L-cysteine biosynthesis III (from L-homocysteine)

gomodel:YeastPathways_HOMOCYSDEGR-PWY-1

L-cysteine biosynthesis III (from L-homocysteine) condenses L-homocysteine with L-serine to form L-cystathionine and then cleaves L-cystathionine to L-cysteine, 2-oxobutanoate, and ammonia in Saccharomyces cerevisiae S288C.

Pathway type

amino acid biosynthesis

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

15 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
L-cysteine biosynthetic process `GO:0019344`	biological process
L-cystathionine dizwitterion `CHEBI:58161`	small molecule
water `CHEBI:15377`	small molecule
cytosol `GO:0005829`	cellular component
L-homocysteine zwitterion `CHEBI:58199`	small molecule
L-serine zwitterion `CHEBI:33384`	small molecule
CYS4 Scer `SGD:S000003387`	protein
L-cysteine zwitterion `CHEBI:35235`	small molecule
CYS3 Scer `SGD:S000000010`	protein
2-oxobutanoate `CHEBI:16763`	lipid
ammonia `CHEBI:16134`	small molecule
cytoplasm `GO:0005737`	cellular component
pyridoxal 5'-phosphate(2-) `CHEBI:597326`	cofactor
cystathionine gamma-lyase activity `gomodel:CYSTAGLY-RXN`	molecular activity
cystathionine beta-synthase activity `gomodel:CYSTATHIONINE-BETA-SYNTHASE-RXN`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
cystathionine beta-synthase activity `gomodel:CYSTATHIONINE-BETA-SYNTHASE-RXN`	part_of	L-cysteine biosynthetic process `GO:0019344`	gomodel:YeastPathways_HOMOCYSDEGR-PWY-1 Source assertion: The model asserts gomodel:CYSTATHIONINE-BETA-SYNTHASE-RXN BFO:0000050 gomodel:YeastPathways_HOMOCYSDEGR-PWY-1/YeastPathways_HOMOCYSDEGR-PWY-1. Source location `./YeastPathways_HOMOCYSDEGR-PWY-1.json#/facts/0; endpoint types: /individuals/9/type; /individuals/27/type`
cystathionine beta-synthase activity `gomodel:CYSTATHIONINE-BETA-SYNTHASE-RXN`	has_output	L-cystathionine dizwitterion `CHEBI:58161`	gomodel:YeastPathways_HOMOCYSDEGR-PWY-1 Source assertion: The model asserts gomodel:CYSTATHIONINE-BETA-SYNTHASE-RXN RO:0002234 gomodel:CHEBI_58161_CYSTATHIONINE-BETA-SYNTHASE-RXN. Source location `./YeastPathways_HOMOCYSDEGR-PWY-1.json#/facts/1; endpoint types: /individuals/9/type; /individuals/6/type`
cystathionine gamma-lyase activity `gomodel:CYSTAGLY-RXN`	has_input	L-cystathionine dizwitterion `CHEBI:58161`	gomodel:YeastPathways_HOMOCYSDEGR-PWY-1 Source assertion: The model asserts gomodel:CYSTAGLY-RXN RO:0002233 gomodel:CHEBI_58161_CYSTATHIONINE-BETA-SYNTHASE-RXN. Source location `./YeastPathways_HOMOCYSDEGR-PWY-1.json#/facts/2; endpoint types: /individuals/8/type; /individuals/6/type`
cystathionine beta-synthase activity `gomodel:CYSTATHIONINE-BETA-SYNTHASE-RXN`	provides_input_for	cystathionine gamma-lyase activity `gomodel:CYSTAGLY-RXN`	gomodel:YeastPathways_HOMOCYSDEGR-PWY-1 Source assertion: The model asserts gomodel:CYSTATHIONINE-BETA-SYNTHASE-RXN RO:0002413 gomodel:CYSTAGLY-RXN. Source location `./YeastPathways_HOMOCYSDEGR-PWY-1.json#/facts/3; endpoint types: /individuals/9/type; /individuals/8/type`
cystathionine beta-synthase activity `gomodel:CYSTATHIONINE-BETA-SYNTHASE-RXN`	has_output	water `CHEBI:15377`	gomodel:YeastPathways_HOMOCYSDEGR-PWY-1 Source assertion: The model asserts gomodel:CYSTATHIONINE-BETA-SYNTHASE-RXN RO:0002234 gomodel:CHEBI_15377_CYSTATHIONINE-BETA-SYNTHASE-RXN. Source location `./YeastPathways_HOMOCYSDEGR-PWY-1.json#/facts/4; endpoint types: /individuals/9/type; /individuals/1/type`
cystathionine beta-synthase activity `gomodel:CYSTATHIONINE-BETA-SYNTHASE-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_HOMOCYSDEGR-PWY-1 Source assertion: The model asserts gomodel:CYSTATHIONINE-BETA-SYNTHASE-RXN BFO:0000066 gomodel:reaction_CYSTATHIONINE-BETA-SYNTHASE-RXN_location_lociGO_0005829. Source location `./YeastPathways_HOMOCYSDEGR-PWY-1.json#/facts/5; endpoint types: /individuals/9/type; /individuals/26/type`
cystathionine gamma-lyase activity `gomodel:CYSTAGLY-RXN`	part_of	L-cysteine biosynthetic process `GO:0019344`	gomodel:YeastPathways_HOMOCYSDEGR-PWY-1 Source assertion: The model asserts gomodel:CYSTAGLY-RXN BFO:0000050 gomodel:YeastPathways_HOMOCYSDEGR-PWY-1/YeastPathways_HOMOCYSDEGR-PWY-1. Source location `./YeastPathways_HOMOCYSDEGR-PWY-1.json#/facts/6; endpoint types: /individuals/8/type; /individuals/27/type`
cystathionine beta-synthase activity `gomodel:CYSTATHIONINE-BETA-SYNTHASE-RXN`	has_input	L-homocysteine zwitterion `CHEBI:58199`	gomodel:YeastPathways_HOMOCYSDEGR-PWY-1 Source assertion: The model asserts gomodel:CYSTATHIONINE-BETA-SYNTHASE-RXN RO:0002233 gomodel:CHEBI_58199_CYSTATHIONINE-BETA-SYNTHASE-RXN. Source location `./YeastPathways_HOMOCYSDEGR-PWY-1.json#/facts/7; endpoint types: /individuals/9/type; /individuals/7/type`
cystathionine gamma-lyase activity `gomodel:CYSTAGLY-RXN`	has_input	water `CHEBI:15377`	gomodel:YeastPathways_HOMOCYSDEGR-PWY-1 Source assertion: The model asserts gomodel:CYSTAGLY-RXN RO:0002233 gomodel:CHEBI_15377_CYSTAGLY-RXN. Source location `./YeastPathways_HOMOCYSDEGR-PWY-1.json#/facts/8; endpoint types: /individuals/8/type; /individuals/0/type`
cystathionine beta-synthase activity `gomodel:CYSTATHIONINE-BETA-SYNTHASE-RXN`	has_input	L-serine zwitterion `CHEBI:33384`	gomodel:YeastPathways_HOMOCYSDEGR-PWY-1 Source assertion: The model asserts gomodel:CYSTATHIONINE-BETA-SYNTHASE-RXN RO:0002233 gomodel:CHEBI_33384_CYSTATHIONINE-BETA-SYNTHASE-RXN. Source location `./YeastPathways_HOMOCYSDEGR-PWY-1.json#/facts/9; endpoint types: /individuals/9/type; /individuals/4/type`
CYS4 Scer `SGD:S000003387`	enables	cystathionine beta-synthase activity `gomodel:CYSTATHIONINE-BETA-SYNTHASE-RXN`	gomodel:YeastPathways_HOMOCYSDEGR-PWY-1 Source assertion: The model asserts gomodel:CYSTATHIONINE-BETA-SYNTHASE-RXN RO:0002333 gomodel:YGR155W-MONOMER_CYSTATHIONINE-BETA-SYNTHASE-RXN_controller. Source location `./YeastPathways_HOMOCYSDEGR-PWY-1.json#/facts/10; endpoint types: /individuals/9/type; /individuals/11/type`
cystathionine gamma-lyase activity `gomodel:CYSTAGLY-RXN`	has_output	L-cysteine zwitterion `CHEBI:35235`	gomodel:YeastPathways_HOMOCYSDEGR-PWY-1 Source assertion: The model asserts gomodel:CYSTAGLY-RXN RO:0002234 gomodel:CHEBI_35235_CYSTAGLY-RXN. Source location `./YeastPathways_HOMOCYSDEGR-PWY-1.json#/facts/11; endpoint types: /individuals/8/type; /individuals/5/type`
CYS3 Scer `SGD:S000000010`	enables	cystathionine gamma-lyase activity `gomodel:CYSTAGLY-RXN`	gomodel:YeastPathways_HOMOCYSDEGR-PWY-1 Source assertion: The model asserts gomodel:CYSTAGLY-RXN RO:0002333 gomodel:YAL012W-MONOMER_CYSTAGLY-RXN_controller. Source location `./YeastPathways_HOMOCYSDEGR-PWY-1.json#/facts/12; endpoint types: /individuals/8/type; /individuals/10/type`
cystathionine gamma-lyase activity `gomodel:CYSTAGLY-RXN`	has_output	2-oxobutanoate `CHEBI:16763`	gomodel:YeastPathways_HOMOCYSDEGR-PWY-1 Source assertion: The model asserts gomodel:CYSTAGLY-RXN RO:0002234 gomodel:CHEBI_16763_CYSTAGLY-RXN. Source location `./YeastPathways_HOMOCYSDEGR-PWY-1.json#/facts/13; endpoint types: /individuals/8/type; /individuals/3/type`
cystathionine gamma-lyase activity `gomodel:CYSTAGLY-RXN`	has_output	ammonia `CHEBI:16134`	gomodel:YeastPathways_HOMOCYSDEGR-PWY-1 Source assertion: The model asserts gomodel:CYSTAGLY-RXN RO:0002234 gomodel:CHEBI_16134_CYSTAGLY-RXN. Source location `./YeastPathways_HOMOCYSDEGR-PWY-1.json#/facts/14; endpoint types: /individuals/8/type; /individuals/2/type`
cystathionine gamma-lyase activity `gomodel:CYSTAGLY-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_HOMOCYSDEGR-PWY-1 Source assertion: The model asserts gomodel:CYSTAGLY-RXN BFO:0000066 gomodel:reaction_CYSTAGLY-RXN_location_lociGO_0005829. Source location `./YeastPathways_HOMOCYSDEGR-PWY-1.json#/facts/15; endpoint types: /individuals/8/type; /individuals/25/type`
CYS3 Scer `SGD:S000000010`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:14562095)	cytoplasm `GO:0005737`	UniProtKB:P31373 Source assertion: UniProtKB:P31373 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/839/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P31373 Source assertion: UniProtKB:P31373 has the exact SGD cross-reference SGD:S000000010. 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/839/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
CYS4 Scer `SGD:S000003387`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: not specified	pyridoxal 5'-phosphate(2-) `CHEBI:597326`	UniProtKB:P32582 Source assertion: UniProtKB:P32582 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/958/comments/0/cofactors/0` UniProtKB:P32582 Source assertion: UniProtKB:P32582 has the exact SGD cross-reference SGD:S000003387. 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/958/uniProtKBCrossReferences/0`
CYS3 Scer `SGD:S000000010`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: ECO:0000269 (PubMed:12715888)	pyridoxal 5'-phosphate(2-) `CHEBI:597326`	UniProtKB:P31373 Source assertion: UniProtKB:P31373 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/839/comments/0/cofactors/0` UniProtKB:P31373 Source assertion: UniProtKB:P31373 has the exact SGD cross-reference SGD:S000000010. 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/839/uniProtKBCrossReferences/0`

References

gomodel:YeastPathways_HOMOCYSDEGR-PWY-1 GO-CAM L-cysteine biosynthesis III from L-homocysteine model YeastPathways_HOMOCYSDEGR-PWY-1 (source version: Pinned Noctua JSON archive; model date 2026-08-03; member ./YeastPathways_HOMOCYSDEGR-PWY-1.json)
UniProtKB:P31373 Reviewed UniProtKB P31373 location annotations (source version: UniProt release 2026_03)
UniProtKB:P32582 UniProtKB P32582 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 1 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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