TraitMech

TraitMech › GENOMICS

PD-Lambda-3 system

traitmech:000382 · CLASS · PROPOSED

A phage defense system in which an organism possesses a PD-Lambda-3 locus represented by DefenseFinder as a two-profile model, PD-Lambda-3__PD-Lambda-3_A and PD-Lambda-3__PD-Lambda-3_B, and experimentally linked to LambdaVir protection when expressed in E. coli.

Trait evidence (10)

PD-Lambda-3 loci restrict LambdaVir

Conservative system-level sketch linking possession of a PD-Lambda-3 locus to protection against LambdaVir.

NONMECHANISTIC · The graph captures PD-Lambda-3 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, the effector mechanism, the third protein in the experimental source locus, and exact PD-Lambda-3 profile-to-protein correspondence unresolved.

PD-Lambda-3 loci restrict LambdaVir Interactive directed graph showing evidence-backed causal relationships for PD-Lambda-3 system.

Edge evidence

Provenance

Identifier source
TraitMech local identifier
Definition source
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-3.md

Parent traits (1)

Synonyms (3)

  • PD-Lambda-3 RELATED_SYNONYM · https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-3.md
  • PD-Lambda-3__PD-Lambda-3_A RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  • PD-Lambda-3__PD-Lambda-3_B RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Discussions and Knowledge Gaps (1)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Resolve PD-Lambda-3 natural host breadth, direct phage trigger, effector mechanism, the third protein in the experimental source locus, and exact profile-to-protein correspondence before minting narrower PD-Lambda-3 mechanism traits.

KNOWLEDGE GAP OPEN pd-lambda-3-mechanism-gap · raised by codex · 2026-09-26

Attached to causal_graphs#pd_lambda_3_locus_restricts_lambda_vir

Vassallo et al. support PD-Lambda-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 LambdaVir, and DefenseFinder represents the system with A and B profiles. Natural host breadth, the direct phage trigger, effector logic, the third protein in the experimental source locus, and exact profile-to-protein correspondence remain unresolved.

Evidence

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted PD-Lambda-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_v259.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    Reviewed PD-Lambda-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 Enterobacter sp. example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-Lambda-3 activity. No paid research was used.