identifier: traitmech:000394
label: PD-T4-10 system
definition: An abortive infection system in which an organism possesses a PD-T4-10
  locus represented by DefenseFinder as a two-profile model, PD-T4-10__PD-T4-10_A
  and PD-T4-10__PD-T4-10_B, and experimentally linked to T2, T4, T6, T5, and SECphi27
  protection when expressed in E. coli.
definition_source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000214
synonyms:
- synonym_text: PD-T4-10
  synonym_type: RELATED_SYNONYM
  source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md
- synonym_text: PD-T4-10__PD-T4-10_A
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
- synonym_text: PD-T4-10__PD-T4-10_B
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
evidence:
- reference: DOI:10.1038/s41564-022-01219-4
  snippet: 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.
  notes: Vassallo et al. developed the agnostic E. coli pangenome selection that uncovered
    PD-T4-10 and related conserved phage-defense systems.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md
  snippet: 'The PD-T4-10 system is composed of 2 proteins: PD-T4-10_B and, PD-T4-10_A.
    These ORFs are overlapping and PD-T4-10_B is toxic while PD-T4-10_A neutralizes
    its toxicity, hinting at a toxin-antitoxin (TA) mechanism. It confers resitance
    to T2, T4, T6 and SECphi27 through an Abi defense mechanism :ref{doi=10.1038/s41564-022-01219-4}.'
  notes: The DefenseFinder wiki describes PD-T4-10 as a two-protein Abi system whose
    overlapping ORFs include a toxic PD-T4-10_B and neutralizing PD-T4-10_A.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md
  snippet: 'The PD-T4-10 is composed of 2 proteins: PD-T4-10_A and PD-T4-10_B.'
  notes: The DefenseFinder wiki names PD-T4-10_A and PD-T4-10_B as the two components
    of the PD-T4-10 system.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md
  snippet: The PD-T4-10 system in *Escherichia fergusonii* (GCF_019047545.1, NZ_CP077242)
    is composed of 2 proteins PD-T4-10_A (WP_032236482.1) PD-T4-10_B (WP_032236481.1)
  notes: The DefenseFinder wiki illustrates a predicted PD-T4-10 locus in RefSeq assembly
    GCF_019047545.1 on NZ_CP077242.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md
  snippet: "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo\
    \ et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO36089.1'>RCO36089.1</a>,\
    \ <a href='https://ncbi.nlm.nih.gov/protein/RCO36088.1'>RCO36088.1</a>] --> Expressed_0[Escherichia\
    \ coli]\n    Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi27"
  notes: The DefenseFinder experimental-validation diagram links Vassallo et al. to
    an E. coli PD-T4-10 source locus expressed in E. coli against T2, T4, T6, T5,
    and SECphi27.
- reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md
  snippet: "subgraph Title4[Protects against]\n        T2\n        T4\n        T6\n\
    \        T5\n        SECphi27"
  notes: The DefenseFinder experimental-validation diagram lists T2, T4, T6, T5, and
    SECphi27 in the PD-T4-10 protects-against subgraph.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: PD-T4-10 | 10\.1101/2022\.05\.12\.491691 | Mapping the landscape of anti-phage
    defense mechanisms in the E\. coli pangenome
  notes: The DefenseFinder article registry maps the named PD-T4-10 system to the
    Vassallo et al. E. coli pangenome phage-defense preprint.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
  snippet: "PD-T4-10\tPD-T4-10\t2\t2\tPD-T4-10__PD-T4-10_A, PD-T4-10__PD-T4-10_B\t\
    \t\t"
  notes: The DefenseFinder rules table models PD-T4-10 as a two-profile system requiring
    PD-T4-10__PD-T4-10_A and PD-T4-10__PD-T4-10_B.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  snippet: '| PD-T4-10__PD-T4-10_A                             | PD-T4-10__PD-T4-10_A                             |
    PD-T4-10               | Custom                  | 20     |

    | PD-T4-10__PD-T4-10_B                             | PD-T4-10__PD-T4-10_B                             |
    PD-T4-10               | Custom                  | 20     |'
  notes: The DefenseFinder HMM inventory records PD-T4-10__PD-T4-10_A and PD-T4-10__PD-T4-10_B
    under the PD-T4-10 system namespace.
causal_graphs:
- graph_id: pd_t4_10_locus_restricts_t2_t4_t6_t5_and_secphi27
  title: PD-T4-10 loci restrict T2, T4, T6, T5, and SECphi27
  description: Conservative system-level sketch linking possession of a PD-T4-10 locus
    to protection against T2, T4, T6, T5, and SECphi27.
  scope_status: NONMECHANISTIC
  scope_notes: The graph captures PD-T4-10 as a named DefenseFinder abortive-infection
    system while leaving natural host breadth, the direct phage trigger, the toxic
    PD-T4-10_B target, and the PD-T4-10_A neutralization logic unresolved.
  nodes:
  - node_id: pd_t4_10_locus
    label: PD-T4-10 locus
    node_type: GENETIC_ELEMENT
    description: A two-profile abortive-infection locus represented by the DefenseFinder
      PD-T4-10_A and PD-T4-10_B profiles.
  - node_id: pd_t4_10_listed_phage_protection
    label: T2, T4, T6, T5, and SECphi27 protection
    node_type: BIOLOGICAL_PROCESS
    description: Protection against T2, T4, T6, T5, and SECphi27 by PD-T4-10.
  - node_id: pd_t4_10_system_trait
    label: PD-T4-10 system
    node_type: TRAIT
    grounding: traitmech:000394
    description: Possession of a genome-encoded PD-T4-10 abortive-infection phage-defense
      system.
  - node_id: abortive_infection_system
    label: abortive infection system
    node_type: TRAIT
    grounding: traitmech:000214
    description: Possession of a genome-encoded abortive-infection phage-defense system.
  edges:
  - subject: pd_t4_10_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: pd_t4_10_listed_phage_protection
    description: The DefenseFinder wiki links a PD-T4-10 locus from Vassallo et al.
      to protection against T2, T4, T6, T5, and SECphi27, and DefenseFinder models
      PD-T4-10 through two mandatory profiles.
    evidence:
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md
      snippet: 'The PD-T4-10 system is composed of 2 proteins: PD-T4-10_B and, PD-T4-10_A.
        These ORFs are overlapping and PD-T4-10_B is toxic while PD-T4-10_A neutralizes
        its toxicity, hinting at a toxin-antitoxin (TA) mechanism. It confers resitance
        to T2, T4, T6 and SECphi27 through an Abi defense mechanism :ref{doi=10.1038/s41564-022-01219-4}.'
      notes: The DefenseFinder wiki describes PD-T4-10 as a two-protein Abi system
        whose overlapping ORFs include a toxic PD-T4-10_B and neutralizing PD-T4-10_A.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md
      snippet: 'The PD-T4-10 is composed of 2 proteins: PD-T4-10_A and PD-T4-10_B.'
      notes: The DefenseFinder wiki names PD-T4-10_A and PD-T4-10_B as the two components
        of the PD-T4-10 system.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md
      snippet: "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo\
        \ et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO36089.1'>RCO36089.1</a>,\
        \ <a href='https://ncbi.nlm.nih.gov/protein/RCO36088.1'>RCO36088.1</a>] -->\
        \ Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2\
        \ & T4 & T6 & T5 & SECphi27"
      notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
        to an E. coli PD-T4-10 source locus expressed in E. coli against T2, T4, T6,
        T5, and SECphi27.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md
      snippet: "subgraph Title4[Protects against]\n        T2\n        T4\n      \
        \  T6\n        T5\n        SECphi27"
      notes: The DefenseFinder experimental-validation diagram lists T2, T4, T6, T5,
        and SECphi27 in the PD-T4-10 protects-against subgraph.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "PD-T4-10\tPD-T4-10\t2\t2\tPD-T4-10__PD-T4-10_A, PD-T4-10__PD-T4-10_B\t\
        \t\t"
      notes: The DefenseFinder rules table models PD-T4-10 as a two-profile system
        requiring PD-T4-10__PD-T4-10_A and PD-T4-10__PD-T4-10_B.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: '| PD-T4-10__PD-T4-10_A                             | PD-T4-10__PD-T4-10_A                             |
        PD-T4-10               | Custom                  | 20     |

        | PD-T4-10__PD-T4-10_B                             | PD-T4-10__PD-T4-10_B                             |
        PD-T4-10               | Custom                  | 20     |'
      notes: The DefenseFinder HMM inventory records PD-T4-10__PD-T4-10_A and PD-T4-10__PD-T4-10_B
        under the PD-T4-10 system namespace.
  - subject: pd_t4_10_listed_phage_protection
    predicate: confers
    predicate_id: METPO:2007700
    object: pd_t4_10_system_trait
    description: Protection against T2, T4, T6, T5, and SECphi27 realizes the PD-T4-10
      system trait.
    evidence:
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md
      snippet: "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo\
        \ et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO36089.1'>RCO36089.1</a>,\
        \ <a href='https://ncbi.nlm.nih.gov/protein/RCO36088.1'>RCO36088.1</a>] -->\
        \ Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2\
        \ & T4 & T6 & T5 & SECphi27"
      notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
        to an E. coli PD-T4-10 source locus expressed in E. coli against T2, T4, T6,
        T5, and SECphi27.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md
      snippet: "subgraph Title4[Protects against]\n        T2\n        T4\n      \
        \  T6\n        T5\n        SECphi27"
      notes: The DefenseFinder experimental-validation diagram lists T2, T4, T6, T5,
        and SECphi27 in the PD-T4-10 protects-against subgraph.
  - subject: pd_t4_10_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: abortive_infection_system
    description: PD-T4-10 system possession is an abortive-infection-system trait.
    evidence:
    - reference: DOI:10.1038/s41564-022-01219-4
      snippet: 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.
      notes: Vassallo et al. developed the agnostic E. coli pangenome selection that
        uncovered PD-T4-10 and related conserved phage-defense systems.
    - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md
      snippet: 'The PD-T4-10 system is composed of 2 proteins: PD-T4-10_B and, PD-T4-10_A.
        These ORFs are overlapping and PD-T4-10_B is toxic while PD-T4-10_A neutralizes
        its toxicity, hinting at a toxin-antitoxin (TA) mechanism. It confers resitance
        to T2, T4, T6 and SECphi27 through an Abi defense mechanism :ref{doi=10.1038/s41564-022-01219-4}.'
      notes: The DefenseFinder wiki describes PD-T4-10 as a two-protein Abi system
        whose overlapping ORFs include a toxic PD-T4-10_B and neutralizing PD-T4-10_A.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: PD-T4-10 | 10\.1101/2022\.05\.12\.491691 | Mapping the landscape of
        anti-phage defense mechanisms in the E\. coli pangenome
      notes: The DefenseFinder article registry maps the named PD-T4-10 system to
        the Vassallo et al. E. coli pangenome phage-defense preprint.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
      snippet: "PD-T4-10\tPD-T4-10\t2\t2\tPD-T4-10__PD-T4-10_A, PD-T4-10__PD-T4-10_B\t\
        \t\t"
      notes: The DefenseFinder rules table models PD-T4-10 as a two-profile system
        requiring PD-T4-10__PD-T4-10_A and PD-T4-10__PD-T4-10_B.
discussions:
- discussion_id: pd-t4-10-mechanism-gap
  prompt: Resolve PD-T4-10 natural host breadth, direct phage trigger, the toxic PD-T4-10_B
    target, and PD-T4-10_A neutralization logic before minting narrower PD-T4-10 mechanism
    traits.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: Vassallo et al. support PD-T4-10 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, T5, and SECphi27, and DefenseFinder
    represents the system with two mandatory profiles and an abortive-infection mechanism
    assignment. Natural host breadth, the direct phage trigger, the toxic PD-T4-10_B
    target, and the PD-T4-10_A neutralization logic remain unresolved.
  evidence:
  - reference: DOI:10.1038/s41564-022-01219-4
    snippet: 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.
    notes: Vassallo et al. developed the agnostic E. coli pangenome selection that
      uncovered PD-T4-10 and related conserved phage-defense systems.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md
    snippet: 'The PD-T4-10 system is composed of 2 proteins: PD-T4-10_B and, PD-T4-10_A.
      These ORFs are overlapping and PD-T4-10_B is toxic while PD-T4-10_A neutralizes
      its toxicity, hinting at a toxin-antitoxin (TA) mechanism. It confers resitance
      to T2, T4, T6 and SECphi27 through an Abi defense mechanism :ref{doi=10.1038/s41564-022-01219-4}.'
    notes: The DefenseFinder wiki describes PD-T4-10 as a two-protein Abi system whose
      overlapping ORFs include a toxic PD-T4-10_B and neutralizing PD-T4-10_A.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md
    snippet: 'The PD-T4-10 is composed of 2 proteins: PD-T4-10_A and PD-T4-10_B.'
    notes: The DefenseFinder wiki names PD-T4-10_A and PD-T4-10_B as the two components
      of the PD-T4-10 system.
  - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-10.md
    snippet: "Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo\
      \ et al., 2022</a>] --> Origin_0\n    Origin_0[Escherichia coli \n<a href='https://ncbi.nlm.nih.gov/protein/RCO36089.1'>RCO36089.1</a>,\
      \ <a href='https://ncbi.nlm.nih.gov/protein/RCO36088.1'>RCO36088.1</a>] -->\
      \ Expressed_0[Escherichia coli]\n    Expressed_0[Escherichia coli] ----> T2\
      \ & T4 & T6 & T5 & SECphi27"
    notes: The DefenseFinder experimental-validation diagram links Vassallo et al.
      to an E. coli PD-T4-10 source locus expressed in E. coli against T2, T4, T6,
      T5, and SECphi27.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    snippet: "PD-T4-10\tPD-T4-10\t2\t2\tPD-T4-10__PD-T4-10_A, PD-T4-10__PD-T4-10_B\t\
      \t\t"
    notes: The DefenseFinder rules table models PD-T4-10 as a two-profile system requiring
      PD-T4-10__PD-T4-10_A and PD-T4-10__PD-T4-10_B.
  - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    snippet: '| PD-T4-10__PD-T4-10_A                             | PD-T4-10__PD-T4-10_A                             |
      PD-T4-10               | Custom                  | 20     |

      | PD-T4-10__PD-T4-10_B                             | PD-T4-10__PD-T4-10_B                             |
      PD-T4-10               | Custom                  | 20     |'
    notes: The DefenseFinder HMM inventory records PD-T4-10__PD-T4-10_A and PD-T4-10__PD-T4-10_B
      under the PD-T4-10 system namespace.
  attaches_to:
  - causal_graphs#pd_t4_10_locus_restricts_t2_t4_t6_t5_and_secphi27
  posed_by: codex
  posed_date: '2026-09-26'
curation_history:
- timestamp: '2026-09-26T20:56:41Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Minted PD-T4-10 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord
    under abortive infection 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_v271.
  llm_assisted: true
- timestamp: '2026-09-26T20:56:42Z'
  curator: codex
  action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP
  changes: Reviewed PD-T4-10 system canonical_examples and left them empty because
    the current sources support an E. coli accession-level experimental validation
    graph, a DefenseFinder two-profile system model, and a RefSeq Escherichia fergusonii
    example, but not a direct native microbial isolate exemplar with experimentally
    verified endogenous PD-T4-10 activity. No paid research was used.
  llm_assisted: true