identifier: traitmech:000388
label: PD-T4-3 system
definition: A phage defense system in which an organism possesses a PD-T4-3 locus
  represented by DefenseFinder as a single-profile model, PD-T4-3__PD-T4-3, and experimentally
  linked to T2, T4, and T6 protection when expressed in E. coli.
definition_source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000209
synonyms:
- synonym_text: PD-T4-3
  synonym_type: RELATED_SYNONYM
  source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md
- synonym_text: PD-T4-3__PD-T4-3
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
evidence:
- reference: DOI:10.1038/s41564-022-01219-4
  snippet: Here we developed an experimental selection scheme agnostic to genomic
    context to identify defence systems in 71 diverse E. coli strains. Our results
    unveil 21 conserved defence systems, none of which were previously detected as
    enriched in defence islands.
  notes: Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered
    PD-T4-3 and related conserved phage-defense systems.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md
  snippet: PD-T4-3 is a single gene system isolated during an experimental screen
    of fosmids derived from 71 strains of diverse *E.coli*, and cloned back in a derivative
    of K12.
  notes: The DefenseFinder wiki describes PD-T4-3 as a single-gene system isolated
    from the Vassallo et al. fosmid screen.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md
  snippet: 'The PD-T4-3 is composed of 1 protein: PD-T4-3.'
  notes: The DefenseFinder wiki names PD-T4-3 as a single-protein system.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md
  snippet: 'The PD-T4-3 system in *Morganella morganii* (GCF_018802485.1, NZ_CP064826)
    is composed of 1 protein: PD-T4-3 (WP_214179544.1)'
  notes: The DefenseFinder wiki illustrates a predicted PD-T4-3 locus in RefSeq assembly
    GCF_018802485.1 on NZ_CP064826.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md
  snippet: "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo\
    \ et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO27183.1'>RCO27183.1</a>]\
    \ --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2\
    \ & T4 & T6"
  notes: The DefenseFinder experimental-validation diagram links Vassallo et al. to
    an E. coli PD-T4-3 source locus expressed in E. coli against T2, T4, and T6.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md
  snippet: "subgraph Title4[Protects against]\n        T2\n        T4\n        T6"
  notes: The DefenseFinder experimental-validation diagram lists T2, T4, and T6 in
    the PD-T4-3 protects-against subgraph.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: PD-T4-3 | 10\.1101/2022\.05\.12\.491691 | Mapping the landscape of anti-phage
    defense mechanisms in the E\. coli pangenome
  notes: The DefenseFinder article registry maps the named PD-T4-3 system to the Vassallo
    et al. E. coli pangenome phage-defense preprint.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
  snippet: "PD-T4-3\tPD-T4-3\t1\t1\tPD-T4-3__PD-T4-3\t\t\t"
  notes: The DefenseFinder rules table models PD-T4-3 as a single-profile system requiring
    PD-T4-3__PD-T4-3.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| PD-T4-3__PD-T4-3                                 | PD-T4-3__PD-T4-3                                 |
    PD-T4-3                | Custom                  | 150    |'
  notes: The DefenseFinder HMM inventory records PD-T4-3__PD-T4-3 under the PD-T4-3
    system namespace.
causal_graphs:
- graph_id: pd_t4_3_locus_restricts_t2_t4_and_t6
  title: PD-T4-3 loci restrict T2, T4, and T6
  description: Conservative system-level sketch linking possession of a PD-T4-3 locus
    to protection against T2, T4, and T6.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures PD-T4-3 as a named DefenseFinder phage-defense system
    while leaving natural host breadth, the direct phage trigger, and the effector
    mechanism unresolved.
  nodes:
  - node_id: pd_t4_3_locus
    label: PD-T4-3 locus
    node_type: GENETIC_ELEMENT
    description: A phage-defense locus represented by the PD-T4-3 DefenseFinder profile.
  - node_id: pd_t4_3_listed_phage_protection
    label: T2, T4, and T6 protection
    node_type: BIOLOGICAL_PROCESS
    description: Protection against T2, T4, and T6 by PD-T4-3.
  - node_id: pd_t4_3_system_trait
    label: PD-T4-3 system
    node_type: TRAIT
    grounding: traitmech:000388
    description: Possession of a genome-encoded PD-T4-3 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: pd_t4_3_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: pd_t4_3_listed_phage_protection
    description: The DefenseFinder wiki links a PD-T4-3 locus from Vassallo et al.
      to protection against T2, T4, and T6, and DefenseFinder models PD-T4-3 through
      one mandatory profile.
    evidence:
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md
      snippet: PD-T4-3 is a single gene system isolated during an experimental screen
        of fosmids derived from 71 strains of diverse *E.coli*, and cloned back in
        a derivative of K12.
      notes: The DefenseFinder wiki describes PD-T4-3 as a single-gene system isolated
        from the Vassallo et al. fosmid screen.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md
      snippet: 'The PD-T4-3 is composed of 1 protein: PD-T4-3.'
      notes: The DefenseFinder wiki names PD-T4-3 as a single-protein system.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md
      snippet: "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo\
        \ et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO27183.1'>RCO27183.1</a>]\
        \ --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ---->\
        \ T2 & T4 & T6"
      notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
        to an E. coli PD-T4-3 source locus expressed in E. coli against T2, T4, and
        T6.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md
      snippet: "subgraph Title4[Protects against]\n        T2\n        T4\n      \
        \  T6"
      notes: The DefenseFinder experimental-validation diagram lists T2, T4, and T6
        in the PD-T4-3 protects-against subgraph.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "PD-T4-3\tPD-T4-3\t1\t1\tPD-T4-3__PD-T4-3\t\t\t"
      notes: The DefenseFinder rules table models PD-T4-3 as a single-profile system
        requiring PD-T4-3__PD-T4-3.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| PD-T4-3__PD-T4-3                                 | PD-T4-3__PD-T4-3                                 |
        PD-T4-3                | Custom                  | 150    |'
      notes: The DefenseFinder HMM inventory records PD-T4-3__PD-T4-3 under the PD-T4-3
        system namespace.
  - subject: pd_t4_3_listed_phage_protection
    predicate: confers
    predicate_id: METPO:2007700
    object: pd_t4_3_system_trait
    description: Protection against T2, T4, and T6 realizes the PD-T4-3 system trait.
    evidence:
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md
      snippet: "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo\
        \ et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO27183.1'>RCO27183.1</a>]\
        \ --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ---->\
        \ T2 & T4 & T6"
      notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
        to an E. coli PD-T4-3 source locus expressed in E. coli against T2, T4, and
        T6.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md
      snippet: "subgraph Title4[Protects against]\n        T2\n        T4\n      \
        \  T6"
      notes: The DefenseFinder experimental-validation diagram lists T2, T4, and T6
        in the PD-T4-3 protects-against subgraph.
  - subject: pd_t4_3_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: PD-T4-3 system possession is a phage-defense-system trait.
    evidence:
    - reference: DOI:10.1038/s41564-022-01219-4
      snippet: Here we developed an experimental selection scheme agnostic to genomic
        context to identify defence systems in 71 diverse E. coli strains. Our results
        unveil 21 conserved defence systems, none of which were previously detected
        as enriched in defence islands.
      notes: Vassallo et al. developed the agnostic E. coli pangenome selection that
        uncovered PD-T4-3 and related conserved phage-defense systems.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: PD-T4-3 | 10\.1101/2022\.05\.12\.491691 | Mapping the landscape of
        anti-phage defense mechanisms in the E\. coli pangenome
      notes: The DefenseFinder article registry maps the named PD-T4-3 system to the
        Vassallo et al. E. coli pangenome phage-defense preprint.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "PD-T4-3\tPD-T4-3\t1\t1\tPD-T4-3__PD-T4-3\t\t\t"
      notes: The DefenseFinder rules table models PD-T4-3 as a single-profile system
        requiring PD-T4-3__PD-T4-3.
discussions:
- discussion_id: pd-t4-3-mechanism-gap
  prompt: Resolve PD-T4-3 natural host breadth, direct phage trigger, and effector
    mechanism before minting narrower PD-T4-3 mechanism traits.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: Vassallo et al. support PD-T4-3 as one of the conserved systems from
    an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the
    source locus to protection against T2, T4, and T6, and DefenseFinder represents
    the system with one mandatory profile. Natural host breadth, the direct phage
    trigger, and effector logic remain unresolved.
  evidence:
  - reference: DOI:10.1038/s41564-022-01219-4
    snippet: Here we developed an experimental selection scheme agnostic to genomic
      context to identify defence systems in 71 diverse E. coli strains. Our results
      unveil 21 conserved defence systems, none of which were previously detected
      as enriched in defence islands.
    notes: Vassallo et al. developed the agnostic E. coli pangenome selection that
      uncovered PD-T4-3 and related conserved phage-defense systems.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md
    snippet: PD-T4-3 is a single gene system isolated during an experimental screen
      of fosmids derived from 71 strains of diverse *E.coli*, and cloned back in a
      derivative of K12.
    notes: The DefenseFinder wiki describes PD-T4-3 as a single-gene system isolated
      from the Vassallo et al. fosmid screen.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md
    snippet: 'The PD-T4-3 is composed of 1 protein: PD-T4-3.'
    notes: The DefenseFinder wiki names PD-T4-3 as a single-protein system.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-3.md
    snippet: "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo\
      \ et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO27183.1'>RCO27183.1</a>]\
      \ --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ---->\
      \ T2 & T4 & T6"
    notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
      to an E. coli PD-T4-3 source locus expressed in E. coli against T2, T4, and
      T6.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    snippet: "PD-T4-3\tPD-T4-3\t1\t1\tPD-T4-3__PD-T4-3\t\t\t"
    notes: The DefenseFinder rules table models PD-T4-3 as a single-profile system
      requiring PD-T4-3__PD-T4-3.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| PD-T4-3__PD-T4-3                                 | PD-T4-3__PD-T4-3                                 |
      PD-T4-3                | Custom                  | 150    |'
    notes: The DefenseFinder HMM inventory records PD-T4-3__PD-T4-3 under the PD-T4-3
      system namespace.
  attaches_to:
  - causal_graphs#pd_t4_3_locus_restricts_t2_t4_and_t6
  posed_by: codex
  posed_date: '2026-09-26'
curation_history:
- timestamp: '2026-09-26T16:05:00Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted PD-T4-3 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_v265.
  llm_assisted: true
- timestamp: '2026-09-26T16:05:01Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed PD-T4-3 system canonical_examples and left them empty because
    the current sources support an E. coli accession-level experimental validation
    graph, a DefenseFinder system model, and a RefSeq Morganella morganii example,
    but not a direct native microbial isolate exemplar with experimentally verified
    endogenous PD-T4-3 activity. No paid research was used.
  llm_assisted: true