Scer `SGD:S000001876`	located_in Physical protein location from reviewed UniProt. evidence code not specified by source	mitochondrial matrix `GO:0005759`	UniProtKB:P09624 Source assertion: UniProtKB:P09624 annotates location Mitochondrion matrix (SL-0170). 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/227/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P09624 Source assertion: UniProtKB:P09624 has the exact SGD cross-reference SGD:S000001876. 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/227/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
GCV1 Scer `SGD:S000002426`	located_in Physical protein location from reviewed UniProt. evidence code not specified by source	mitochondrion `GO:0005739`	UniProtKB:P48015 Source assertion: UniProtKB:P48015 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/3893/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P48015 Source assertion: UniProtKB:P48015 has the exact SGD cross-reference SGD:S000002426. 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/3893/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
GCV2 Scer `SGD:S000004801`	located_in Physical protein location from reviewed UniProt. ECO:0000250	mitochondrion `GO:0005739`	UniProtKB:P49095 Source assertion: UniProtKB:P49095 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/2023/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P49095 Source assertion: UniProtKB:P49095 has the exact SGD cross-reference SGD:S000004801. 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/2023/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
LPD1 Scer `SGD:S000001876`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000269 (PubMed:9538259); ECO:0000269 (Reference:Ref.13) Binds 1 FAD per subunit. UniProt note evidence: ECO:0000269 (PubMed:9538259); ECO:0000269 (Reference:Ref.13)	FAD(3-) `CHEBI:57692`	UniProtKB:P09624 Source assertion: UniProtKB:P09624 annotates CHEBI:57692 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/227/comments/0/cofactors/0; /results/227/comments/0/note` UniProtKB:P09624 Source assertion: UniProtKB:P09624 has the exact SGD cross-reference SGD:S000001876. 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/227/uniProtKBCrossReferences/0`
GCV2 Scer `SGD:S000004801`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000250	pyridoxal 5'-phosphate(2-) `CHEBI:597326`	UniProtKB:P49095 Source assertion: UniProtKB:P49095 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/2023/comments/0/cofactors/0` UniProtKB:P49095 Source assertion: UniProtKB:P49095 has the exact SGD cross-reference SGD:S000004801. 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/2023/uniProtKBCrossReferences/0`

References

gomodel:YeastPathways_GLYCLEAV-PWY GO-CAM glycine cleavage model YeastPathways_GLYCLEAV-PWY (source version: Pinned Noctua JSON archive; model date 2024-07-12; member ./YeastPathways_GLYCLEAV-PWY.json)
UniProtKB:P09624 Reviewed UniProtKB P09624 location annotations (source version: UniProt release 2026_03)
UniProtKB:P48015 Reviewed UniProtKB P48015 location annotations (source version: UniProt release 2026_03)
UniProtKB:P49095 Reviewed UniProtKB P49095 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 3 activity location assignments and 3 mapped physical proteins against reviewed S288C UniProt release2026_03 location/function/caution batch SHA256 95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d. Added 3 independently supported location edges and quarantined 3 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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