identifier: traitmech:000378
label: PD-Lambda-2 system
definition: A phage defense system in which an organism possesses a PD-Lambda-2 locus
  represented by DefenseFinder as a model with two mandatory profiles, PD-Lambda-2__PD-Lambda-2_A
  and PD-Lambda-2__PD-Lambda-2_B, plus the accessory PD-Lambda-2__PD-Lambda-2_C profile.
definition_source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000209
synonyms:
- synonym_text: PD-Lambda-2
  synonym_type: RELATED_SYNONYM
  source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md
- synonym_text: PD-Lambda-2__PD-Lambda-2_A
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
- synonym_text: PD-Lambda-2__PD-Lambda-2_B
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
- synonym_text: PD-Lambda-2__PD-Lambda-2_C
  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-Lambda-2 and related conserved phage-defense systems.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md
  snippet: 'The PD-Lambda-2 is composed of 3 proteins: PD-Lambda-2_A, PD-Lambda-2_B
    and PD-Lambda-2_C.'
  notes: The DefenseFinder wiki names PD-Lambda-2 as a three-protein system.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md
  snippet: The PD-Lambda-2 system in *Vibrio parahaemolyticus* (GCF_013393845.1, NZ_CP040100)
    is composed of 3 proteins PD-Lambda-2_C (WP_116869984.1) PD-Lambda-2_B (WP_029809306.1)
    PD-Lambda-2_A (WP_029809305.1)
  notes: The DefenseFinder wiki illustrates a predicted PD-Lambda-2 locus in RefSeq
    assembly GCF_013393845.1 on NZ_CP040100.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-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/RCO93357.1'>RCO93357.1</a>,\
    \ <a href='https://ncbi.nlm.nih.gov/protein/RCO93356.1'>RCO93356.1</a>,\n<a href='https://ncbi.nlm.nih.gov/protein/RCO93355.1'>RCO93355.1</a>]\
    \ --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir\
    \ & SECphi17 & SECphi18 & SECphi27 & T3"
  notes: The DefenseFinder experimental-validation diagram links Vassallo et al. to
    an E. coli PD-Lambda-2 source locus and testing in E. coli against LambdaVir,
    SECphi17, SECphi18, SECphi27, and T3.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md
  snippet: "subgraph Title4[Protects against]\n        LambdaVir\n        SECphi17\n\
    \        SECphi18\n        SECphi27\n        T3"
  notes: The DefenseFinder experimental-validation diagram lists LambdaVir, SECphi17,
    SECphi18, SECphi27, and T3 in the PD-Lambda-2 protects-against subgraph.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: PD-Lambda-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-Lambda-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-Lambda-2\tPD-Lambda-2\t2\t2\tPD-Lambda-2__PD-Lambda-2_A, PD-Lambda-2__PD-Lambda-2_B\t\
    PD-Lambda-2__PD-Lambda-2_C\t\t"
  notes: The DefenseFinder rules table models PD-Lambda-2 with PD-Lambda-2__PD-Lambda-2_A
    and PD-Lambda-2__PD-Lambda-2_B as mandatory profiles and PD-Lambda-2__PD-Lambda-2_C
    as an accessory profile.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| PD-Lambda-2__PD-Lambda-2_A                       | PD-Lambda-2__PD-Lambda-2_A                       |
    PD-Lambda-2            | Custom                  | 60     |'
  notes: The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_A under
    the PD-Lambda-2 system namespace.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| PD-Lambda-2__PD-Lambda-2_B                       | PD-Lambda-2__PD-Lambda-2_B                       |
    PD-Lambda-2            | Custom                  | 100    |'
  notes: The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_B under
    the PD-Lambda-2 system namespace.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| PD-Lambda-2__PD-Lambda-2_C                       | PD-Lambda-2__PD-Lambda-2_C                       |
    PD-Lambda-2            | Custom                  | 20     |'
  notes: The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_C under
    the PD-Lambda-2 system namespace.
causal_graphs:
- graph_id: pd_lambda_2_locus_restricts_phages
  title: PD-Lambda-2 loci restrict LambdaVir, SECphi17, SECphi18, SECphi27, and T3
  description: Conservative system-level sketch linking possession of a PD-Lambda-2
    locus to protection against LambdaVir, SECphi17, SECphi18, SECphi27, and T3.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures PD-Lambda-2 as a named DefenseFinder phage-defense
    system while leaving natural host breadth, the direct phage trigger, the effector
    mechanism, and exact PD-Lambda-2 profile-to-protein correspondence unresolved.
  nodes:
  - node_id: pd_lambda_2_locus
    label: PD-Lambda-2 locus
    node_type: GENETIC_ELEMENT
    description: A phage-defense locus represented by the PD-Lambda-2 DefenseFinder
      profiles.
  - node_id: pd_lambda_2_listed_phage_protection
    label: LambdaVir, SECphi17, SECphi18, SECphi27, and T3 protection
    node_type: BIOLOGICAL_PROCESS
    description: Protection against LambdaVir, SECphi17, SECphi18, SECphi27, and T3
      by PD-Lambda-2.
  - node_id: pd_lambda_2_system_trait
    label: PD-Lambda-2 system
    node_type: TRAIT
    grounding: traitmech:000378
    description: Possession of a genome-encoded PD-Lambda-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_lambda_2_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: pd_lambda_2_listed_phage_protection
    description: The DefenseFinder wiki links a PD-Lambda-2 locus from Vassallo et
      al. to protection against LambdaVir, SECphi17, SECphi18, SECphi27, and T3, and
      DefenseFinder models PD-Lambda-2 through A, B, and C profiles.
    evidence:
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md
      snippet: 'The PD-Lambda-2 is composed of 3 proteins: PD-Lambda-2_A, PD-Lambda-2_B
        and PD-Lambda-2_C.'
      notes: The DefenseFinder wiki names PD-Lambda-2 as a three-protein system.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-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/RCO93357.1'>RCO93357.1</a>,\
        \ <a href='https://ncbi.nlm.nih.gov/protein/RCO93356.1'>RCO93356.1</a>,\n\
        <a href='https://ncbi.nlm.nih.gov/protein/RCO93355.1'>RCO93355.1</a>] -->\
        \ Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir\
        \ & SECphi17 & SECphi18 & SECphi27 & T3"
      notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
        to an E. coli PD-Lambda-2 source locus and testing in E. coli against LambdaVir,
        SECphi17, SECphi18, SECphi27, and T3.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md
      snippet: "subgraph Title4[Protects against]\n        LambdaVir\n        SECphi17\n\
        \        SECphi18\n        SECphi27\n        T3"
      notes: The DefenseFinder experimental-validation diagram lists LambdaVir, SECphi17,
        SECphi18, SECphi27, and T3 in the PD-Lambda-2 protects-against subgraph.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "PD-Lambda-2\tPD-Lambda-2\t2\t2\tPD-Lambda-2__PD-Lambda-2_A, PD-Lambda-2__PD-Lambda-2_B\t\
        PD-Lambda-2__PD-Lambda-2_C\t\t"
      notes: The DefenseFinder rules table models PD-Lambda-2 with PD-Lambda-2__PD-Lambda-2_A
        and PD-Lambda-2__PD-Lambda-2_B as mandatory profiles and PD-Lambda-2__PD-Lambda-2_C
        as an accessory profile.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| PD-Lambda-2__PD-Lambda-2_A                       | PD-Lambda-2__PD-Lambda-2_A                       |
        PD-Lambda-2            | Custom                  | 60     |'
      notes: The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_A under
        the PD-Lambda-2 system namespace.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| PD-Lambda-2__PD-Lambda-2_B                       | PD-Lambda-2__PD-Lambda-2_B                       |
        PD-Lambda-2            | Custom                  | 100    |'
      notes: The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_B under
        the PD-Lambda-2 system namespace.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| PD-Lambda-2__PD-Lambda-2_C                       | PD-Lambda-2__PD-Lambda-2_C                       |
        PD-Lambda-2            | Custom                  | 20     |'
      notes: The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_C under
        the PD-Lambda-2 system namespace.
  - subject: pd_lambda_2_listed_phage_protection
    predicate: confers
    predicate_id: METPO:2007700
    object: pd_lambda_2_system_trait
    description: Protection against LambdaVir, SECphi17, SECphi18, SECphi27, and T3
      realizes the PD-Lambda-2 system trait.
    evidence:
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-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/RCO93357.1'>RCO93357.1</a>,\
        \ <a href='https://ncbi.nlm.nih.gov/protein/RCO93356.1'>RCO93356.1</a>,\n\
        <a href='https://ncbi.nlm.nih.gov/protein/RCO93355.1'>RCO93355.1</a>] -->\
        \ Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir\
        \ & SECphi17 & SECphi18 & SECphi27 & T3"
      notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
        to an E. coli PD-Lambda-2 source locus and testing in E. coli against LambdaVir,
        SECphi17, SECphi18, SECphi27, and T3.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md
      snippet: "subgraph Title4[Protects against]\n        LambdaVir\n        SECphi17\n\
        \        SECphi18\n        SECphi27\n        T3"
      notes: The DefenseFinder experimental-validation diagram lists LambdaVir, SECphi17,
        SECphi18, SECphi27, and T3 in the PD-Lambda-2 protects-against subgraph.
  - subject: pd_lambda_2_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: PD-Lambda-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-Lambda-2 and related conserved phage-defense systems.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: PD-Lambda-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-Lambda-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-Lambda-2\tPD-Lambda-2\t2\t2\tPD-Lambda-2__PD-Lambda-2_A, PD-Lambda-2__PD-Lambda-2_B\t\
        PD-Lambda-2__PD-Lambda-2_C\t\t"
      notes: The DefenseFinder rules table models PD-Lambda-2 with PD-Lambda-2__PD-Lambda-2_A
        and PD-Lambda-2__PD-Lambda-2_B as mandatory profiles and PD-Lambda-2__PD-Lambda-2_C
        as an accessory profile.
discussions:
- discussion_id: pd-lambda-2-mechanism-gap
  prompt: Resolve PD-Lambda-2 natural host breadth, direct phage trigger, effector
    mechanism, and exact profile-to-protein correspondence before minting narrower
    PD-Lambda-2 mechanism traits.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: Vassallo et al. support PD-Lambda-2 as one of the conserved systems from
    an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the
    source locus to protection against LambdaVir, SECphi17, SECphi18, SECphi27, and
    T3, and DefenseFinder represents the system with A, B, and C profiles. Natural
    host breadth, the direct phage trigger, effector logic, and exact profile-to-protein
    correspondence 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-Lambda-2 and related conserved phage-defense systems.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md
    snippet: 'The PD-Lambda-2 is composed of 3 proteins: PD-Lambda-2_A, PD-Lambda-2_B
      and PD-Lambda-2_C.'
    notes: The DefenseFinder wiki names PD-Lambda-2 as a three-protein system.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-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/RCO93357.1'>RCO93357.1</a>,\
      \ <a href='https://ncbi.nlm.nih.gov/protein/RCO93356.1'>RCO93356.1</a>,\n<a\
      \ href='https://ncbi.nlm.nih.gov/protein/RCO93355.1'>RCO93355.1</a>] --> Expressed_0[Escherichia\
      \ coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir & SECphi17 & SECphi18\
      \ & SECphi27 & T3"
    notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
      to an E. coli PD-Lambda-2 source locus and testing in E. coli against LambdaVir,
      SECphi17, SECphi18, SECphi27, and T3.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    snippet: "PD-Lambda-2\tPD-Lambda-2\t2\t2\tPD-Lambda-2__PD-Lambda-2_A, PD-Lambda-2__PD-Lambda-2_B\t\
      PD-Lambda-2__PD-Lambda-2_C\t\t"
    notes: The DefenseFinder rules table models PD-Lambda-2 with PD-Lambda-2__PD-Lambda-2_A
      and PD-Lambda-2__PD-Lambda-2_B as mandatory profiles and PD-Lambda-2__PD-Lambda-2_C
      as an accessory profile.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| PD-Lambda-2__PD-Lambda-2_A                       | PD-Lambda-2__PD-Lambda-2_A                       |
      PD-Lambda-2            | Custom                  | 60     |'
    notes: The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_A under
      the PD-Lambda-2 system namespace.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| PD-Lambda-2__PD-Lambda-2_B                       | PD-Lambda-2__PD-Lambda-2_B                       |
      PD-Lambda-2            | Custom                  | 100    |'
    notes: The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_B under
      the PD-Lambda-2 system namespace.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| PD-Lambda-2__PD-Lambda-2_C                       | PD-Lambda-2__PD-Lambda-2_C                       |
      PD-Lambda-2            | Custom                  | 20     |'
    notes: The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_C under
      the PD-Lambda-2 system namespace.
  attaches_to:
  - causal_graphs#pd_lambda_2_locus_restricts_phages
  posed_by: codex
  posed_date: '2026-09-26'
curation_history:
- timestamp: '2026-09-26T09:48:10Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted PD-Lambda-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_v255.
  llm_assisted: true
- timestamp: '2026-09-26T09:48:11Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed PD-Lambda-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 Vibrio parahaemolyticus example,
    but not a direct native microbial isolate exemplar with experimentally verified
    endogenous PD-Lambda-2 activity. No paid research was used.
  llm_assisted: true