id: gomodel:68b0f0d000008746
title: nitrogen utilization (GO:0019740) (ammonia, proline,  D-alanine, L-alanine)
taxon: NCBITaxon:4896
status: production
date_modified: '2026-04-07'
comments:
- need terms "nitrogen utilization, ammonium nitrogen source', "nitrogen utilization,  proline
  nitrogen source' (different pathways), unless a better way can be identified.
activities:
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    - term: ECO:0000255
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      with_objects:
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      provenances:
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        date: '2025-11-29'
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      date: '2025-09-23'
      provided_by:
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    term: PomBase:SPBC1683.13c
  molecular_function:
    type: MolecularFunctionAssociation
    term: GO:0000981
  occurs_in:
    type: CellularAnatomicalEntityAssociation
    evidence: []
    provenances:
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      date: '2025-09-23'
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    term: GO:0000785
  part_of:
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    evidence:
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      reference: PMID:20404084
      provenances:
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    term: GO:0060261
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          date: '2025-09-23'
          provided_by:
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        term: GO:0071235
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      with_objects:
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    predicate: RO:0002409
    downstream_activity: gomodel:68b0f0d000008746/68b0f0d000008899
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  enabled_by:
    type: EnabledByProteinComplexAssociation
    evidence: []
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      date: '2025-09-23'
      provided_by:
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    term: GO:0016591
  molecular_function:
    type: MolecularFunctionAssociation
    term: GO:0003968
  occurs_in:
    type: CellularAnatomicalEntityAssociation
    evidence: []
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    term: GO:0006366
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    term: GO:0005829
- id: gomodel:68b0f0d000008746/68b0f0d000009244
  term: CHEBI:57416
  located_in:
    type: CellularAnatomicalEntityAssociation
    evidence: []
    provenances:
    - contributor:
      - https://orcid.org/0000-0001-6330-7526
      date: '2025-09-24'
      provided_by:
      - http://www.pombase.org
    term: GO:0005829
- id: gomodel:68b0f0d000008746/68b0f0d000009323
  term: CHEBI:15361
  located_in:
    type: CellularAnatomicalEntityAssociation
    evidence: []
    provenances:
    - contributor:
      - https://orcid.org/0000-0001-6330-7526
      date: '2025-09-24'
      provided_by:
      - http://www.pombase.org
    term: GO:0005777
- id: gomodel:68b0f0d000008746/68b0f0d000008908
  term: CHEBI:60039
  located_in:
    type: CellularAnatomicalEntityAssociation
    evidence: []
    provenances:
    - contributor:
      - https://orcid.org/0000-0001-6330-7526
      date: '2025-09-23'
      provided_by:
      - http://www.pombase.org
    term: GO:0005576
- id: gomodel:68b0f0d000008746/68b0f0d000009310
  term: CHEBI:57972
  located_in:
    type: CellularAnatomicalEntityAssociation
    evidence: []
    provenances:
    - contributor:
      - https://orcid.org/0000-0001-6330-7526
      date: '2025-09-24'
      provided_by:
      - http://www.pombase.org
    term: GO:0005829
- id: gomodel:68b0f0d000008746/68b0f0d000009298
  term: CHEBI:57416
  located_in:
    type: CellularAnatomicalEntityAssociation
    evidence: []
    provenances:
    - contributor:
      - https://orcid.org/0000-0001-6330-7526
      date: '2025-09-24'
      provided_by:
      - http://www.pombase.org
    term: GO:0005777
- id: gomodel:68b0f0d000008746/68b0f0d000009341
  term: CHEBI:28938
  located_in:
    type: CellularAnatomicalEntityAssociation
    evidence: []
    provenances:
    - contributor:
      - https://orcid.org/0000-0001-6330-7526
      date: '2025-09-24'
      provided_by:
      - http://www.pombase.org
    term: GO:0005777
- id: gomodel:68b0f0d000008746/68b0f0d000009242
  term: CHEBI:57416
  located_in:
    type: CellularAnatomicalEntityAssociation
    evidence: []
    provenances:
    - contributor:
      - https://orcid.org/0000-0001-6330-7526
      date: '2025-09-24'
      provided_by:
      - http://www.pombase.org
    term: GO:0005576
objects:
- id: GO:0004674
  label: protein serine/threonine kinase activity
  type: gocam:Object
- id: PomBase:SPCC1020.10
  label: oca2 Spom
  type: gocam:Object
- id: GO:0000122
  label: negative regulation of transcription by RNA polymerase II
  type: gocam:Object
- id: GO:0006808
  label: regulation of nitrogen utilization
  type: gocam:Object
- id: GO:0000785
  label: chromatin
  type: gocam:Object
- id: ECO:0000314
  label: direct assay evidence used in manual assertion
  type: gocam:Object
- id: ECO:0000315
  label: mutant phenotype evidence used in manual assertion
  type: gocam:Object
- id: ECO:0000353
  label: physical interaction evidence used in manual assertion
  type: gocam:Object
- id: GO:0140937
  label: histone H4K12 deacetylase activity, hydrolytic mechanism
  type: gocam:Object
- id: GO:0033698
  label: Rpd3L complex
  type: gocam:Object
- id: GO:0045815
  label: transcription initiation-coupled chromatin remodeling
  type: gocam:Object
- id: ECO:0000318
  label: biological aspect of ancestor evidence used in manual assertion
  type: gocam:Object
- id: GO:0003968
  label: RNA-directed RNA polymerase activity
  type: gocam:Object
- id: GO:0016591
  label: RNA polymerase II, holoenzyme
  type: gocam:Object
- id: GO:0006366
  label: transcription by RNA polymerase II
  type: gocam:Object
- id: GO:0071235
  label: cellular response to proline
  type: gocam:Object
- id: GO:0071242
  label: cellular response to ammonium ion
  type: gocam:Object
- id: GO:0000981
  label: DNA-binding transcription factor activity, RNA polymerase II-specific
  type: gocam:Object
- id: PomBase:SPBC1683.13c
  label: cha4 Spom
  type: gocam:Object
- id: GO:0060261
  label: positive regulation of transcription initiation by RNA polymerase II
  type: gocam:Object
- id: ECO:0000255
  label: match to sequence model evidence used in manual assertion
  type: gocam:Object
- id: PomBase:SPAC29A4.18
  label: prw1 Spom
  type: gocam:Object
- id: PomBase:SPBC36.05c
  label: clr6 Spom
  type: gocam:Object
- id: GO:0015171
  label: amino acid transmembrane transporter activity
  type: gocam:Object
- id: PomBase:SPAP7G5.06
  label: per1 Spom
  type: gocam:Object
- id: GO:0035524
  label: proline transmembrane transport
  type: gocam:Object
- id: GO:0005886
  label: plasma membrane
  type: gocam:Object
- id: ECO:0000270
  label: expression pattern evidence used in manual assertion
  type: gocam:Object
- id: ECO:0000266
  label: sequence orthology evidence used in manual assertion
  type: gocam:Object
- id: GO:0015193
  label: L-proline transmembrane transporter activity
  type: gocam:Object
- id: PomBase:SPAC869.10c
  label: put4 Spom
  type: gocam:Object
- id: GO:1905647
  label: proline import across plasma membrane
  type: gocam:Object
- id: ECO:0000303
  label: author statement without traceable support used in manual assertion
  type: gocam:Object
- id: CHEBI:60039
  label: L-proline zwitterion
  type: gocam:Object
- id: GO:0005576
  label: extracellular region
  type: gocam:Object
- id: GO:0005829
  label: cytosol
  type: gocam:Object
- id: GO:0019740
  label: nitrogen utilization
  type: gocam:Object
- id: GO:0042944
  label: D-alanine transmembrane transporter activity
  type: gocam:Object
- id: CHEBI:36080
  label: protein
  type: gocam:Object
- id: GO:0042941
  label: D-alanine transmembrane transport
  type: gocam:Object
- id: CHEBI:57416
  label: D-alanine zwitterion
  type: gocam:Object
- id: GO:0008784
  label: alanine racemase activity
  type: gocam:Object
- id: PomBase:SPCC965.08c
  label: alr1 Spom
  type: gocam:Object
- id: GO:0055130
  label: D-alanine catabolic process
  type: gocam:Object
- id: GO:0003884
  label: D-amino-acid oxidase activity
  type: gocam:Object
- id: PomBase:SPCC1450.07c
  label: dao1 Spom
  type: gocam:Object
- id: GO:0019478
  label: D-amino acid catabolic process
  type: gocam:Object
- id: GO:0005737
  label: cytoplasm
  type: gocam:Object
- id: GO:0005778
  label: peroxisomal membrane
  type: gocam:Object
- id: GO:0005777
  label: peroxisome
  type: gocam:Object
- id: CHEBI:57972
  label: L-alanine zwitterion
  type: gocam:Object
- id: CHEBI:15361
  label: pyruvate
  type: gocam:Object
- id: CHEBI:28938
  label: ammonium
  type: gocam:Object
- id: PomBase:SPBC359.02
  label: alr2 Spom
  type: gocam:Object
- id: ECO:0000250
  label: sequence similarity evidence used in manual assertion
  type: gocam:Object
provenances:
- contributor:
  - https://orcid.org/0000-0001-6330-7526
  date: '2026-04-07'
  provided_by:
  - http://www.pombase.org
