identifier: traitmech:000389
label: PD-T4-4 system
definition: A phage defense system in which an organism possesses a PD-T4-4 locus
  represented by DefenseFinder as a two-profile model requiring PD-T4-4__PD-T4-4_A
  and PD-T4-4__PD-T4-4_B, and experimentally linked to T2, T4, T6, and SECphi17 protection
  when expressed in E. coli.
definition_source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000209
synonyms:
- synonym_text: PD-T4-4
  synonym_type: RELATED_SYNONYM
  source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md
- synonym_text: PD-T4-4__PD-T4-4_A
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
- synonym_text: PD-T4-4__PD-T4-4_B
  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-T4-4 and related conserved phage-defense systems.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md
  snippet: PD-T4-4 is a defense system composed of two proteins, a P-loop NTPase and
    a nuclease, that is most likely protecting the bacterial population through abortive
    infection. It was identified from an ICE in an *E. coli* genome.
  notes: The DefenseFinder wiki describes PD-T4-4 as a two-protein system from an
    E. coli integrative and conjugative element.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md
  snippet: 'The PD-T4-4 is composed of 2 proteins: PD-T4-4_A and PD-T4-4_B.'
  notes: The DefenseFinder wiki names PD-T4-4 as a two-protein system with PD-T4-4_A
    and PD-T4-4_B components.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md
  snippet: The PD-T4-4 system in *Thiothrix subterranea* (GCF_016772315.1, NZ_CP053482)
    is composed of 2 proteins PD-T4-4_A (WP_202716711.1) PD-T4-4_B (WP_202716712.1)
  notes: The DefenseFinder wiki illustrates a predicted two-protein PD-T4-4 locus
    in RefSeq assembly GCF_016772315.1 on NZ_CP053482.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.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/RCO57999.1'>RCO57999.1</a>,\
    \ <a href='https://ncbi.nlm.nih.gov/protein/RCO57988.1'>RCO57988.1</a>] --> Expressed_0[Escherichia\
    \ coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi17"
  notes: The DefenseFinder experimental-validation diagram links Vassallo et al. to
    an E. coli PD-T4-4 source locus expressed in E. coli against T2, T4, T6, and SECphi17.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md
  snippet: "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n\
    \        SECphi17"
  notes: The DefenseFinder experimental-validation diagram lists T2, T4, T6, and SECphi17
    in the PD-T4-4 protects-against subgraph.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: PD-T4-4 | 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-T4-4 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-T4-4\tPD-T4-4\t2\t2\tPD-T4-4__PD-T4-4_A, PD-T4-4__PD-T4-4_B\t\t\t"
  notes: The DefenseFinder rules table models PD-T4-4 as a two-profile system requiring
    PD-T4-4__PD-T4-4_A and PD-T4-4__PD-T4-4_B.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| PD-T4-4__PD-T4-4_A                               | PD-T4-4__PD-T4-4_A                               |
    PD-T4-4                | Custom                  | 75     |'
  notes: The DefenseFinder HMM inventory records PD-T4-4__PD-T4-4_A under the PD-T4-4
    system namespace.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| PD-T4-4__PD-T4-4_B                               | PD-T4-4__PD-T4-4_B                               |
    PD-T4-4                | Custom                  | 25     |'
  notes: The DefenseFinder HMM inventory records PD-T4-4__PD-T4-4_B under the PD-T4-4
    system namespace.
causal_graphs:
- graph_id: pd_t4_4_locus_restricts_t2_t4_t6_and_secphi17
  title: PD-T4-4 loci restrict T2, T4, T6, and SECphi17
  description: Conservative system-level sketch linking possession of a PD-T4-4 locus
    to protection against T2, T4, T6, and SECphi17.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures PD-T4-4 as a named DefenseFinder phage-defense system
    while leaving natural host breadth, the direct phage trigger, and the hinted abortive-infection
    effector mechanism unmodeled until direct mechanism evidence is available.
  nodes:
  - node_id: pd_t4_4_locus
    label: PD-T4-4 locus
    node_type: GENETIC_ELEMENT
    description: A phage-defense locus represented by the two PD-T4-4 DefenseFinder
      profiles.
  - node_id: pd_t4_4_listed_phage_protection
    label: T2, T4, T6, and SECphi17 protection
    node_type: BIOLOGICAL_PROCESS
    description: Protection against T2, T4, T6, and SECphi17 by PD-T4-4.
  - node_id: pd_t4_4_system_trait
    label: PD-T4-4 system
    node_type: TRAIT
    grounding: traitmech:000389
    description: Possession of a genome-encoded PD-T4-4 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_4_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: pd_t4_4_listed_phage_protection
    description: The DefenseFinder wiki links a PD-T4-4 locus from Vassallo et al.
      to protection against T2, T4, T6, and SECphi17, and DefenseFinder models PD-T4-4
      through two mandatory profiles.
    evidence:
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md
      snippet: PD-T4-4 is a defense system composed of two proteins, a P-loop NTPase
        and a nuclease, that is most likely protecting the bacterial population through
        abortive infection. It was identified from an ICE in an *E. coli* genome.
      notes: The DefenseFinder wiki describes PD-T4-4 as a two-protein system from
        an E. coli integrative and conjugative element.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md
      snippet: 'The PD-T4-4 is composed of 2 proteins: PD-T4-4_A and PD-T4-4_B.'
      notes: The DefenseFinder wiki names PD-T4-4 as a two-protein system with PD-T4-4_A
        and PD-T4-4_B components.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.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/RCO57999.1'>RCO57999.1</a>,\
        \ <a href='https://ncbi.nlm.nih.gov/protein/RCO57988.1'>RCO57988.1</a>] -->\
        \ Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2\
        \ & T4 & T6 & SECphi17"
      notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
        to an E. coli PD-T4-4 source locus expressed in E. coli against T2, T4, T6,
        and SECphi17.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md
      snippet: "subgraph Title4[Protects against]\n        T2\n        T4\n      \
        \  T6\n        SECphi17"
      notes: The DefenseFinder experimental-validation diagram lists T2, T4, T6, and
        SECphi17 in the PD-T4-4 protects-against subgraph.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "PD-T4-4\tPD-T4-4\t2\t2\tPD-T4-4__PD-T4-4_A, PD-T4-4__PD-T4-4_B\t\t\
        \t"
      notes: The DefenseFinder rules table models PD-T4-4 as a two-profile system
        requiring PD-T4-4__PD-T4-4_A and PD-T4-4__PD-T4-4_B.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| PD-T4-4__PD-T4-4_A                               | PD-T4-4__PD-T4-4_A                               |
        PD-T4-4                | Custom                  | 75     |'
      notes: The DefenseFinder HMM inventory records PD-T4-4__PD-T4-4_A under the
        PD-T4-4 system namespace.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| PD-T4-4__PD-T4-4_B                               | PD-T4-4__PD-T4-4_B                               |
        PD-T4-4                | Custom                  | 25     |'
      notes: The DefenseFinder HMM inventory records PD-T4-4__PD-T4-4_B under the
        PD-T4-4 system namespace.
  - subject: pd_t4_4_listed_phage_protection
    predicate: confers
    predicate_id: METPO:2007700
    object: pd_t4_4_system_trait
    description: Protection against T2, T4, T6, and SECphi17 realizes the PD-T4-4
      system trait.
    evidence:
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.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/RCO57999.1'>RCO57999.1</a>,\
        \ <a href='https://ncbi.nlm.nih.gov/protein/RCO57988.1'>RCO57988.1</a>] -->\
        \ Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2\
        \ & T4 & T6 & SECphi17"
      notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
        to an E. coli PD-T4-4 source locus expressed in E. coli against T2, T4, T6,
        and SECphi17.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md
      snippet: "subgraph Title4[Protects against]\n        T2\n        T4\n      \
        \  T6\n        SECphi17"
      notes: The DefenseFinder experimental-validation diagram lists T2, T4, T6, and
        SECphi17 in the PD-T4-4 protects-against subgraph.
  - subject: pd_t4_4_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: PD-T4-4 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-T4-4 and related conserved phage-defense systems.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: PD-T4-4 | 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-T4-4 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-T4-4\tPD-T4-4\t2\t2\tPD-T4-4__PD-T4-4_A, PD-T4-4__PD-T4-4_B\t\t\
        \t"
      notes: The DefenseFinder rules table models PD-T4-4 as a two-profile system
        requiring PD-T4-4__PD-T4-4_A and PD-T4-4__PD-T4-4_B.
discussions:
- discussion_id: pd-t4-4-mechanism-gap
  prompt: Resolve PD-T4-4 natural host breadth, direct phage trigger, and effector
    mechanism before minting narrower PD-T4-4 mechanism traits.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: Vassallo et al. support PD-T4-4 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, T6, and SECphi17, and DefenseFinder
    represents the system with two mandatory profiles. Natural host breadth, the direct
    phage trigger, and direct effector logic remain unresolved, so the likely abortive-infection
    hypothesis is left unmodeled.
  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-T4-4 and related conserved phage-defense systems.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md
    snippet: PD-T4-4 is a defense system composed of two proteins, a P-loop NTPase
      and a nuclease, that is most likely protecting the bacterial population through
      abortive infection. It was identified from an ICE in an *E. coli* genome.
    notes: The DefenseFinder wiki describes PD-T4-4 as a two-protein system from an
      E. coli integrative and conjugative element.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md
    snippet: 'The PD-T4-4 is composed of 2 proteins: PD-T4-4_A and PD-T4-4_B.'
    notes: The DefenseFinder wiki names PD-T4-4 as a two-protein system with PD-T4-4_A
      and PD-T4-4_B components.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.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/RCO57999.1'>RCO57999.1</a>,\
      \ <a href='https://ncbi.nlm.nih.gov/protein/RCO57988.1'>RCO57988.1</a>] -->\
      \ Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2\
      \ & T4 & T6 & SECphi17"
    notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
      to an E. coli PD-T4-4 source locus expressed in E. coli against T2, T4, T6,
      and SECphi17.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    snippet: "PD-T4-4\tPD-T4-4\t2\t2\tPD-T4-4__PD-T4-4_A, PD-T4-4__PD-T4-4_B\t\t\t"
    notes: The DefenseFinder rules table models PD-T4-4 as a two-profile system requiring
      PD-T4-4__PD-T4-4_A and PD-T4-4__PD-T4-4_B.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| PD-T4-4__PD-T4-4_A                               | PD-T4-4__PD-T4-4_A                               |
      PD-T4-4                | Custom                  | 75     |'
    notes: The DefenseFinder HMM inventory records PD-T4-4__PD-T4-4_A under the PD-T4-4
      system namespace.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| PD-T4-4__PD-T4-4_B                               | PD-T4-4__PD-T4-4_B                               |
      PD-T4-4                | Custom                  | 25     |'
    notes: The DefenseFinder HMM inventory records PD-T4-4__PD-T4-4_B under the PD-T4-4
      system namespace.
  attaches_to:
  - causal_graphs#pd_t4_4_locus_restricts_t2_t4_t6_and_secphi17
  posed_by: codex
  posed_date: '2026-09-26'
curation_history:
- timestamp: '2026-09-26T16:51:00Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted PD-T4-4 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_v266.
  llm_assisted: true
- timestamp: '2026-09-26T16:51:01Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed PD-T4-4 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 Thiothrix subterranea example,
    but not a direct native microbial isolate exemplar with experimentally verified
    endogenous PD-T4-4 activity. No paid research was used.
  llm_assisted: true
- timestamp: '2026-09-26T17:24:43Z'
  curator: codex
  action: ADDRESS_SCOPE_NOTE_REVIEW
  changes: Clarified after Claude Code Review issue 1288 that the DefenseFinder wiki
    names abortive infection as the likely PD-T4-4 population-level protection route,
    but the graph leaves that hypothesis unmodeled until direct mechanism evidence
    is available.
  llm_assisted: true