identifier: traitmech:000404
label: PD-Lambda-1 system
definition: A phage defense system in which an organism possesses a PD-Lambda-1 locus
  represented by DefenseFinder as a single-profile model, PD-Lambda-1__PD-Lambda-1,
  and experimentally linked to LambdaVir protection when expressed in E. coli.
definition_source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000209
synonyms:
- synonym_text: PD-Lambda-1
  synonym_type: RELATED_SYNONYM
  source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md
- synonym_text: PD-Lambda-1__PD-Lambda-1
  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-1 and related conserved phage-defense systems.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md
  snippet: The PD-Lambda-1 system is composed of one protein, PD-Lambda-1, and confers
    resistance to LambdaVir :ref{doi=10.1038/s41564-022-01219-4}.
  notes: The DefenseFinder wiki describes PD-Lambda-1 as a one-protein system that
    can confer LambdaVir resistance.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md
  snippet: As far as we are aware, the molecular mechanism is unknown.
  notes: The DefenseFinder wiki records the PD-Lambda-1 molecular mechanism as unresolved.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md
  snippet: 'The PD-Lambda-1 is composed of 1 protein: PD-Lambda-1.'
  notes: The DefenseFinder wiki names PD-Lambda-1 as a single-protein system.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md
  snippet: 'The PD-Lambda-1 system in *Gemmata massiliana* (GCF_901538265.1, NZ_LR593886)
    is composed of 1 protein: PD-Lambda-1 (WP_197909633.1)'
  notes: The DefenseFinder wiki illustrates a predicted one-protein PD-Lambda-1 locus
    in RefSeq assembly GCF_901538265.1 on NZ_LR593886.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.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/RCP76574.1'>RCP76574.1</a>]\
    \ --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> LambdaVir"
  notes: The DefenseFinder experimental-validation diagram links Vassallo et al. to
    an E. coli PD-Lambda-1 source locus expressed in E. coli against LambdaVir.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md
  snippet: "subgraph Title4[Protects against]\n        LambdaVir"
  notes: The DefenseFinder experimental-validation diagram lists LambdaVir in the
    PD-Lambda-1 protects-against subgraph.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
  snippet: "PD-Lambda-1\tPD-Lambda-1\t1\t1\tPD-Lambda-1__PD-Lambda-1\t\t\t"
  notes: The DefenseFinder rules table models PD-Lambda-1 as a single-profile system
    requiring PD-Lambda-1__PD-Lambda-1.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| PD-Lambda-1__PD-Lambda-1                         | PD-Lambda-1__PD-Lambda-1                         |
    PD-Lambda-1            | Custom                  | 200    |'
  notes: The DefenseFinder HMM inventory records PD-Lambda-1__PD-Lambda-1 under the
    PD-Lambda-1 system namespace.
causal_graphs:
- graph_id: pd_lambda_1_locus_restricts_lambda_vir
  title: PD-Lambda-1 loci restrict LambdaVir
  description: Conservative system-level sketch linking possession of a PD-Lambda-1
    locus to LambdaVir protection.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures PD-Lambda-1 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_lambda_1_locus
    label: PD-Lambda-1 locus
    node_type: GENETIC_ELEMENT
    description: A phage-defense locus represented by the PD-Lambda-1 DefenseFinder
      profile.
  - node_id: pd_lambda_1_listed_phage_protection
    label: LambdaVir protection
    node_type: BIOLOGICAL_PROCESS
    description: Protection against LambdaVir by PD-Lambda-1.
  - node_id: pd_lambda_1_system_trait
    label: PD-Lambda-1 system
    node_type: TRAIT
    grounding: traitmech:000404
    description: Possession of a genome-encoded PD-Lambda-1 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_1_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: pd_lambda_1_listed_phage_protection
    description: The DefenseFinder wiki links a PD-Lambda-1 locus from Vassallo et
      al. to LambdaVir protection, and DefenseFinder models PD-Lambda-1 through one
      mandatory profile.
    evidence:
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md
      snippet: The PD-Lambda-1 system is composed of one protein, PD-Lambda-1, and
        confers resistance to LambdaVir :ref{doi=10.1038/s41564-022-01219-4}.
      notes: The DefenseFinder wiki describes PD-Lambda-1 as a one-protein system
        that can confer LambdaVir resistance.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md
      snippet: 'The PD-Lambda-1 is composed of 1 protein: PD-Lambda-1.'
      notes: The DefenseFinder wiki names PD-Lambda-1 as a single-protein system.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.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/RCP76574.1'>RCP76574.1</a>]\
        \ --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ---->\
        \ LambdaVir"
      notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
        to an E. coli PD-Lambda-1 source locus expressed in E. coli against LambdaVir.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md
      snippet: "subgraph Title4[Protects against]\n        LambdaVir"
      notes: The DefenseFinder experimental-validation diagram lists LambdaVir in
        the PD-Lambda-1 protects-against subgraph.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "PD-Lambda-1\tPD-Lambda-1\t1\t1\tPD-Lambda-1__PD-Lambda-1\t\t\t"
      notes: The DefenseFinder rules table models PD-Lambda-1 as a single-profile
        system requiring PD-Lambda-1__PD-Lambda-1.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| PD-Lambda-1__PD-Lambda-1                         | PD-Lambda-1__PD-Lambda-1                         |
        PD-Lambda-1            | Custom                  | 200    |'
      notes: The DefenseFinder HMM inventory records PD-Lambda-1__PD-Lambda-1 under
        the PD-Lambda-1 system namespace.
  - subject: pd_lambda_1_listed_phage_protection
    predicate: confers
    predicate_id: METPO:2007700
    object: pd_lambda_1_system_trait
    description: Protection against LambdaVir realizes the PD-Lambda-1 system trait.
    evidence:
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md
      snippet: The PD-Lambda-1 system is composed of one protein, PD-Lambda-1, and
        confers resistance to LambdaVir :ref{doi=10.1038/s41564-022-01219-4}.
      notes: The DefenseFinder wiki describes PD-Lambda-1 as a one-protein system
        that can confer LambdaVir resistance.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.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/RCP76574.1'>RCP76574.1</a>]\
        \ --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ---->\
        \ LambdaVir"
      notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
        to an E. coli PD-Lambda-1 source locus expressed in E. coli against LambdaVir.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md
      snippet: "subgraph Title4[Protects against]\n        LambdaVir"
      notes: The DefenseFinder experimental-validation diagram lists LambdaVir in
        the PD-Lambda-1 protects-against subgraph.
  - subject: pd_lambda_1_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: PD-Lambda-1 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-1 and related conserved phage-defense systems.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md
      snippet: 'The PD-Lambda-1 is composed of 1 protein: PD-Lambda-1.'
      notes: The DefenseFinder wiki names PD-Lambda-1 as a single-protein system.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "PD-Lambda-1\tPD-Lambda-1\t1\t1\tPD-Lambda-1__PD-Lambda-1\t\t\t"
      notes: The DefenseFinder rules table models PD-Lambda-1 as a single-profile
        system requiring PD-Lambda-1__PD-Lambda-1.
discussions:
- discussion_id: pd-lambda-1-mechanism-gap
  prompt: Resolve PD-Lambda-1 natural host breadth, direct phage trigger, and effector
    mechanism before minting narrower PD-Lambda-1 mechanism traits.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: Vassallo et al. support PD-Lambda-1 as one of the conserved systems from
    an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the
    source locus to LambdaVir protection, and DefenseFinder represents the system
    with one 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-Lambda-1 and related conserved phage-defense systems.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md
    snippet: The PD-Lambda-1 system is composed of one protein, PD-Lambda-1, and confers
      resistance to LambdaVir :ref{doi=10.1038/s41564-022-01219-4}.
    notes: The DefenseFinder wiki describes PD-Lambda-1 as a one-protein system that
      can confer LambdaVir resistance.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md
    snippet: As far as we are aware, the molecular mechanism is unknown.
    notes: The DefenseFinder wiki records the PD-Lambda-1 molecular mechanism as unresolved.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.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/RCP76574.1'>RCP76574.1</a>]\
      \ --> Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ---->\
      \ LambdaVir"
    notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
      to an E. coli PD-Lambda-1 source locus expressed in E. coli against LambdaVir.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    snippet: "PD-Lambda-1\tPD-Lambda-1\t1\t1\tPD-Lambda-1__PD-Lambda-1\t\t\t"
    notes: The DefenseFinder rules table models PD-Lambda-1 as a single-profile system
      requiring PD-Lambda-1__PD-Lambda-1.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| PD-Lambda-1__PD-Lambda-1                         | PD-Lambda-1__PD-Lambda-1                         |
      PD-Lambda-1            | Custom                  | 200    |'
    notes: The DefenseFinder HMM inventory records PD-Lambda-1__PD-Lambda-1 under
      the PD-Lambda-1 system namespace.
  attaches_to:
  - causal_graphs#pd_lambda_1_locus_restricts_lambda_vir
  posed_by: codex
  posed_date: '2026-09-27'
- discussion_id: pd-lambda-1-defensefinder-article-registry-gap
  prompt: Recheck whether DefenseFinder adds a PD-Lambda-1 List_system_article.md
    row before using the article registry as direct PD-Lambda-1 model-to-paper evidence.
  kind: CURATION_TODO
  status: OPEN
  rationale: The pinned DefenseFinder wiki, rules table, and HMM inventory all represent
    PD-Lambda-1, but the pinned List_system_article.md registry omits a PD-Lambda-1
    row. The PD-Lambda-1 record therefore cites the pinned wiki plus the DOI-backed
    Vassallo et al. screen instead of inventing a missing article-registry entry.
  evidence:
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md
    snippet: The PD-Lambda-1 system is composed of one protein, PD-Lambda-1, and confers
      resistance to LambdaVir :ref{doi=10.1038/s41564-022-01219-4}.
    notes: The DefenseFinder wiki describes PD-Lambda-1 as a one-protein system that
      can confer LambdaVir resistance.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    snippet: "PD-Lambda-1\tPD-Lambda-1\t1\t1\tPD-Lambda-1__PD-Lambda-1\t\t\t"
    notes: The DefenseFinder rules table models PD-Lambda-1 as a single-profile system
      requiring PD-Lambda-1__PD-Lambda-1.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| PD-Lambda-1__PD-Lambda-1                         | PD-Lambda-1__PD-Lambda-1                         |
      PD-Lambda-1            | Custom                  | 200    |'
    notes: The DefenseFinder HMM inventory records PD-Lambda-1__PD-Lambda-1 under
      the PD-Lambda-1 system namespace.
  posed_by: codex
  posed_date: '2026-09-27'
curation_history:
- timestamp: '2026-09-27T07:17:46Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted PD-Lambda-1 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_v281.
  llm_assisted: true
- timestamp: '2026-09-27T07:17:47Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed PD-Lambda-1 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 Gemmata massiliana example,
    but not a direct native microbial isolate exemplar with experimentally verified
    endogenous PD-Lambda-1 activity. No paid research was used.
  llm_assisted: true