PD-Lambda-2 system

traitmech:000378 · CLASS · PROPOSED

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.

Trait evidence (10)

DOI:10.1038/s41564-022-01219-4
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.

Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-Lambda-2 and related conserved phage-defense systems.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md
The PD-Lambda-2 is composed of 3 proteins: PD-Lambda-2_A, PD-Lambda-2_B and PD-Lambda-2_C.

The DefenseFinder wiki names PD-Lambda-2 as a three-protein system.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md
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)

The DefenseFinder wiki illustrates a predicted PD-Lambda-2 locus in RefSeq assembly GCF_013393845.1 on NZ_CP040100.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli <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>, <a href='https://ncbi.nlm.nih.gov/protein/RCO93355.1'>RCO93355.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3

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.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md
subgraph Title4[Protects against] LambdaVir SECphi17 SECphi18 SECphi27 T3

The DefenseFinder experimental-validation diagram lists LambdaVir, SECphi17, SECphi18, SECphi27, and T3 in the PD-Lambda-2 protects-against subgraph.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
PD-Lambda-2 | 10\.1101/2022\.05\.12\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\. coli pangenome

The DefenseFinder article registry maps the named PD-Lambda-2 system to the Vassallo et al. E. coli pangenome phage-defense preprint.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
PD-Lambda-2 PD-Lambda-2 2 2 PD-Lambda-2__PD-Lambda-2_A, PD-Lambda-2__PD-Lambda-2_B PD-Lambda-2__PD-Lambda-2_C

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.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PD-Lambda-2__PD-Lambda-2_A | PD-Lambda-2__PD-Lambda-2_A | PD-Lambda-2 | Custom | 60 |

The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_A under the PD-Lambda-2 system namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PD-Lambda-2__PD-Lambda-2_B | PD-Lambda-2__PD-Lambda-2_B | PD-Lambda-2 | Custom | 100 |

The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_B under the PD-Lambda-2 system namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PD-Lambda-2__PD-Lambda-2_C | PD-Lambda-2__PD-Lambda-2_C | PD-Lambda-2 | Custom | 20 |

The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_C under the PD-Lambda-2 system namespace.

PD-Lambda-2 loci restrict LambdaVir, SECphi17, SECphi18, SECphi27, and T3

Conservative system-level sketch linking possession of a PD-Lambda-2 locus to protection against LambdaVir, SECphi17, SECphi18, SECphi27, and T3.

NONMECHANISTIC · 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.

Edge evidence

PD-Lambda-2 locus contributes to LambdaVir, SECphi17, SECphi18, SECphi27, and T3 protection RO:0002326
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.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md The PD-Lambda-2 is composed of 3 proteins: PD-Lambda-2_A, PD-Lambda-2_B and PD-Lambda-2_C. The DefenseFinder wiki names PD-Lambda-2 as a three-protein system.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli <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>, <a href='https://ncbi.nlm.nih.gov/protein/RCO93355.1'>RCO93355.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3 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.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md subgraph Title4[Protects against] LambdaVir SECphi17 SECphi18 SECphi27 T3 The DefenseFinder experimental-validation diagram lists LambdaVir, SECphi17, SECphi18, SECphi27, and T3 in the PD-Lambda-2 protects-against subgraph.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv PD-Lambda-2 PD-Lambda-2 2 2 PD-Lambda-2__PD-Lambda-2_A, PD-Lambda-2__PD-Lambda-2_B PD-Lambda-2__PD-Lambda-2_C 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.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | PD-Lambda-2__PD-Lambda-2_A | PD-Lambda-2__PD-Lambda-2_A | PD-Lambda-2 | Custom | 60 | The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_A under the PD-Lambda-2 system namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | PD-Lambda-2__PD-Lambda-2_B | PD-Lambda-2__PD-Lambda-2_B | PD-Lambda-2 | Custom | 100 | The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_B under the PD-Lambda-2 system namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | PD-Lambda-2__PD-Lambda-2_C | PD-Lambda-2__PD-Lambda-2_C | PD-Lambda-2 | Custom | 20 | The DefenseFinder HMM inventory records PD-Lambda-2__PD-Lambda-2_C under the PD-Lambda-2 system namespace.
LambdaVir, SECphi17, SECphi18, SECphi27, and T3 protection confers PD-Lambda-2 system METPO:2007700
Protection against LambdaVir, SECphi17, SECphi18, SECphi27, and T3 realizes the PD-Lambda-2 system trait.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli <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>, <a href='https://ncbi.nlm.nih.gov/protein/RCO93355.1'>RCO93355.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3 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.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md subgraph Title4[Protects against] LambdaVir SECphi17 SECphi18 SECphi27 T3 The DefenseFinder experimental-validation diagram lists LambdaVir, SECphi17, SECphi18, SECphi27, and T3 in the PD-Lambda-2 protects-against subgraph.
PD-Lambda-2 system is a phage defense system rdfs:subClassOf
PD-Lambda-2 system possession is a phage-defense-system trait.
- DOI:10.1038/s41564-022-01219-4 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. Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered PD-Lambda-2 and related conserved phage-defense systems.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md PD-Lambda-2 | 10\.1101/2022\.05\.12\.491691 | Mapping the landscape of anti-phage defense mechanisms in the E\. coli pangenome The DefenseFinder article registry maps the named PD-Lambda-2 system to the Vassallo et al. E. coli pangenome phage-defense preprint.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv PD-Lambda-2 PD-Lambda-2 2 2 PD-Lambda-2__PD-Lambda-2_A, PD-Lambda-2__PD-Lambda-2_B PD-Lambda-2__PD-Lambda-2_C 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.

Provenance

Identifier source: TraitMech local identifier
Definition source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md

Parent traits (1)

phage defense system traitmech:000209

Synonyms (4)

PD-Lambda-2 RELATED_SYNONYM · https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md
PD-Lambda-2__PD-Lambda-2_A RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
PD-Lambda-2__PD-Lambda-2_B RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
PD-Lambda-2__PD-Lambda-2_C 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-2 natural host breadth, direct phage trigger, effector mechanism, and exact profile-to-protein correspondence before minting narrower PD-Lambda-2 mechanism traits.

KNOWLEDGE GAP OPEN pd-lambda-2-mechanism-gap · raised by codex · 2026-09-26

Attached to causal_graphs#pd_lambda_2_locus_restricts_phages

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

DOI:10.1038/s41564-022-01219-4
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.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md
The PD-Lambda-2 is composed of 3 proteins: PD-Lambda-2_A, PD-Lambda-2_B and PD-Lambda-2_C.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-2.md
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0 Origin_0[Escherichia coli <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>, <a href='https://ncbi.nlm.nih.gov/protein/RCO93355.1'>RCO93355.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
PD-Lambda-2 PD-Lambda-2 2 2 PD-Lambda-2__PD-Lambda-2_A, PD-Lambda-2__PD-Lambda-2_B PD-Lambda-2__PD-Lambda-2_C
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PD-Lambda-2__PD-Lambda-2_A | PD-Lambda-2__PD-Lambda-2_A | PD-Lambda-2 | Custom | 60 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PD-Lambda-2__PD-Lambda-2_B | PD-Lambda-2__PD-Lambda-2_B | PD-Lambda-2 | Custom | 100 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PD-Lambda-2__PD-Lambda-2_C | PD-Lambda-2__PD-Lambda-2_C | PD-Lambda-2 | Custom | 20 |

Curation history

2026-09-26T09:48:10Z · MINTED_TRAITMECH_ID · codex
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.
2026-09-26T09:48:11Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
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.