L-proline degradation

gomodel:YeastPathways_PROUT-PWY

L-proline degradation in Saccharomyces cerevisiae S288C oxidizes L-proline to (S)-1-pyrroline-5-carboxylate, hydrates that intermediate to L-glutamic 5-semialdehyde, and oxidizes it to L-glutamate.

Pathway type

amino acid degradation

Organism scope

Saccharomyces cerevisiae S288C NCBITaxon:559292

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Pathway network

20 nodes · 25 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-proline catabolic process `GO:0006562`	biological process
NADH(2-) `CHEBI:57945`	small molecule
hydron `CHEBI:15378`	small molecule
cytosol `GO:0005829`	cellular component
PUT1 Scer `SGD:S000004132`	protein
hydroquinone `CHEBI:17594`	small molecule
(S)-1-pyrroline-5-carboxylate `CHEBI:17388`	small molecule
water `CHEBI:15377`	small molecule
L-proline zwitterion `CHEBI:60039`	small molecule
PUT2 Scer `SGD:S000001079`	protein
quinone `CHEBI:36141`	small molecule
L-glutamic 5-semialdehyde zwitterion `CHEBI:58066`	small molecule
NAD(1-) `CHEBI:57540`	small molecule
L-glutamate(1-) `CHEBI:29985`	small molecule
mitochondrial matrix `GO:0005759`	cellular component
mitochondrial inner membrane `GO:0005743`	cellular component
FAD(3-) `CHEBI:57692`	cofactor
L-glutamate gamma-semialdehyde dehydrogenase (NAD+) activity `gomodel:RXN-14116`	molecular activity
proline dehydrogenase activity `gomodel:RXN-14903`	molecular activity
(S)-1-pyrroline-5-carboxylate + H+ + H2O <-> L-glutamate-5-semialdehyde `gomodel:SPONTPRO-RXN`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
(S)-1-pyrroline-5-carboxylate + H+ + H2O <-> L-glutamate-5-semialdehyde `gomodel:SPONTPRO-RXN`	part_of	L-proline catabolic process `GO:0006562`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:SPONTPRO-RXN BFO:0000050 gomodel:YeastPathways_PROUT-PWY/YeastPathways_PROUT-PWY. Source location `./YeastPathways_PROUT-PWY.json#/facts/0; endpoint types: /individuals/15/type; /individuals/39/type`
L-glutamate gamma-semialdehyde dehydrogenase (NAD+) activity `gomodel:RXN-14116`	has_output	NADH(2-) `CHEBI:57945`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:RXN-14116 RO:0002234 gomodel:CHEBI_57945_RXN-14116. Source location `./YeastPathways_PROUT-PWY.json#/facts/1; endpoint types: /individuals/13/type; /individuals/10/type`
L-glutamate gamma-semialdehyde dehydrogenase (NAD+) activity `gomodel:RXN-14116`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:RXN-14116 RO:0002234 gomodel:CHEBI_15378_RXN-14116. Source location `./YeastPathways_PROUT-PWY.json#/facts/2; endpoint types: /individuals/13/type; /individuals/2/type`
PUT1 Scer `SGD:S000004132`	enables	proline dehydrogenase activity `gomodel:RXN-14903`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:RXN-14903 RO:0002333 gomodel:YLR142W-MONOMER_RXN-14903_controller. Source location `./YeastPathways_PROUT-PWY.json#/facts/4; endpoint types: /individuals/14/type; /individuals/16/type`
(S)-1-pyrroline-5-carboxylate + H+ + H2O <-> L-glutamate-5-semialdehyde `gomodel:SPONTPRO-RXN`	has_input	hydron `CHEBI:15378`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:SPONTPRO-RXN RO:0002233 gomodel:CHEBI_15378_SPONTPRO-RXN. Source location `./YeastPathways_PROUT-PWY.json#/facts/5; endpoint types: /individuals/15/type; /individuals/4/type`
proline dehydrogenase activity `gomodel:RXN-14903`	has_output	hydroquinone `CHEBI:17594`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:RXN-14903 RO:0002234 gomodel:CHEBI_17594_RXN-14903. Source location `./YeastPathways_PROUT-PWY.json#/facts/6; endpoint types: /individuals/14/type; /individuals/6/type`
(S)-1-pyrroline-5-carboxylate + H+ + H2O <-> L-glutamate-5-semialdehyde `gomodel:SPONTPRO-RXN`	has_input	(S)-1-pyrroline-5-carboxylate `CHEBI:17388`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:SPONTPRO-RXN RO:0002233 gomodel:CHEBI_17388_RXN-14903. Source location `./YeastPathways_PROUT-PWY.json#/facts/7; endpoint types: /individuals/15/type; /individuals/5/type`
L-glutamate gamma-semialdehyde dehydrogenase (NAD+) activity `gomodel:RXN-14116`	has_input	water `CHEBI:15377`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:RXN-14116 RO:0002233 gomodel:CHEBI_15377_RXN-14116. Source location `./YeastPathways_PROUT-PWY.json#/facts/8; endpoint types: /individuals/13/type; /individuals/0/type`
(S)-1-pyrroline-5-carboxylate + H+ + H2O <-> L-glutamate-5-semialdehyde `gomodel:SPONTPRO-RXN`	has_input	water `CHEBI:15377`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:SPONTPRO-RXN RO:0002233 gomodel:CHEBI_15377_SPONTPRO-RXN. Source location `./YeastPathways_PROUT-PWY.json#/facts/9; endpoint types: /individuals/15/type; /individuals/1/type`
L-glutamate gamma-semialdehyde dehydrogenase (NAD+) activity `gomodel:RXN-14116`	part_of	L-proline catabolic process `GO:0006562`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:RXN-14116 BFO:0000050 gomodel:YeastPathways_PROUT-PWY/YeastPathways_PROUT-PWY. Source location `./YeastPathways_PROUT-PWY.json#/facts/11; endpoint types: /individuals/13/type; /individuals/39/type`
(S)-1-pyrroline-5-carboxylate + H+ + H2O <-> L-glutamate-5-semialdehyde `gomodel:SPONTPRO-RXN`	occurs_in	cytosol `GO:0005829`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:SPONTPRO-RXN BFO:0000066 gomodel:reaction_SPONTPRO-RXN_location_lociGO_0005829. Source location `./YeastPathways_PROUT-PWY.json#/facts/12; endpoint types: /individuals/15/type; /individuals/38/type`
proline dehydrogenase activity `gomodel:RXN-14903`	has_output	hydron `CHEBI:15378`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:RXN-14903 RO:0002234 gomodel:CHEBI_15378_RXN-14903. Source location `./YeastPathways_PROUT-PWY.json#/facts/13; endpoint types: /individuals/14/type; /individuals/3/type`
proline dehydrogenase activity `gomodel:RXN-14903`	has_input	L-proline zwitterion `CHEBI:60039`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:RXN-14903 RO:0002233 gomodel:CHEBI_60039_RXN-14903. Source location `./YeastPathways_PROUT-PWY.json#/facts/14; endpoint types: /individuals/14/type; /individuals/12/type`
proline dehydrogenase activity `gomodel:RXN-14903`	causally_upstream_of	L-glutamate gamma-semialdehyde dehydrogenase (NAD+) activity `gomodel:RXN-14116`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:RXN-14903 RO:0002411 gomodel:RXN-14116. Source location `./YeastPathways_PROUT-PWY.json#/facts/15; endpoint types: /individuals/14/type; /individuals/13/type`
PUT2 Scer `SGD:S000001079`	enables	L-glutamate gamma-semialdehyde dehydrogenase (NAD+) activity `gomodel:RXN-14116`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:RXN-14116 RO:0002333 gomodel:YeastPathways_PROUT-PWY/6690711d00000539. Source location `./YeastPathways_PROUT-PWY.json#/facts/16; endpoint types: /individuals/13/type; /individuals/41/type`
proline dehydrogenase activity `gomodel:RXN-14903`	has_input	quinone `CHEBI:36141`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:RXN-14903 RO:0002233 gomodel:CHEBI_36141_RXN-14903. Source location `./YeastPathways_PROUT-PWY.json#/facts/17; endpoint types: /individuals/14/type; /individuals/8/type`
(S)-1-pyrroline-5-carboxylate + H+ + H2O <-> L-glutamate-5-semialdehyde `gomodel:SPONTPRO-RXN`	has_output	L-glutamic 5-semialdehyde zwitterion `CHEBI:58066`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:SPONTPRO-RXN RO:0002234 gomodel:CHEBI_58066_SPONTPRO-RXN. Source location `./YeastPathways_PROUT-PWY.json#/facts/18; endpoint types: /individuals/15/type; /individuals/11/type`
L-glutamate gamma-semialdehyde dehydrogenase (NAD+) activity `gomodel:RXN-14116`	has_input	NAD(1-) `CHEBI:57540`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:RXN-14116 RO:0002233 gomodel:CHEBI_57540_RXN-14116. Source location `./YeastPathways_PROUT-PWY.json#/facts/19; endpoint types: /individuals/13/type; /individuals/9/type`
proline dehydrogenase activity `gomodel:RXN-14903`	has_output	(S)-1-pyrroline-5-carboxylate `CHEBI:17388`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:RXN-14903 RO:0002234 gomodel:CHEBI_17388_RXN-14903. Source location `./YeastPathways_PROUT-PWY.json#/facts/20; endpoint types: /individuals/14/type; /individuals/5/type`
L-glutamate gamma-semialdehyde dehydrogenase (NAD+) activity `gomodel:RXN-14116`	has_output	L-glutamate(1-) `CHEBI:29985`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:RXN-14116 RO:0002234 gomodel:CHEBI_29985_RXN-14116. Source location `./YeastPathways_PROUT-PWY.json#/facts/21; endpoint types: /individuals/13/type; /individuals/7/type`
L-glutamate gamma-semialdehyde dehydrogenase (NAD+) activity `gomodel:RXN-14116`	has_input	L-glutamic 5-semialdehyde zwitterion `CHEBI:58066`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:RXN-14116 RO:0002233 gomodel:CHEBI_58066_SPONTPRO-RXN. Source location `./YeastPathways_PROUT-PWY.json#/facts/22; endpoint types: /individuals/13/type; /individuals/11/type`
proline dehydrogenase activity `gomodel:RXN-14903`	part_of	L-proline catabolic process `GO:0006562`	gomodel:YeastPathways_PROUT-PWY Source assertion: The model asserts gomodel:RXN-14903 BFO:0000050 gomodel:YeastPathways_PROUT-PWY/YeastPathways_PROUT-PWY. Source location `./YeastPathways_PROUT-PWY.json#/facts/23; endpoint types: /individuals/14/type; /individuals/39/type`
PUT1 Scer `SGD:S000004132`	located_in Physical protein location from reviewed UniProt. evidence code not specified by source	mitochondrial matrix `GO:0005759`	UniProtKB:P09368 Source assertion: UniProtKB:P09368 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/3256/comments/1/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P09368 Source assertion: UniProtKB:P09368 has the exact SGD cross-reference SGD:S000004132. 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/3256/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
PUT2 Scer `SGD:S000001079`	located_in Physical protein location from reviewed UniProt. ECO:0000269 (PubMed:11502169)	mitochondrial inner membrane `GO:0005743`	UniProtKB:P07275 Source assertion: UniProtKB:P07275 annotates location Mitochondrion inner membrane (SL-0168). 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/3249/comments/0/subcellularLocations/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d` UniProtKB:P07275 Source assertion: UniProtKB:P07275 has the exact SGD cross-reference SGD:S000001079. 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/3249/uniProtKBCrossReferences/0; sha256=95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d`
PUT1 Scer `SGD:S000004132`	has_cofactor UniProtKB reviewed (Swiss-Prot) annotation. UniProt evidence: not specified	FAD(3-) `CHEBI:57692`	UniProtKB:P09368 Source assertion: UniProtKB:P09368 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/3256/comments/0/cofactors/0` UniProtKB:P09368 Source assertion: UniProtKB:P09368 has the exact SGD cross-reference SGD:S000004132. 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/3256/uniProtKBCrossReferences/0`

References

gomodel:YeastPathways_PROUT-PWY GO-CAM L-proline degradation model YeastPathways_PROUT-PWY (source version: Pinned Noctua JSON archive; model date 2026-07-23; member ./YeastPathways_PROUT-PWY.json)
UniProtKB:P09368 Reviewed UniProtKB P09368 location annotations (source version: UniProt release 2026_03)
UniProtKB:P07275 Reviewed UniProtKB P07275 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 2 mapped physical proteins against reviewed S288C UniProt release2026_03 location/function/caution batch SHA256 95f72dcc644358c480e0e59f996cf88533558b5fa4256460a030e0a1eaf9678d. Added 2 independently supported location edges and quarantined 2 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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