PD-T4-7 system

traitmech:000392 · CLASS · PROPOSED

An abortive infection system in which an organism possesses a PD-T4-7 locus represented by DefenseFinder as a single-profile model, PD-T4-7__PD-T4-7, and experimentally linked to T2, T4, and T6 protection when expressed in E. coli.

Trait evidence (9)

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-T4-7 and related conserved phage-defense systems.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md
The PD-T4-7 is composed of 1 protein: PD-T4-7.

The DefenseFinder wiki names PD-T4-7 as a single-protein system.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md
Vassalo et al. :ref{doi=10.1038/s41564-022-01219-4} state that PD-T4-7 functions through an abortive infection mechanism.

The DefenseFinder wiki reports an abortive-infection mechanism assignment for PD-T4-7 while leaving the direct substrate and effector logic unresolved.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md
The PD-T4-7 system in *Thalassospira sp. B30-1* (GCF_015767575.1, NZ_CP065232) is composed of 1 protein: PD-T4-7 (WP_139190007.1)

The DefenseFinder wiki illustrates a predicted PD-T4-7 locus in RefSeq assembly GCF_015767575.1 on NZ_CP065232.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.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/RRN43039.1'>RRN43039.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6

The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-7 source locus expressed in E. coli against T2, T4, and T6.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md
subgraph Title4[Protects against] T2 T4 T6

The DefenseFinder experimental-validation diagram lists T2, T4, and T6 in the PD-T4-7 protects-against subgraph.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
PD-T4-7 | 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-T4-7 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-T4-7 PD-T4-7 1 1 PD-T4-7__PD-T4-7

The DefenseFinder rules table models PD-T4-7 as a single-profile system requiring PD-T4-7__PD-T4-7.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PD-T4-7__PD-T4-7 | PD-T4-7__PD-T4-7 | PD-T4-7 | Custom | 80 |

The DefenseFinder HMM inventory records PD-T4-7__PD-T4-7 under the PD-T4-7 system namespace.

PD-T4-7 loci restrict T2, T4, and T6

Conservative system-level sketch linking possession of a PD-T4-7 locus to protection against T2, T4, and T6.

NONMECHANISTIC · The graph captures PD-T4-7 as a named DefenseFinder abortive-infection system while leaving natural host breadth, the direct phage trigger, and the direct effector logic unresolved.

Edge evidence

PD-T4-7 locus contributes to T2, T4, and T6 protection RO:0002326
The DefenseFinder wiki links a PD-T4-7 locus from Vassallo et al. to protection against T2, T4, and T6, and DefenseFinder models PD-T4-7 through one mandatory profile.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md The PD-T4-7 is composed of 1 protein: PD-T4-7. The DefenseFinder wiki names PD-T4-7 as a single-protein system.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.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/RRN43039.1'>RRN43039.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-7 source locus expressed in E. coli against T2, T4, and T6.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md subgraph Title4[Protects against] T2 T4 T6 The DefenseFinder experimental-validation diagram lists T2, T4, and T6 in the PD-T4-7 protects-against subgraph.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv PD-T4-7 PD-T4-7 1 1 PD-T4-7__PD-T4-7 The DefenseFinder rules table models PD-T4-7 as a single-profile system requiring PD-T4-7__PD-T4-7.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | PD-T4-7__PD-T4-7 | PD-T4-7__PD-T4-7 | PD-T4-7 | Custom | 80 | The DefenseFinder HMM inventory records PD-T4-7__PD-T4-7 under the PD-T4-7 system namespace.
T2, T4, and T6 protection confers PD-T4-7 system METPO:2007700
Protection against T2, T4, and T6 realizes the PD-T4-7 system trait.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.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/RRN43039.1'>RRN43039.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6 The DefenseFinder experimental-validation diagram links Vassallo et al. to an E. coli PD-T4-7 source locus expressed in E. coli against T2, T4, and T6.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md subgraph Title4[Protects against] T2 T4 T6 The DefenseFinder experimental-validation diagram lists T2, T4, and T6 in the PD-T4-7 protects-against subgraph.
PD-T4-7 system is a abortive infection system rdfs:subClassOf
PD-T4-7 system possession is an abortive-infection-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-T4-7 and related conserved phage-defense systems.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md Vassalo et al. :ref{doi=10.1038/s41564-022-01219-4} state that PD-T4-7 functions through an abortive infection mechanism. The DefenseFinder wiki reports an abortive-infection mechanism assignment for PD-T4-7 while leaving the direct substrate and effector logic unresolved.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md PD-T4-7 | 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-T4-7 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-T4-7 PD-T4-7 1 1 PD-T4-7__PD-T4-7 The DefenseFinder rules table models PD-T4-7 as a single-profile system requiring PD-T4-7__PD-T4-7.

Provenance

Identifier source: TraitMech local identifier
Definition source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md

Parent traits (1)

abortive infection system traitmech:000214

Synonyms (2)

PD-T4-7 RELATED_SYNONYM · https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md
PD-T4-7__PD-T4-7 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-T4-7 natural host breadth, direct phage trigger, and direct abortive-infection effector logic before minting narrower PD-T4-7 mechanism traits.

KNOWLEDGE GAP OPEN pd-t4-7-mechanism-gap · raised by codex · 2026-09-26

Attached to causal_graphs#pd_t4_7_locus_restricts_t2_t4_and_t6

Vassallo et al. support PD-T4-7 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, and T6, and DefenseFinder represents the system with one mandatory profile and an abortive-infection mechanism assignment. Natural host breadth, the direct phage trigger, and direct effector logic 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-t4-7.md
The PD-T4-7 is composed of 1 protein: PD-T4-7.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.md
Vassalo et al. :ref{doi=10.1038/s41564-022-01219-4} state that PD-T4-7 functions through an abortive infection mechanism.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-7.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/RRN43039.1'>RRN43039.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T2 & T4 & T6
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
PD-T4-7 PD-T4-7 1 1 PD-T4-7__PD-T4-7
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| PD-T4-7__PD-T4-7 | PD-T4-7__PD-T4-7 | PD-T4-7 | Custom | 80 |

Curation history

2026-09-26T19:13:36Z · MINTED_TRAITMECH_ID · codex
Minted PD-T4-7 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_v269.
2026-09-26T19:13:37Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed PD-T4-7 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 Thalassospira example, but not a direct native microbial isolate exemplar with experimentally verified endogenous PD-T4-7 activity. No paid research was used.
2026-09-26T19:42:30Z · ADDRESS_SCOPE_NOTE_REVIEW · codex
Addressed PR 1292 review issue 1293 by reparenting PD-T4-7 under abortive infection system, updating the subclass graph node, and naming the DefenseFinder abortive-infection assignment while leaving natural host breadth, the direct phage trigger, and direct effector logic unresolved.
2026-09-26T19:55:00Z · RESTORE_MINT_EVENT_PROVENANCE · codex
Addressed PR 1292 review issue 1294 by restoring the original mint event to say PD-T4-7 was minted under phage defense system; the later ADDRESS_SCOPE_NOTE_REVIEW event records the abortive-infection reparenting.