identifier: METPO:1000804
label: Substrate-level phosphorylation
definition: A metabolism in which ATP is formed directly by transfer of a phosphoryl
  group from a substrate to ADP.
definition_source: DOI:10.1111/1751-7915.13746
trait_category: METABOLISM
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000060
evidence:
- reference: DOI:10.1111/1751-7915.13746
  snippet: Substrate-level phosphorylation is one of the main sources
  notes: Review supports SLP as microbial energy conservation in fermentative metabolism.
- reference: DOI:10.1128/MMBR.69.1.12-50.2005
  snippet: phosphotransacetylase [PTA], acetate kinase [ACK]
  notes: Review supports acetate kinase and phosphotransacetylase as central acetate-switch
    enzymes.
canonical_examples:
- taxon_id: NCBITaxon:1314
  taxon_label: Streptococcus pyogenes
  note: "ATP via glycolytic substrate-level phosphorylation"
  reference: PMID:27442496
- taxon_id: NCBITaxon:1488
  taxon_label: Clostridium acetobutylicum
  note: "fermentative substrate-level phosphorylation"
  reference: PMID:11466286
causal_graphs:
- graph_id: substrate_level_phosphorylation_direct_atp
  title: Substrate-level phosphorylation direct ATP formation
  description: DOI-backed graph connecting high-energy phosphorylated intermediates,
    kinase reactions, ADP phosphorylation, and ATP formation.
  nodes:
  - node_id: substrate_level_phosphorylation_trait
    label: Substrate-level phosphorylation
    node_type: TRAIT
    grounding: METPO:1000804
    description: ATP generation by direct phosphoryl transfer from a metabolic intermediate.
  - node_id: fermentative_condition
    label: fermentative condition
    node_type: ENVIRONMENTAL_FACTOR
    description: Metabolic context where SLP is a major ATP source.
  - node_id: high_energy_phosphorylated_intermediate
    label: high-energy phosphorylated intermediate
    node_type: CHEMICAL
    description: Metabolite carrying a transferable phosphoryl group.
  - node_id: adp
    label: ADP
    node_type: CHEMICAL
    description: Phosphoryl acceptor converted to ATP.
    grounding: CHEBI:16761
  - node_id: kinase_reaction
    label: kinase reaction
    node_type: MOLECULAR_FUNCTION
    description: Enzymatic phosphoryl transfer to ADP.
    grounding: GO:0016301
  - node_id: atp
    label: ATP
    node_type: CHEMICAL
    grounding: CHEBI:30616
    description: Energy carrier produced by SLP.
  - node_id: acetyl_phosphate
    label: acetyl phosphate
    node_type: CHEMICAL
    description: High-energy intermediate in acetate dissimilation.
    grounding: CHEBI:15350
  - node_id: acetate_kinase
    label: acetate kinase
    node_type: GENE_OR_PROTEIN
    description: Enzyme that converts acetyl phosphate and ADP to acetate and ATP.
    grounding: UniProtKB:A0A081KVG3
  - node_id: acetate
    label: acetate
    node_type: CHEMICAL
    grounding: CHEBI:30089
    description: Product of the acetate kinase SLP reaction.
  - node_id: anaerobiosis
    label: anaerobiosis / low oxygen
    node_type: ENVIRONMENTAL_FACTOR
    description: Absence of oxygen enabling anaerobic catabolism such as fermentation.
  - node_id: fermentation
    label: fermentation
    node_type: BIOLOGICAL_PROCESS
    description: Anaerobic catabolism in which ATP is produced by substrate-level
      phosphorylation.
    grounding: GO:0006113
  - node_id: acka_pta_pathway
    label: AckA-Pta pathway
    node_type: PATHWAY
    description: Phosphotransacetylase/acetate kinase reaction set that produces ATP
      via SLP.
  - node_id: carbamate_kinase_arginine_deiminase
    label: carbamate kinase (arginine deiminase pathway)
    node_type: GENE_OR_PROTEIN
    description: Carbamate kinase of the arginine deiminase pathway that generates
      ATP by SLP.
  edges:
  - subject: substrate_level_phosphorylation_trait
    predicate: occurs in
    object: fermentative_condition
    description: SLP is a major ATP source in fermentative energy metabolism.
    evidence:
    - reference: DOI:10.1111/1751-7915.13746
      snippet: main sources of energy under fermentative conditions
      notes: Supports fermentative context for SLP.
    predicate_id: biolink:occurs_in
  - subject: high_energy_phosphorylated_intermediate
    predicate: donates phosphoryl group to
    object: adp
    description: SLP transfers phosphoryl groups from metabolic intermediates to ADP.
    evidence:
    - reference: DOI:10.1111/1751-7915.13746
      snippet: transferring a phosphate group to ADP
      notes: Supports direct phosphoryl transfer to ADP.
  - subject: kinase_reaction
    predicate: produces
    object: atp
    description: Kinase reactions convert phosphorylated intermediates and ADP to
      ATP.
    evidence:
    - reference: DOI:10.1111/1751-7915.13746
      snippet: kinase-catalysed reactions can be applied for SLP
      notes: Supports kinase-mediated ATP formation.
    predicate_id: METPO:2000202
  - subject: acetyl_phosphate
    predicate: substrate for
    object: acetate_kinase
    description: Acetyl phosphate is converted by acetate kinase during acetate dissimilation.
    evidence:
    - reference: DOI:10.1128/MMBR.69.1.12-50.2005
      snippet: Acetyl phosphate ... high-energy intermediate
      notes: Supports acetyl phosphate as the high-energy acetate-switch intermediate.
  - subject: acetate_kinase
    predicate: produces
    object: acetate
    description: Acetate kinase forms acetate from acetyl phosphate.
    evidence:
    - reference: DOI:10.1128/MMBR.69.1.12-50.2005
      snippet: phosphotransacetylase [PTA], acetate kinase [ACK]
      notes: Supports acetate kinase as a central acetate-switch component.
    predicate_id: METPO:2000202
  - subject: acetate_kinase
    predicate: produces
    object: atp
    description: Acetate kinase contributes ATP formation through substrate-level
      phosphorylation.
    evidence:
    - reference: DOI:10.1111/1751-7915.13746
      snippet: acetyl-phosphate to acetate
      notes: Review lists acetyl-phosphate to acetate among SLP energy-conserving
        reactions.
    predicate_id: METPO:2000202
  - subject: anaerobiosis
    predicate: enables
    object: fermentation
    description: Absence of oxygen enables fermentative metabolism.
    evidence:
    - reference: DOI:10.1093/femsre/fuae016
      notes: Fermentation is a type of metabolism carried out by organisms in environments
        without oxygen.
    predicate_id: RO:0002327
  - subject: fermentation
    predicate: produces ATP via
    object: substrate_level_phosphorylation_trait
    description: In fermentation, ATP is produced by substrate-level phosphorylation.
    evidence:
    - reference: DOI:10.1093/femsre/fuae016
      notes: ATP is produced by substrate-level phosphorylation; strong definitional
        edge.
  - subject: acka_pta_pathway
    predicate: allows ATP production via
    object: substrate_level_phosphorylation_trait
    description: The AckA-Pta reaction set allows ATP production via substrate-level
      phosphorylation.
    evidence:
    - reference: DOI:10.1042/ETLS20220092
      notes: AckA-Pta, a set of reactions that allows ATP production via substrate-level
        phosphorylation.
  - subject: carbamate_kinase_arginine_deiminase
    predicate: generates ATP via
    object: substrate_level_phosphorylation_trait
    description: Carbamate kinase in the arginine deiminase pathway is an additional
      SLP route for ATP production.
    evidence:
    - reference: DOI:10.1039/d4cb00099d
      notes: The carbamate kinase reaction has been reported to be effective for ATP
        production in several acetogens.
curation_history:
- timestamp: '2026-05-05T01:35:46.913184+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-08T00:00:00-07:00'
  curator: codex
  action: ADDED_CAUSAL_GRAPH
  changes: Added DOI-backed causal graph for direct phosphoryl transfer to ADP and
    acetate kinase-linked ATP formation.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:30Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000202×3).
  llm_assisted: true
- timestamp: '2026-05-20T05:49:24Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:occurs_in×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:38:00Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0016301×1).
  llm_assisted: true
- timestamp: '2026-05-24T05:05:14Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A081KVG3×1).
  llm_assisted: true
- timestamp: '2026-06-14T05:51:46Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:16761×1, CHEBI:15350×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 4 evidence-backed generic edges (4 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:12Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:21:19Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0006113×1).
  llm_assisted: true