PD-T4-4 system

traitmech:000389 · CLASS · PROPOSED

A phage defense system in which an organism possesses a PD-T4-4 locus represented by DefenseFinder as a two-profile model requiring PD-T4-4__PD-T4-4_A and PD-T4-4__PD-T4-4_B, and experimentally linked to T2, T4, T6, and SECphi17 protection when expressed in E. coli.

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-T4-4 and related conserved phage-defense systems.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md
PD-T4-4 is a defense system composed of two proteins, a P-loop NTPase and a nuclease, that is most likely protecting the bacterial population through abortive infection. It was identified from an ICE in an *E. coli* genome.

The DefenseFinder wiki describes PD-T4-4 as a two-protein system from an E. coli integrative and conjugative element.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md
The PD-T4-4 is composed of 2 proteins: PD-T4-4_A and PD-T4-4_B.

The DefenseFinder wiki names PD-T4-4 as a two-protein system with PD-T4-4_A and PD-T4-4_B components.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md
The PD-T4-4 system in *Thiothrix subterranea* (GCF_016772315.1, NZ_CP053482) is composed of 2 proteins PD-T4-4_A (WP_202716711.1) PD-T4-4_B (WP_202716712.1)

The DefenseFinder wiki illustrates a predicted two-protein PD-T4-4 locus in RefSeq assembly GCF_016772315.1 on NZ_CP053482.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.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/RCO57999.1'>RCO57999.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO57988.1'>RCO57988.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi17

The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-4 source locus expressed in E. coli against T2, T4, T6, and SECphi17.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md
subgraph Title4[Protects against] T2 T4 T6 SECphi17

The DefenseFinder experimental-validation diagram lists T2, T4, T6, and SECphi17 in the PD-T4-4 protects-against subgraph.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
PD-T4-4 | 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-T4-4 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-T4-4 PD-T4-4 2 2 PD-T4-4__PD-T4-4_A, PD-T4-4__PD-T4-4_B

The DefenseFinder rules table models PD-T4-4 as a two-profile system requiring PD-T4-4__PD-T4-4_A and PD-T4-4__PD-T4-4_B.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PD-T4-4__PD-T4-4_A | PD-T4-4__PD-T4-4_A | PD-T4-4 | Custom | 75 |

The DefenseFinder HMM inventory records PD-T4-4__PD-T4-4_A under the PD-T4-4 system namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PD-T4-4__PD-T4-4_B | PD-T4-4__PD-T4-4_B | PD-T4-4 | Custom | 25 |

The DefenseFinder HMM inventory records PD-T4-4__PD-T4-4_B under the PD-T4-4 system namespace.

PD-T4-4 loci restrict T2, T4, T6, and SECphi17

Conservative system-level sketch linking possession of a PD-T4-4 locus to protection against T2, T4, T6, and SECphi17.

NONMECHANISTIC · The graph captures PD-T4-4 as a named DefenseFinder phage-defense system while leaving natural host breadth, the direct phage trigger, and the hinted abortive-infection effector mechanism unmodeled until direct mechanism evidence is available.

Edge evidence

PD-T4-4 locus contributes to T2, T4, T6, and SECphi17 protection RO:0002326
The DefenseFinder wiki links a PD-T4-4 locus from Vassallo et al. to protection against T2, T4, T6, and SECphi17, and DefenseFinder models PD-T4-4 through two mandatory profiles.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md PD-T4-4 is a defense system composed of two proteins, a P-loop NTPase and a nuclease, that is most likely protecting the bacterial population through abortive infection. It was identified from an ICE in an *E. coli* genome. The DefenseFinder wiki describes PD-T4-4 as a two-protein system from an E. coli integrative and conjugative element.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md The PD-T4-4 is composed of 2 proteins: PD-T4-4_A and PD-T4-4_B. The DefenseFinder wiki names PD-T4-4 as a two-protein system with PD-T4-4_A and PD-T4-4_B components.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.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/RCO57999.1'>RCO57999.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO57988.1'>RCO57988.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi17 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-4 source locus expressed in E. coli against T2, T4, T6, and SECphi17.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md subgraph Title4[Protects against] T2 T4 T6 SECphi17 The DefenseFinder experimental-validation diagram lists T2, T4, T6, and SECphi17 in the PD-T4-4 protects-against subgraph.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv PD-T4-4 PD-T4-4 2 2 PD-T4-4__PD-T4-4_A, PD-T4-4__PD-T4-4_B The DefenseFinder rules table models PD-T4-4 as a two-profile system requiring PD-T4-4__PD-T4-4_A and PD-T4-4__PD-T4-4_B.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | PD-T4-4__PD-T4-4_A | PD-T4-4__PD-T4-4_A | PD-T4-4 | Custom | 75 | The DefenseFinder HMM inventory records PD-T4-4__PD-T4-4_A under the PD-T4-4 system namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | PD-T4-4__PD-T4-4_B | PD-T4-4__PD-T4-4_B | PD-T4-4 | Custom | 25 | The DefenseFinder HMM inventory records PD-T4-4__PD-T4-4_B under the PD-T4-4 system namespace.
T2, T4, T6, and SECphi17 protection confers PD-T4-4 system METPO:2007700
Protection against T2, T4, T6, and SECphi17 realizes the PD-T4-4 system trait.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.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/RCO57999.1'>RCO57999.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO57988.1'>RCO57988.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi17 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-4 source locus expressed in E. coli against T2, T4, T6, and SECphi17.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md subgraph Title4[Protects against] T2 T4 T6 SECphi17 The DefenseFinder experimental-validation diagram lists T2, T4, T6, and SECphi17 in the PD-T4-4 protects-against subgraph.
PD-T4-4 system is a phage defense system rdfs:subClassOf
PD-T4-4 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-T4-4 and related conserved phage-defense systems.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md PD-T4-4 | 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-T4-4 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-T4-4 PD-T4-4 2 2 PD-T4-4__PD-T4-4_A, PD-T4-4__PD-T4-4_B The DefenseFinder rules table models PD-T4-4 as a two-profile system requiring PD-T4-4__PD-T4-4_A and PD-T4-4__PD-T4-4_B.

Provenance

Identifier source: TraitMech local identifier
Definition source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md

Parent traits (1)

phage defense system traitmech:000209

Synonyms (3)

PD-T4-4 RELATED_SYNONYM · https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md
PD-T4-4__PD-T4-4_A RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
PD-T4-4__PD-T4-4_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-T4-4 natural host breadth, direct phage trigger, and effector mechanism before minting narrower PD-T4-4 mechanism traits.

KNOWLEDGE GAP OPEN pd-t4-4-mechanism-gap · raised by codex · 2026-09-26

Attached to causal_graphs#pd_t4_4_locus_restricts_t2_t4_t6_and_secphi17

Vassallo et al. support PD-T4-4 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, and SECphi17, and DefenseFinder represents the system with two mandatory profiles. Natural host breadth, the direct phage trigger, and direct effector logic remain unresolved, so the likely abortive-infection hypothesis is left unmodeled.

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-t4-4.md
PD-T4-4 is a defense system composed of two proteins, a P-loop NTPase and a nuclease, that is most likely protecting the bacterial population through abortive infection. It was identified from an ICE in an *E. coli* genome.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.md
The PD-T4-4 is composed of 2 proteins: PD-T4-4_A and PD-T4-4_B.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-4.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/RCO57999.1'>RCO57999.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO57988.1'>RCO57988.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi17
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
PD-T4-4 PD-T4-4 2 2 PD-T4-4__PD-T4-4_A, PD-T4-4__PD-T4-4_B
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PD-T4-4__PD-T4-4_A | PD-T4-4__PD-T4-4_A | PD-T4-4 | Custom | 75 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PD-T4-4__PD-T4-4_B | PD-T4-4__PD-T4-4_B | PD-T4-4 | Custom | 25 |

Curation history

2026-09-26T16:51:00Z · MINTED_TRAITMECH_ID · codex
Minted PD-T4-4 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_v266.
2026-09-26T16:51:01Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed PD-T4-4 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 Thiothrix subterranea example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-T4-4 activity. No paid research was used.
2026-09-26T17:24:43Z · ADDRESS_SCOPE_NOTE_REVIEW · codex
Clarified after Claude Code Review issue 1288 that the DefenseFinder wiki names abortive infection as the likely PD-T4-4 population-level protection route, but the graph leaves that hypothesis unmodeled until direct mechanism evidence is available.