identifier: traitmech:000396
label: PD-T7-2 system
definition: A phage defense system in which an organism possesses a PD-T7-2 locus
  represented by DefenseFinder as a two-profile model, PD-T7-2__PD-T7-2_A and PD-T7-2__PD-T7-2_B,
  and experimentally linked to T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3,
  and T7 protection when expressed in E. coli.
definition_source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000209
synonyms:
- synonym_text: PD-T7-2
  synonym_type: RELATED_SYNONYM
  source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md
- synonym_text: PD-T7-2__PD-T7-2_A
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
- synonym_text: PD-T7-2__PD-T7-2_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-T7-2 and related conserved phage-defense systems.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md
  snippet: 'The PD-T7-2 is composed of 2 proteins: PD-T7-2_A and PD-T7-2_B.'
  notes: The DefenseFinder wiki names PD-T7-2 as a two-protein system with PD-T7-2_A
    and PD-T7-2_B.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md
  snippet: The PD-T7-2 system in *Lederbergia lenta* (GCF_900478165.1, NZ_LS483476)
    is composed of 2 proteins PD-T7-2_A (WP_066145327.1) PD-T7-2_B (WP_066145329.1)
  notes: The DefenseFinder wiki illustrates a predicted two-protein PD-T7-2 locus
    in RefSeq assembly GCF_900478165.1 on NZ_LS483476.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.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/RRM73498.1'>RRM73498.1</a>,\
    \ <a href='https://ncbi.nlm.nih.gov/protein/RRM73410.1'>RRM73410.1</a>] --> Expressed_0[Escherichia\
    \ coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & T5\
    \ & SECphi18 & SECphi27 & T3 & T7"
  notes: The DefenseFinder experimental-validation diagram links Vassallo et al. to
    an E. coli PD-T7-2 source locus expressed in E. coli against T2, T4, T6, LambdaVir,
    T5, SECphi18, SECphi27, T3, and T7.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md
  snippet: "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n\
    \        LambdaVir\n        T5\n        SECphi18\n        SECphi27\n        T3\n\
    \        T7"
  notes: The DefenseFinder experimental-validation diagram lists T2, T4, T6, LambdaVir,
    T5, SECphi18, SECphi27, T3, and T7 in the PD-T7-2 protects-against subgraph.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: PD-T7-2 | 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-T7-2 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-T7-2\tPD-T7-2\t2\t2\tPD-T7-2__PD-T7-2_A, PD-T7-2__PD-T7-2_B\t\t\t"
  notes: The DefenseFinder rules table models PD-T7-2 as a two-profile system requiring
    PD-T7-2__PD-T7-2_A and PD-T7-2__PD-T7-2_B.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| PD-T7-2__PD-T7-2_A                               | PD-T7-2__PD-T7-2_A                               |
    PD-T7-2                | Custom                  | 50     |'
  notes: The DefenseFinder HMM inventory records PD-T7-2__PD-T7-2_A under the PD-T7-2
    system namespace.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| PD-T7-2__PD-T7-2_B                               | PD-T7-2__PD-T7-2_B                               |
    PD-T7-2                | Custom                  | 100    |'
  notes: The DefenseFinder HMM inventory records PD-T7-2__PD-T7-2_B under the PD-T7-2
    system namespace.
causal_graphs:
- graph_id: pd_t7_2_locus_restricts_phages
  title: PD-T7-2 loci restrict T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3,
    and T7
  description: Conservative system-level sketch linking possession of a PD-T7-2 locus
    to protection against T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, and T7.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures PD-T7-2 as a named DefenseFinder phage-defense system
    while leaving natural host breadth, the direct phage trigger, the effector mechanism,
    and exact profile-to-protein correspondence unresolved.
  nodes:
  - node_id: pd_t7_2_locus
    label: PD-T7-2 locus
    node_type: GENETIC_ELEMENT
    description: A phage-defense locus represented by the PD-T7-2_A and PD-T7-2_B
      DefenseFinder profiles.
  - node_id: pd_t7_2_listed_phage_protection
    label: T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, and T7 protection
    node_type: BIOLOGICAL_PROCESS
    description: Protection against T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27,
      T3, and T7 by PD-T7-2.
  - node_id: pd_t7_2_system_trait
    label: PD-T7-2 system
    node_type: TRAIT
    grounding: traitmech:000396
    description: Possession of a genome-encoded PD-T7-2 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_t7_2_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: pd_t7_2_listed_phage_protection
    description: The DefenseFinder wiki links a PD-T7-2 locus from Vassallo et al.
      to broad phage protection, and DefenseFinder models PD-T7-2 through two mandatory
      profiles.
    evidence:
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md
      snippet: 'The PD-T7-2 is composed of 2 proteins: PD-T7-2_A and PD-T7-2_B.'
      notes: The DefenseFinder wiki names PD-T7-2 as a two-protein system with PD-T7-2_A
        and PD-T7-2_B.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.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/RRM73498.1'>RRM73498.1</a>,\
        \ <a href='https://ncbi.nlm.nih.gov/protein/RRM73410.1'>RRM73410.1</a>] -->\
        \ Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2\
        \ & T4 & T6 & LambdaVir & T5 & SECphi18 & SECphi27 & T3 & T7"
      notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
        to an E. coli PD-T7-2 source locus expressed in E. coli against T2, T4, T6,
        LambdaVir, T5, SECphi18, SECphi27, T3, and T7.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md
      snippet: "subgraph Title4[Protects against]\n        T2\n        T4\n      \
        \  T6\n        LambdaVir\n        T5\n        SECphi18\n        SECphi27\n\
        \        T3\n        T7"
      notes: The DefenseFinder experimental-validation diagram lists T2, T4, T6, LambdaVir,
        T5, SECphi18, SECphi27, T3, and T7 in the PD-T7-2 protects-against subgraph.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "PD-T7-2\tPD-T7-2\t2\t2\tPD-T7-2__PD-T7-2_A, PD-T7-2__PD-T7-2_B\t\t\
        \t"
      notes: The DefenseFinder rules table models PD-T7-2 as a two-profile system
        requiring PD-T7-2__PD-T7-2_A and PD-T7-2__PD-T7-2_B.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| PD-T7-2__PD-T7-2_A                               | PD-T7-2__PD-T7-2_A                               |
        PD-T7-2                | Custom                  | 50     |'
      notes: The DefenseFinder HMM inventory records PD-T7-2__PD-T7-2_A under the
        PD-T7-2 system namespace.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| PD-T7-2__PD-T7-2_B                               | PD-T7-2__PD-T7-2_B                               |
        PD-T7-2                | Custom                  | 100    |'
      notes: The DefenseFinder HMM inventory records PD-T7-2__PD-T7-2_B under the
        PD-T7-2 system namespace.
  - subject: pd_t7_2_listed_phage_protection
    predicate: confers
    predicate_id: METPO:2007700
    object: pd_t7_2_system_trait
    description: Protection against the listed phages realizes the PD-T7-2 system
      trait.
    evidence:
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.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/RRM73498.1'>RRM73498.1</a>,\
        \ <a href='https://ncbi.nlm.nih.gov/protein/RRM73410.1'>RRM73410.1</a>] -->\
        \ Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2\
        \ & T4 & T6 & LambdaVir & T5 & SECphi18 & SECphi27 & T3 & T7"
      notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
        to an E. coli PD-T7-2 source locus expressed in E. coli against T2, T4, T6,
        LambdaVir, T5, SECphi18, SECphi27, T3, and T7.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md
      snippet: "subgraph Title4[Protects against]\n        T2\n        T4\n      \
        \  T6\n        LambdaVir\n        T5\n        SECphi18\n        SECphi27\n\
        \        T3\n        T7"
      notes: The DefenseFinder experimental-validation diagram lists T2, T4, T6, LambdaVir,
        T5, SECphi18, SECphi27, T3, and T7 in the PD-T7-2 protects-against subgraph.
  - subject: pd_t7_2_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: PD-T7-2 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-T7-2 and related conserved phage-defense systems.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: PD-T7-2 | 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-T7-2 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-T7-2\tPD-T7-2\t2\t2\tPD-T7-2__PD-T7-2_A, PD-T7-2__PD-T7-2_B\t\t\
        \t"
      notes: The DefenseFinder rules table models PD-T7-2 as a two-profile system
        requiring PD-T7-2__PD-T7-2_A and PD-T7-2__PD-T7-2_B.
discussions:
- discussion_id: pd-t7-2-mechanism-gap
  prompt: Resolve PD-T7-2 natural host breadth, direct phage trigger, effector mechanism,
    and profile-to-protein correspondence before minting narrower PD-T7-2 mechanism
    traits.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: Vassallo et al. support PD-T7-2 as one of the conserved systems from
    an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the
    source locus to broad phage protection, and DefenseFinder represents the system
    with two profiles. Natural host breadth, the direct phage trigger, exact effector
    logic, and the exact correspondence between the two profiles and proteins 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-T7-2 and related conserved phage-defense systems.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.md
    snippet: 'The PD-T7-2 is composed of 2 proteins: PD-T7-2_A and PD-T7-2_B.'
    notes: The DefenseFinder wiki names PD-T7-2 as a two-protein system with PD-T7-2_A
      and PD-T7-2_B.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t7-2.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/RRM73498.1'>RRM73498.1</a>,\
      \ <a href='https://ncbi.nlm.nih.gov/protein/RRM73410.1'>RRM73410.1</a>] -->\
      \ Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2\
      \ & T4 & T6 & LambdaVir & T5 & SECphi18 & SECphi27 & T3 & T7"
    notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
      to an E. coli PD-T7-2 source locus expressed in E. coli against T2, T4, T6,
      LambdaVir, T5, SECphi18, SECphi27, T3, and T7.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    snippet: "PD-T7-2\tPD-T7-2\t2\t2\tPD-T7-2__PD-T7-2_A, PD-T7-2__PD-T7-2_B\t\t\t"
    notes: The DefenseFinder rules table models PD-T7-2 as a two-profile system requiring
      PD-T7-2__PD-T7-2_A and PD-T7-2__PD-T7-2_B.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| PD-T7-2__PD-T7-2_A                               | PD-T7-2__PD-T7-2_A                               |
      PD-T7-2                | Custom                  | 50     |'
    notes: The DefenseFinder HMM inventory records PD-T7-2__PD-T7-2_A under the PD-T7-2
      system namespace.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| PD-T7-2__PD-T7-2_B                               | PD-T7-2__PD-T7-2_B                               |
      PD-T7-2                | Custom                  | 100    |'
    notes: The DefenseFinder HMM inventory records PD-T7-2__PD-T7-2_B under the PD-T7-2
      system namespace.
  attaches_to:
  - causal_graphs#pd_t7_2_locus_restricts_phages
  posed_by: codex
  posed_date: '2026-09-26'
curation_history:
- timestamp: '2026-09-26T23:48:04Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted PD-T7-2 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_v273.
  llm_assisted: true
- timestamp: '2026-09-26T23:48:05Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed PD-T7-2 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 Lederbergia lenta example, but
    not a direct native microbial isolate exemplar with experimentally verified endogenous
    PD-T7-2 activity. No paid research was used.
  llm_assisted: true