identifier: traitmech:000381
label: GAPS6 system
definition: A phage defense system in which an organism possesses a GMT-encoded GAPS6
  locus represented by DefenseFinder as a two-profile model, GAPS6__GAPS6a and GAPS6__GAPS6b,
  and experimentally linked to T7, T4, P1-vir, and lambda-vir protection when expressed
  in E. coli.
definition_source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000209
synonyms:
- synonym_text: GAPS6
  synonym_type: EXACT_SYNONYM
  source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md
- synonym_text: GAPS6__GAPS6a
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
- synonym_text: GAPS6__GAPS6b
  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: 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 four anti-phage defense systems in Gamma-Mobile-Trio
    islands.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md
  snippet: GAPS6 is composed of two proteins, [GAPS6a](https://www.ncbi.nlm.nih.gov/protein/WP_248387294.1/)
    and [GAPS6b](https://www.ncbi.nlm.nih.gov/protein/WP_248387295.1/). These two
    proteins are encoded together in diverse Gram-negative bacteria.
  notes: The DefenseFinder wiki describes GAPS6 as a two-protein system with GAPS6a
    and GAPS6b encoded together.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md
  snippet: GAPS6b is essential for the defense phenotype, however it is not known
    whether GAPS6b could be sufficient.
  notes: The DefenseFinder wiki reports that GAPS6b is essential for GAPS6 defense
    but leaves GAPS6b sufficiency unresolved.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md
  snippet: GAPS6b is composed of TPR repeats at the N-terminus, possibly allowing
    ligand binding and a predicted RNAse domain (PINc, PF08745.14) at the C-terminus.
    PINc domains have been implicated as toxins in bacterial toxin-antitoxin modules
    :ref{doi=10.1093/protein/gzq081}. The PINc domain is required for the anti-phage
    defense activity of GAPS6.
  notes: The DefenseFinder wiki reports that GAPS6b carries TPR repeats and a PINc
    domain required for GAPS6 anti-phage activity.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md
  snippet: The GAPS6 system in *Escherichia coli* (GCF_013372365.1, NZ_CP054227) is
    composed of 2 proteins GAPS6b (WP_096985931.1) GAPS6a (WP_000346990.1)
  notes: The DefenseFinder wiki illustrates a predicted two-protein GAPS6 locus in
    RefSeq assembly GCF_013372365.1 on NZ_CP054227.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md
  snippet: "Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata\
    \ et al., 2023</a>] --> Origin_0\n    Origin_0[Vibrio parahaemolyticus \n<a href='https://ncbi.nlm.nih.gov/protein/WP_248387294.1'>WP_248387294.1</a>,\
    \ <a href='https://ncbi.nlm.nih.gov/protein/WP_248387295.1'>WP_248387295.1</a>]\
    \ --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T7\
    \ & T4 & P1-vir & Lambda-vir"
  notes: The DefenseFinder experimental-validation diagram links Mahata et al. to
    a Vibrio parahaemolyticus GAPS6 source locus expressed in E. coli against T7,
    T4, P1-vir, and Lambda-vir.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: GAPS6 | 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 GAPS6 system to the Mahata
    et al. preprint.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
  snippet: "GAPS6\tGAPS6\t2\t2\tGAPS6__GAPS6a, GAPS6__GAPS6b\t\t\t"
  notes: The DefenseFinder rules table models GAPS6 as a two-profile system requiring
    GAPS6__GAPS6a and GAPS6__GAPS6b.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| GAPS6__GAPS6a                                    | GAPS6__GAPS6a                                    |
    GAPS6                  | Custom                  | 20     |'
  notes: The DefenseFinder HMM inventory records GAPS6__GAPS6a under the GAPS6 system
    namespace.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| GAPS6__GAPS6b                                    | GAPS6__GAPS6b                                    |
    GAPS6                  | Custom                  | 20     |'
  notes: The DefenseFinder HMM inventory records GAPS6__GAPS6b under the GAPS6 system
    namespace.
causal_graphs:
- graph_id: gaps6_locus_restricts_phages
  title: GAPS6 loci protect against T7, T4, P1-vir, and lambda-vir
  description: Conservative system-level sketch linking GAPS6 locus possession to
    protection against T7, T4, P1-vir, and lambda-vir.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures GAPS6 as a named two-profile DefenseFinder phage-defense
    system while leaving natural host breadth, the activity of GAPS6a, GAPS6b sufficiency
    and trigger specificity, and exact GAPS6a/GAPS6b profile-to-protein correspondence
    unresolved.
  nodes:
  - node_id: gaps6_locus
    label: GAPS6 locus
    node_type: GENETIC_ELEMENT
    description: A GMT-encoded phage-defense locus represented by the GAPS6__GAPS6a
      and GAPS6__GAPS6b DefenseFinder profiles.
  - node_id: gaps6_listed_phage_protection
    label: T7, T4, P1-vir, and lambda-vir protection
    node_type: BIOLOGICAL_PROCESS
    description: Protection against T7, T4, P1-vir, and lambda-vir by GAPS6.
  - node_id: gaps6_system_trait
    label: GAPS6 system
    node_type: TRAIT
    grounding: traitmech:000381
    description: Possession of a genome-encoded GAPS6 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: gaps6_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: gaps6_listed_phage_protection
    description: The DefenseFinder wiki links a Vibrio parahaemolyticus GAPS6 locus
      from Mahata et al. to protection against T7, T4, P1-vir, and lambda-vir, and
      DefenseFinder models GAPS6 through two mandatory profiles.
    evidence:
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md
      snippet: GAPS6 is composed of two proteins, [GAPS6a](https://www.ncbi.nlm.nih.gov/protein/WP_248387294.1/)
        and [GAPS6b](https://www.ncbi.nlm.nih.gov/protein/WP_248387295.1/). These
        two proteins are encoded together in diverse Gram-negative bacteria.
      notes: The DefenseFinder wiki describes GAPS6 as a two-protein system with GAPS6a
        and GAPS6b encoded together.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md
      snippet: "Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata\
        \ et al., 2023</a>] --> Origin_0\n    Origin_0[Vibrio parahaemolyticus \n\
        <a href='https://ncbi.nlm.nih.gov/protein/WP_248387294.1'>WP_248387294.1</a>,\
        \ <a href='https://ncbi.nlm.nih.gov/protein/WP_248387295.1'>WP_248387295.1</a>]\
        \ --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ---->\
        \ T7 & T4 & P1-vir & Lambda-vir"
      notes: The DefenseFinder experimental-validation diagram links Mahata et al.
        to a Vibrio parahaemolyticus GAPS6 source locus expressed in E. coli against
        T7, T4, P1-vir, and Lambda-vir.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "GAPS6\tGAPS6\t2\t2\tGAPS6__GAPS6a, GAPS6__GAPS6b\t\t\t"
      notes: The DefenseFinder rules table models GAPS6 as a two-profile system requiring
        GAPS6__GAPS6a and GAPS6__GAPS6b.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| GAPS6__GAPS6a                                    | GAPS6__GAPS6a                                    |
        GAPS6                  | Custom                  | 20     |'
      notes: The DefenseFinder HMM inventory records GAPS6__GAPS6a under the GAPS6
        system namespace.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| GAPS6__GAPS6b                                    | GAPS6__GAPS6b                                    |
        GAPS6                  | Custom                  | 20     |'
      notes: The DefenseFinder HMM inventory records GAPS6__GAPS6b under the GAPS6
        system namespace.
  - subject: gaps6_listed_phage_protection
    predicate: confers
    predicate_id: METPO:2007700
    object: gaps6_system_trait
    description: Protection against T7, T4, P1-vir, and lambda-vir realizes the GAPS6
      system trait.
    evidence:
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md
      snippet: "Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata\
        \ et al., 2023</a>] --> Origin_0\n    Origin_0[Vibrio parahaemolyticus \n\
        <a href='https://ncbi.nlm.nih.gov/protein/WP_248387294.1'>WP_248387294.1</a>,\
        \ <a href='https://ncbi.nlm.nih.gov/protein/WP_248387295.1'>WP_248387295.1</a>]\
        \ --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ---->\
        \ T7 & T4 & P1-vir & Lambda-vir"
      notes: The DefenseFinder experimental-validation diagram links Mahata et al.
        to a Vibrio parahaemolyticus GAPS6 source locus expressed in E. coli against
        T7, T4, P1-vir, and Lambda-vir.
  - subject: gaps6_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: GAPS6 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 four anti-phage defense systems in Gamma-Mobile-Trio
        islands.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: GAPS6 | 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 GAPS6 system to the
        Mahata et al. preprint.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "GAPS6\tGAPS6\t2\t2\tGAPS6__GAPS6a, GAPS6__GAPS6b\t\t\t"
      notes: The DefenseFinder rules table models GAPS6 as a two-profile system requiring
        GAPS6__GAPS6a and GAPS6__GAPS6b.
discussions:
- discussion_id: gaps6-mechanism-gap
  prompt: Resolve GAPS6 natural host breadth, GAPS6a activity, GAPS6b sufficiency
    and trigger specificity, and exact GAPS6a/GAPS6b profile-to-protein correspondence
    before minting narrower GAPS6 mechanism traits.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: Mahata et al. support GAPS6 as a GMT-encoded anti-phage defense system
    that protects E. coli against T7, T4, P1-vir, and lambda-vir when expressed from
    a Vibrio parahaemolyticus locus, and DefenseFinder represents GAPS6 as a two-profile
    system. Natural host breadth, GAPS6a activity, GAPS6b sufficiency, the phage trigger,
    and exact profile-to-protein correspondence remain unresolved.
  evidence:
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md
    snippet: GAPS6 is composed of two proteins, [GAPS6a](https://www.ncbi.nlm.nih.gov/protein/WP_248387294.1/)
      and [GAPS6b](https://www.ncbi.nlm.nih.gov/protein/WP_248387295.1/). These two
      proteins are encoded together in diverse Gram-negative bacteria.
    notes: The DefenseFinder wiki describes GAPS6 as a two-protein system with GAPS6a
      and GAPS6b encoded together.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md
    snippet: GAPS6b is essential for the defense phenotype, however it is not known
      whether GAPS6b could be sufficient.
    notes: The DefenseFinder wiki reports that GAPS6b is essential for GAPS6 defense
      but leaves GAPS6b sufficiency unresolved.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md
    snippet: GAPS6b is composed of TPR repeats at the N-terminus, possibly allowing
      ligand binding and a predicted RNAse domain (PINc, PF08745.14) at the C-terminus.
      PINc domains have been implicated as toxins in bacterial toxin-antitoxin modules
      :ref{doi=10.1093/protein/gzq081}. The PINc domain is required for the anti-phage
      defense activity of GAPS6.
    notes: The DefenseFinder wiki reports that GAPS6b carries TPR repeats and a PINc
      domain required for GAPS6 anti-phage activity.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md
    snippet: "Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata\
      \ et al., 2023</a>] --> Origin_0\n    Origin_0[Vibrio parahaemolyticus \n<a\
      \ href='https://ncbi.nlm.nih.gov/protein/WP_248387294.1'>WP_248387294.1</a>,\
      \ <a href='https://ncbi.nlm.nih.gov/protein/WP_248387295.1'>WP_248387295.1</a>]\
      \ --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ---->\
      \ T7 & T4 & P1-vir & Lambda-vir"
    notes: The DefenseFinder experimental-validation diagram links Mahata et al. to
      a Vibrio parahaemolyticus GAPS6 source locus expressed in E. coli against T7,
      T4, P1-vir, and Lambda-vir.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    snippet: "GAPS6\tGAPS6\t2\t2\tGAPS6__GAPS6a, GAPS6__GAPS6b\t\t\t"
    notes: The DefenseFinder rules table models GAPS6 as a two-profile system requiring
      GAPS6__GAPS6a and GAPS6__GAPS6b.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| GAPS6__GAPS6a                                    | GAPS6__GAPS6a                                    |
      GAPS6                  | Custom                  | 20     |'
    notes: The DefenseFinder HMM inventory records GAPS6__GAPS6a under the GAPS6 system
      namespace.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| GAPS6__GAPS6b                                    | GAPS6__GAPS6b                                    |
      GAPS6                  | Custom                  | 20     |'
    notes: The DefenseFinder HMM inventory records GAPS6__GAPS6b under the GAPS6 system
      namespace.
  attaches_to:
  - causal_graphs#gaps6_locus_restricts_phages
  posed_by: codex
  posed_date: '2026-09-26'
curation_history:
- timestamp: '2026-09-26T11:58:13Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted GAPS6 system as a DOI- and DefenseFinder-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_v258.
  llm_assisted: true
- timestamp: '2026-09-26T11:58:14Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed GAPS6 system canonical_examples and left them empty because the
    current sources support a Vibrio parahaemolyticus accession-level experimental
    validation graph, a DefenseFinder system model, and a RefSeq Escherichia coli
    example, but not a direct native microbial isolate exemplar with experimentally
    verified endogenous GAPS6 activity. No paid research was used.
  llm_assisted: true