TraitMech

TraitMech › GENOMICS

PD-Lambda-1 system

traitmech:000404 · CLASS · PROPOSED

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.

Trait evidence (9)

PD-Lambda-1 loci restrict LambdaVir

Conservative system-level sketch linking possession of a PD-Lambda-1 locus to LambdaVir protection.

NONMECHANISTIC · 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.

PD-Lambda-1 loci restrict LambdaVir Interactive directed graph showing evidence-backed causal relationships for PD-Lambda-1 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-1.md

Parent traits (1)

Synonyms (2)

  • PD-Lambda-1 RELATED_SYNONYM · https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-1.md
  • PD-Lambda-1__PD-Lambda-1 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 (2)

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

Resolve PD-Lambda-1 natural host breadth, direct phage trigger, and effector mechanism before minting narrower PD-Lambda-1 mechanism traits.

KNOWLEDGE GAP OPEN pd-lambda-1-mechanism-gap · raised by codex · 2026-09-27

Attached to causal_graphs#pd_lambda_1_locus_restricts_lambda_vir

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

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.

CURATION TODO OPEN pd-lambda-1-defensefinder-article-registry-gap · raised by codex · 2026-09-27

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

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

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    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.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    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.