identifier: traitmech:000371
label: GAPS1 system
definition: A phage defense system in which an organism possesses a Gamma-Mobile-Trio
  island-associated GAPS1 locus that can be triggered by a phage capsid protein to
  induce cell dormancy.
definition_source: DOI:10.1038/s41564-024-01840-5
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000209
synonyms:
- synonym_text: GAPS1
  synonym_type: EXACT_SYNONYM
  source: DOI:10.1038/s41564-024-01840-5
- synonym_text: GAPS1__GAPS1
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
evidence:
- reference: DOI:10.1038/s41564-024-01840-5
  snippet: GMT islands' cargoes contain various anti-phage defence systems
  notes: Mahata et al. identify GMT islands as carriers of anti-phage defense-system
    cargo.
- reference: DOI:10.1038/s41564-024-01840-5
  snippet: We reveal four anti-phage defence systems encoded within GMT islands and
    further characterize one system, GAPS1, showing it is triggered by a phage capsid
    protein to induce cell dormancy
  notes: Mahata et al. identify GAPS1 as one of four GMT-island anti-phage defense
    systems and connect GAPS1 activation to phage-capsid-protein-triggered cell dormancy.
- reference: DOI:10.1101/2023.03.28.534373
  snippet: Gamma-Mobile-Trio systems define a new class of mobile elements rich in
    bacterial defensive and offensive tools
  notes: The bioRxiv version of Mahata et al. is the DOI cited in DefenseFinder's
    GAPS1 article-registry row.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: GAPS1 | 10\.1101/2023\.03\.28\.534373 | Gamma-Mobile-Trio systems define
    a new class of mobile elements rich in bacterial defensive and offensive tools
  notes: The DefenseFinder article registry maps the named GAPS1 system to the Mahata
    et al. preprint.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
  snippet: "GAPS1\tGAPS1\t1\t1\tGAPS1__GAPS1\t\t\t"
  notes: The DefenseFinder rules table models GAPS1 as a single-profile system requiring
    GAPS1__GAPS1.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| GAPS1__GAPS1                                     | GAPS1__GAPS1                                     |
    GAPS1                  | Custom                  | 100    |'
  notes: The DefenseFinder HMM inventory records GAPS1__GAPS1 under the GAPS1 model
    namespace.
causal_graphs:
- graph_id: gaps1_capsid_triggered_dormancy
  title: GAPS1 loci induce cell dormancy during phage defense
  description: Conservative system-level sketch connecting the named GAPS1 locus model
    and the phage-capsid-protein-triggered dormancy phenotype to the GAPS1 system
    trait.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures GAPS1 as a named GMT-island anti-phage defense system
    represented in DefenseFinder by a single GAPS1__GAPS1 profile while leaving its
    universal host range, the molecular activity of the GAPS1 component, and the exact
    capsid-protein trigger unresolved.
  nodes:
  - node_id: gaps1_locus
    label: GAPS1 locus
    node_type: GENETIC_ELEMENT
    description: A GMT-island-associated GAPS1 phage-defense locus represented by
      the custom DefenseFinder GAPS1__GAPS1 profile.
  - node_id: gaps1_cell_dormancy
    label: GAPS1-induced cell dormancy
    node_type: STATE
    description: Cellular dormancy induced by a GAPS1 system after recognition of
      a phage capsid-protein trigger.
  - node_id: gaps1_system_trait
    label: GAPS1 system
    node_type: TRAIT
    grounding: traitmech:000371
    description: Possession of a genome-encoded GAPS1 phage-defense system.
  - node_id: phage_defense_system
    label: phage defense system
    node_type: TRAIT
    grounding: traitmech:000209
    description: Possession of one or more genome-encoded immune systems that inhibit
      bacteriophage infection.
  edges:
  - subject: gaps1_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: gaps1_system_trait
    description: DefenseFinder records GAPS1 as a named system and models it as a
      single-profile GAPS1__GAPS1 rule.
    evidence:
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: GAPS1 | 10\.1101/2023\.03\.28\.534373 | Gamma-Mobile-Trio systems define
        a new class of mobile elements rich in bacterial defensive and offensive tools
      notes: The DefenseFinder article registry maps the named GAPS1 system to the
        Mahata et al. preprint.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "GAPS1\tGAPS1\t1\t1\tGAPS1__GAPS1\t\t\t"
      notes: The DefenseFinder rules table models GAPS1 as a single-profile system
        requiring GAPS1__GAPS1.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| GAPS1__GAPS1                                     | GAPS1__GAPS1                                     |
        GAPS1                  | Custom                  | 100    |'
      notes: The DefenseFinder HMM inventory records GAPS1__GAPS1 under the GAPS1
        model namespace.
  - subject: gaps1_cell_dormancy
    predicate: confers
    predicate_id: METPO:2007700
    object: gaps1_system_trait
    description: Phage-capsid-protein-triggered cell dormancy is the characterized
      output that realizes the GAPS1 system trait.
    evidence:
    - reference: DOI:10.1038/s41564-024-01840-5
      snippet: We reveal four anti-phage defence systems encoded within GMT islands
        and further characterize one system, GAPS1, showing it is triggered by a phage
        capsid protein to induce cell dormancy
      notes: Mahata et al. identify GAPS1 as one of four GMT-island anti-phage defense
        systems and connect GAPS1 activation to phage-capsid-protein-triggered cell
        dormancy.
  - subject: gaps1_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: GAPS1 system possession is a phage-defense-system trait.
    evidence:
    - reference: DOI:10.1038/s41564-024-01840-5
      snippet: We reveal four anti-phage defence systems encoded within GMT islands
        and further characterize one system, GAPS1, showing it is triggered by a phage
        capsid protein to induce cell dormancy
      notes: Mahata et al. identify GAPS1 as one of four GMT-island anti-phage defense
        systems and connect GAPS1 activation to phage-capsid-protein-triggered cell
        dormancy.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: GAPS1 | 10\.1101/2023\.03\.28\.534373 | Gamma-Mobile-Trio systems define
        a new class of mobile elements rich in bacterial defensive and offensive tools
      notes: The DefenseFinder article registry maps the named GAPS1 system to the
        Mahata et al. preprint.
discussions:
- discussion_id: gaps1-trigger-sibling-gap
  prompt: Resolve GAPS1 component activity and natural-host exemplars before minting
    narrower GAPS traits.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: Mahata et al. support GAPS1 as one GMT-island anti-phage defense system
    triggered by a phage capsid protein to induce cell dormancy, and DefenseFinder
    represents GAPS1 as one GAPS1__GAPS1 profile. This first system-level record does
    not assert the GAPS1 component's molecular activity, the capsid trigger identity,
    or a universal GAPS1 host range.
  evidence:
  - reference: DOI:10.1038/s41564-024-01840-5
    snippet: We reveal four anti-phage defence systems encoded within GMT islands
      and further characterize one system, GAPS1, showing it is triggered by a phage
      capsid protein to induce cell dormancy
    notes: Mahata et al. identify GAPS1 as one of four GMT-island anti-phage defense
      systems and connect GAPS1 activation to phage-capsid-protein-triggered cell
      dormancy.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    snippet: "GAPS1\tGAPS1\t1\t1\tGAPS1__GAPS1\t\t\t"
    notes: The DefenseFinder rules table models GAPS1 as a single-profile system requiring
      GAPS1__GAPS1.
  attaches_to:
  - causal_graphs#gaps1_capsid_triggered_dormancy
  posed_by: codex
  posed_date: '2026-09-24'
curation_history:
- timestamp: '2026-09-25T04:19:09Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted GAPS1 system as a DOI-backed GENOMICS TraitRecord under phage defense
    system after an ignored-and-hidden duplicate review found no exact live TraitMech,
    METPO, history, or prior proposal record; the replacement placeholder is reserved
    in proposals/metpo_traitmech_v248.
  llm_assisted: true
- timestamp: '2026-09-26T11:02:35Z'
  curator: codex
  action: UPDATED_DISCUSSION
  changes: 'Resolved GitHub issue #1274 by narrowing stale GAPS1 sibling-boundary
    references to GAPS2/GAPS6 after GAPS4 was split into its own TraitRecord.'
  llm_assisted: true
- timestamp: '2026-09-26T11:26:43Z'
  curator: codex
  action: UPDATED_DISCUSSION
  changes: Narrowed stale GAPS1 sibling-boundary references to GAPS6 after GAPS2 was
    split into its own TraitRecord.
  llm_assisted: true
- timestamp: '2026-09-26T11:58:15Z'
  curator: codex
  action: UPDATED_DISCUSSION
  changes: Resolved the remaining stale GAPS1 sibling-boundary reference after GAPS6
    was split into its own TraitRecord.
  llm_assisted: true