identifier: traitmech:000379
label: GAPS4 system
definition: A phage defense system in which an organism possesses a GMT-encoded GAPS4
  locus represented by DefenseFinder as a two-profile model, GAPS4__GAPS4a and GAPS4__GAPS4b,
  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/gaps4.md
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000209
synonyms:
- synonym_text: GAPS4
  synonym_type: EXACT_SYNONYM
  source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
- synonym_text: GAPS4__GAPS4a
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
- synonym_text: GAPS4__GAPS4b
  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/gaps4.md
  snippet: GAPS4 is a two genes system (GAPS4a and GAPS4b). GAPS stands for GMT-encoded
    Anti-Phage System.
  notes: The DefenseFinder wiki describes GAPS4 as a two-gene GMT-encoded anti-phage
    system.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
  snippet: GAPS4 is present in both Gram-positive and Gram-negative GAPS4 activity
    was assessed in *E. coli* and was shown to be active against T4, P1-vir and lambda-vir
    and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}.
  notes: The DefenseFinder wiki summarizes GAPS4 activity against T4, P1-vir, lambda-vir,
    and T7 plaque lysis in an E. coli assay.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
  snippet: GAPS4a is a nuclease containing a domain from the PDDEXK clan (CL0236)
    suggesting that the GAPS4 defense system is acting via DNA degradation. Both genes
    are required for phage defense and were predicted to form a heterodimer. It was
    shown that the system causes host DNA degradation upon infection by lambda-vir
    only, which would suggest that GAPS4 is an abortive infection system :ref{doi=10.1101/2023.03.28.534373}.
  notes: The DefenseFinder wiki summarizes evidence for PDDEXK-domain GAPS4a, dual-gene
    requirement, and lambda-vir-associated host DNA degradation.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
  snippet: The GAPS4 system in *Hafnia alvei* (GCF_902387815.1, NZ_LR699008) is composed
    of 2 proteins GAPS4a (WP_111329122.1) GAPS4b (WP_111329123.1)
  notes: The DefenseFinder wiki illustrates a predicted two-protein GAPS4 locus in
    RefSeq assembly GCF_902387815.1 on NZ_LR699008.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.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_055466293.1'>WP_055466293.1</a>,\
    \ <a href='https://ncbi.nlm.nih.gov/protein/WP_055466294.1'>WP_055466294.1</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 GAPS4 source locus expressed in E. coli against T7,
    T4, P1-vir, and Lambda-vir.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
  snippet: "subgraph Title4[Protects against]\n        T7\n        T4\n        P1-vir\n\
    \        Lambda-vir"
  notes: The DefenseFinder experimental-validation diagram lists T7, T4, P1-vir, and
    Lambda-vir in the GAPS4 protects-against subgraph.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: GAPS4 | 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 GAPS4 system to the Mahata
    et al. preprint.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
  snippet: "GAPS4\tGAPS4\t2\t2\tGAPS4__GAPS4a, GAPS4__GAPS4b\t\t\t"
  notes: The DefenseFinder rules table models GAPS4 as a two-profile system requiring
    GAPS4__GAPS4a and GAPS4__GAPS4b.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| GAPS4__GAPS4a                                    | GAPS4__GAPS4a                                    |
    GAPS4                  | Custom                  | 20     |'
  notes: The DefenseFinder HMM inventory records GAPS4__GAPS4a under the GAPS4 system
    namespace.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| GAPS4__GAPS4b                                    | GAPS4__GAPS4b                                    |
    GAPS4                  | Custom                  | 20     |'
  notes: The DefenseFinder HMM inventory records GAPS4__GAPS4b under the GAPS4 system
    namespace.
causal_graphs:
- graph_id: gaps4_locus_restricts_phages
  title: GAPS4 loci protect against T7, T4, P1-vir, and lambda-vir
  description: Conservative system-level sketch linking GAPS4 locus possession to
    protection against T7, T4, P1-vir, and lambda-vir.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures GAPS4 as a named two-profile DefenseFinder phage-defense
    system while leaving natural host breadth, the lambda-vir trigger of host DNA
    degradation, the abortive-infection mechanism, and exact GAPS4a/GAPS4b profile-to-protein
    correspondence unresolved.
  nodes:
  - node_id: gaps4_locus
    label: GAPS4 locus
    node_type: GENETIC_ELEMENT
    description: A GMT-encoded phage-defense locus represented by the GAPS4a and GAPS4b
      DefenseFinder profiles.
  - node_id: gaps4_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 GAPS4.
  - node_id: gaps4_system_trait
    label: GAPS4 system
    node_type: TRAIT
    grounding: traitmech:000379
    description: Possession of a genome-encoded GAPS4 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: gaps4_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: gaps4_listed_phage_protection
    description: The DefenseFinder wiki links a Vibrio parahaemolyticus GAPS4 locus
      from Mahata et al. to protection against T7, T4, P1-vir, and lambda-vir, and
      DefenseFinder models GAPS4 through GAPS4a and GAPS4b profiles.
    evidence:
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
      snippet: GAPS4 is a two genes system (GAPS4a and GAPS4b). GAPS stands for GMT-encoded
        Anti-Phage System.
      notes: The DefenseFinder wiki describes GAPS4 as a two-gene GMT-encoded anti-phage
        system.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
      snippet: GAPS4 is present in both Gram-positive and Gram-negative GAPS4 activity
        was assessed in *E. coli* and was shown to be active against T4, P1-vir and
        lambda-vir and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}.
      notes: The DefenseFinder wiki summarizes GAPS4 activity against T4, P1-vir,
        lambda-vir, and T7 plaque lysis in an E. coli assay.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.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_055466293.1'>WP_055466293.1</a>,\
        \ <a href='https://ncbi.nlm.nih.gov/protein/WP_055466294.1'>WP_055466294.1</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 GAPS4 source locus expressed in E. coli against
        T7, T4, P1-vir, and Lambda-vir.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
      snippet: "subgraph Title4[Protects against]\n        T7\n        T4\n      \
        \  P1-vir\n        Lambda-vir"
      notes: The DefenseFinder experimental-validation diagram lists T7, T4, P1-vir,
        and Lambda-vir in the GAPS4 protects-against subgraph.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "GAPS4\tGAPS4\t2\t2\tGAPS4__GAPS4a, GAPS4__GAPS4b\t\t\t"
      notes: The DefenseFinder rules table models GAPS4 as a two-profile system requiring
        GAPS4__GAPS4a and GAPS4__GAPS4b.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| GAPS4__GAPS4a                                    | GAPS4__GAPS4a                                    |
        GAPS4                  | Custom                  | 20     |'
      notes: The DefenseFinder HMM inventory records GAPS4__GAPS4a under the GAPS4
        system namespace.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| GAPS4__GAPS4b                                    | GAPS4__GAPS4b                                    |
        GAPS4                  | Custom                  | 20     |'
      notes: The DefenseFinder HMM inventory records GAPS4__GAPS4b under the GAPS4
        system namespace.
  - subject: gaps4_listed_phage_protection
    predicate: confers
    predicate_id: METPO:2007700
    object: gaps4_system_trait
    description: Protection against T7, T4, P1-vir, and lambda-vir realizes the GAPS4
      system trait.
    evidence:
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
      snippet: GAPS4 is present in both Gram-positive and Gram-negative GAPS4 activity
        was assessed in *E. coli* and was shown to be active against T4, P1-vir and
        lambda-vir and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}.
      notes: The DefenseFinder wiki summarizes GAPS4 activity against T4, P1-vir,
        lambda-vir, and T7 plaque lysis in an E. coli assay.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.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_055466293.1'>WP_055466293.1</a>,\
        \ <a href='https://ncbi.nlm.nih.gov/protein/WP_055466294.1'>WP_055466294.1</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 GAPS4 source locus expressed in E. coli against
        T7, T4, P1-vir, and Lambda-vir.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
      snippet: "subgraph Title4[Protects against]\n        T7\n        T4\n      \
        \  P1-vir\n        Lambda-vir"
      notes: The DefenseFinder experimental-validation diagram lists T7, T4, P1-vir,
        and Lambda-vir in the GAPS4 protects-against subgraph.
  - subject: gaps4_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: GAPS4 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: GAPS4 | 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 GAPS4 system to the
        Mahata et al. preprint.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "GAPS4\tGAPS4\t2\t2\tGAPS4__GAPS4a, GAPS4__GAPS4b\t\t\t"
      notes: The DefenseFinder rules table models GAPS4 as a two-profile system requiring
        GAPS4__GAPS4a and GAPS4__GAPS4b.
discussions:
- discussion_id: gaps4-mechanism-gap
  prompt: Resolve GAPS4 natural host breadth, lambda-vir host-DNA-degradation triggers,
    abortive-infection mechanism, and exact GAPS4a/GAPS4b profile-to-protein correspondence
    before minting narrower GAPS4 mechanism traits.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: Mahata et al. support GAPS4 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 GAPS4 as a two-profile
    system. Natural host breadth, the lambda-vir-specific trigger of host DNA degradation,
    the abortive-infection mechanism, and exact profile-to-protein correspondence
    remain unresolved.
  evidence:
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
    snippet: GAPS4 is present in both Gram-positive and Gram-negative GAPS4 activity
      was assessed in *E. coli* and was shown to be active against T4, P1-vir and
      lambda-vir and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}.
    notes: The DefenseFinder wiki summarizes GAPS4 activity against T4, P1-vir, lambda-vir,
      and T7 plaque lysis in an E. coli assay.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.md
    snippet: GAPS4a is a nuclease containing a domain from the PDDEXK clan (CL0236)
      suggesting that the GAPS4 defense system is acting via DNA degradation. Both
      genes are required for phage defense and were predicted to form a heterodimer.
      It was shown that the system causes host DNA degradation upon infection by lambda-vir
      only, which would suggest that GAPS4 is an abortive infection system :ref{doi=10.1101/2023.03.28.534373}.
    notes: The DefenseFinder wiki summarizes evidence for PDDEXK-domain GAPS4a, dual-gene
      requirement, and lambda-vir-associated host DNA degradation.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps4.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_055466293.1'>WP_055466293.1</a>,\
      \ <a href='https://ncbi.nlm.nih.gov/protein/WP_055466294.1'>WP_055466294.1</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 GAPS4 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: "GAPS4\tGAPS4\t2\t2\tGAPS4__GAPS4a, GAPS4__GAPS4b\t\t\t"
    notes: The DefenseFinder rules table models GAPS4 as a two-profile system requiring
      GAPS4__GAPS4a and GAPS4__GAPS4b.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| GAPS4__GAPS4a                                    | GAPS4__GAPS4a                                    |
      GAPS4                  | Custom                  | 20     |'
    notes: The DefenseFinder HMM inventory records GAPS4__GAPS4a under the GAPS4 system
      namespace.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| GAPS4__GAPS4b                                    | GAPS4__GAPS4b                                    |
      GAPS4                  | Custom                  | 20     |'
    notes: The DefenseFinder HMM inventory records GAPS4__GAPS4b under the GAPS4 system
      namespace.
  attaches_to:
  - causal_graphs#gaps4_locus_restricts_phages
  posed_by: codex
  posed_date: '2026-09-26'
curation_history:
- timestamp: '2026-09-26T10:47:13Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted GAPS4 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_v256.
  llm_assisted: true
- timestamp: '2026-09-26T10:47:14Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed GAPS4 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 Hafnia alvei example,
    but not a direct native microbial isolate exemplar with experimentally verified
    endogenous GAPS4 activity. No paid research was used.
  llm_assisted: true