PD-Lambda-5 system

traitmech:000385 · CLASS · PROPOSED

A phage defense system in which an organism possesses a PD-Lambda-5 locus represented by DefenseFinder as a two-profile model, PD-Lambda-5__PD-Lambda-5_A and PD-Lambda-5__PD-Lambda-5_B, and experimentally linked to T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7 protection when expressed in E. coli.

Trait evidence (11)

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-5 and related conserved phage-defense systems.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
PD-lambda-5 is a two-gene system identified in a P2-like prophage. It encodes a protein with a nuclease and a HEPN domain, and a predicted methyltransferase. It confers broad anti-phage defense and does not seem to mediate abortive infection.

The DefenseFinder wiki describes PD-Lambda-5 as a two-gene system from a P2-like prophage that can confer broad anti-phage defense.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
PD-lambda-5 molecular mechanism has not been described to date.

The DefenseFinder wiki records the PD-Lambda-5 molecular mechanism as not yet described.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
The PD-Lambda-5 is composed of 2 proteins: PD-Lambda-5_A and PD-Lambda-5_B.

The DefenseFinder wiki names PD-Lambda-5 as a two-protein system with PD-Lambda-5_A and PD-Lambda-5_B.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
The PD-Lambda-5 system in *Plantactinospora sp. BB1* (GCF_003030385.1, NZ_CP028159) is composed of 2 proteins PD-Lambda-5_A (WP_159104731.1) PD-Lambda-5_B (WP_199853739.1)

The DefenseFinder wiki illustrates a predicted two-protein PD-Lambda-5 locus in RefSeq assembly GCF_003030385.1 on NZ_CP028159.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.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/RCQ13837.1'>RCQ13837.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCQ13838.1'>RCQ13838.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3 & T7

The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-5 source locus expressed in E. coli against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
subgraph Title4[Protects against] T2 T4 T6 LambdaVir SECphi17 SECphi18 SECphi27 T3 T7

The DefenseFinder experimental-validation diagram lists T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7 in the PD-Lambda-5 protects-against subgraph.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
PD-Lambda-5 | 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-5 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-5 PD-Lambda-5 2 2 PD-Lambda-5__PD-Lambda-5_A, PD-Lambda-5__PD-Lambda-5_B

The DefenseFinder rules table models PD-Lambda-5 as a two-profile system requiring PD-Lambda-5__PD-Lambda-5_A and PD-Lambda-5__PD-Lambda-5_B.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PD-Lambda-5__PD-Lambda-5_A | PD-Lambda-5__PD-Lambda-5_A | PD-Lambda-5 | Custom | 20 |

The DefenseFinder HMM inventory records PD-Lambda-5__PD-Lambda-5_A under the PD-Lambda-5 system namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PD-Lambda-5__PD-Lambda-5_B | PD-Lambda-5__PD-Lambda-5_B | PD-Lambda-5 | Custom | 20 |

The DefenseFinder HMM inventory records PD-Lambda-5__PD-Lambda-5_B under the PD-Lambda-5 system namespace.

PD-Lambda-5 loci restrict T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7

Conservative system-level sketch linking possession of a PD-Lambda-5 locus to protection against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7.

NONMECHANISTIC · The graph captures PD-Lambda-5 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, the effector mechanism, and exact PD-Lambda-5 profile-to-protein correspondence unresolved.

Edge evidence

PD-Lambda-5 locus contributes to T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7 protection RO:0002326
The DefenseFinder wiki links a PD-Lambda-5 locus from Vassallo et al. to protection against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7, and DefenseFinder models PD-Lambda-5 through two mandatory profiles.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md PD-lambda-5 is a two-gene system identified in a P2-like prophage. It encodes a protein with a nuclease and a HEPN domain, and a predicted methyltransferase. It confers broad anti-phage defense and does not seem to mediate abortive infection. The DefenseFinder wiki describes PD-Lambda-5 as a two-gene system from a P2-like prophage that can confer broad anti-phage defense.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md The PD-Lambda-5 is composed of 2 proteins: PD-Lambda-5_A and PD-Lambda-5_B. The DefenseFinder wiki names PD-Lambda-5 as a two-protein system with PD-Lambda-5_A and PD-Lambda-5_B.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.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/RCQ13837.1'>RCQ13837.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCQ13838.1'>RCQ13838.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3 & T7 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-5 source locus expressed in E. coli against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md subgraph Title4[Protects against] T2 T4 T6 LambdaVir SECphi17 SECphi18 SECphi27 T3 T7 The DefenseFinder experimental-validation diagram lists T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7 in the PD-Lambda-5 protects-against subgraph.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv PD-Lambda-5 PD-Lambda-5 2 2 PD-Lambda-5__PD-Lambda-5_A, PD-Lambda-5__PD-Lambda-5_B The DefenseFinder rules table models PD-Lambda-5 as a two-profile system requiring PD-Lambda-5__PD-Lambda-5_A and PD-Lambda-5__PD-Lambda-5_B.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | PD-Lambda-5__PD-Lambda-5_A | PD-Lambda-5__PD-Lambda-5_A | PD-Lambda-5 | Custom | 20 | The DefenseFinder HMM inventory records PD-Lambda-5__PD-Lambda-5_A under the PD-Lambda-5 system namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | PD-Lambda-5__PD-Lambda-5_B | PD-Lambda-5__PD-Lambda-5_B | PD-Lambda-5 | Custom | 20 | The DefenseFinder HMM inventory records PD-Lambda-5__PD-Lambda-5_B under the PD-Lambda-5 system namespace.
T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7 protection confers PD-Lambda-5 system METPO:2007700
Protection against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7 realizes the PD-Lambda-5 system trait.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.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/RCQ13837.1'>RCQ13837.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCQ13838.1'>RCQ13838.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3 & T7 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-Lambda-5 source locus expressed in E. coli against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md subgraph Title4[Protects against] T2 T4 T6 LambdaVir SECphi17 SECphi18 SECphi27 T3 T7 The DefenseFinder experimental-validation diagram lists T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7 in the PD-Lambda-5 protects-against subgraph.
PD-Lambda-5 system is a phage defense system rdfs:subClassOf
PD-Lambda-5 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-5 and related conserved phage-defense systems.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md PD-Lambda-5 | 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-5 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-5 PD-Lambda-5 2 2 PD-Lambda-5__PD-Lambda-5_A, PD-Lambda-5__PD-Lambda-5_B The DefenseFinder rules table models PD-Lambda-5 as a two-profile system requiring PD-Lambda-5__PD-Lambda-5_A and PD-Lambda-5__PD-Lambda-5_B.

Provenance

Identifier source: TraitMech local identifier
Definition source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md

Parent traits (1)

phage defense system traitmech:000209

Synonyms (3)

PD-Lambda-5 RELATED_SYNONYM · https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
PD-Lambda-5__PD-Lambda-5_A RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
PD-Lambda-5__PD-Lambda-5_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-5 natural host breadth, direct phage trigger, effector mechanism, and profile-to-protein correspondence before minting narrower PD-Lambda-5 mechanism traits.

KNOWLEDGE GAP OPEN pd-lambda-5-mechanism-gap · raised by codex · 2026-09-26

Attached to causal_graphs#pd_lambda_5_locus_restricts_phages

Vassallo et al. support PD-Lambda-5 as one of the conserved systems from an E. coli pangenome phage-defense selection, the DefenseFinder wiki maps the source locus to protection against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7, and DefenseFinder represents the system with two mandatory 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-5.md
PD-lambda-5 is a two-gene system identified in a P2-like prophage. It encodes a protein with a nuclease and a HEPN domain, and a predicted methyltransferase. It confers broad anti-phage defense and does not seem to mediate abortive infection.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
PD-lambda-5 molecular mechanism has not been described to date.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.md
The PD-Lambda-5 is composed of 2 proteins: PD-Lambda-5_A and PD-Lambda-5_B.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-lambda-5.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/RCQ13837.1'>RCQ13837.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCQ13838.1'>RCQ13838.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3 & T7
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
PD-Lambda-5 PD-Lambda-5 2 2 PD-Lambda-5__PD-Lambda-5_A, PD-Lambda-5__PD-Lambda-5_B
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PD-Lambda-5__PD-Lambda-5_A | PD-Lambda-5__PD-Lambda-5_A | PD-Lambda-5 | Custom | 20 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PD-Lambda-5__PD-Lambda-5_B | PD-Lambda-5__PD-Lambda-5_B | PD-Lambda-5 | Custom | 20 |

Curation history

2026-09-26T14:07:45Z · MINTED_TRAITMECH_ID · codex
Minted PD-Lambda-5 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_v262.
2026-09-26T14:07:46Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed PD-Lambda-5 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 Plantactinospora sp. BB1 example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-Lambda-5 activity. No paid research was used.