identifier: traitmech:000323 label: Pif system definition: An abortive infection system in which an organism possesses an F-plasmid pif-family locus represented by the DefenseFinder Pif__PifA and Pif__PifC profiles and exemplified by the pif region that specifies abortive infection of T7 phage. definition_source: DOI:10.1007/BF00327934 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000214 synonyms: - synonym_text: Pif synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md evidence: - reference: PMID:6096670 snippet: Molecular analysis of F plasmid pif region specifying abortive infection of T7 phage. notes: Cram et al. title the paper around F-plasmid pif-region specification of the T7 abortive-infection phenotype. - reference: DOI:10.1007/BF00327934 snippet: We report the molecular cloning of the pif region of the F plasmid and its physical dissection by subcloning and deletion analysis. notes: Cram et al. cloned and deletion-mapped the F-plasmid pif region. - reference: DOI:10.1007/BF00327934 snippet: Examination of the polypeptide products synthesized in maxicells by plasmids carrying defined pif sequences has shown that the region specifies at least two proteins of molecular weights 80,000 and 40,000, the genes for which appear to lie in the same transcriptional unit. notes: Cram et al. support a multigene pif region without resolving a direct PifA or PifC molecular function. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Pif | 10\.1007/BF00327934 | Molecular analysis of F plasmid pif region specifying abortive infection of T7 phage notes: The DefenseFinder article registry maps the named Pif model namespace to the F-plasmid pif-region molecular analysis paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Pif\tPif\t2\t2\tPif__PifA, Pif__PifC" notes: The DefenseFinder rules table models Pif as a two-component system requiring both the Pif__PifA and Pif__PifC profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Pif__PifA | Pif__PifA | Pif | Custom | 20 |' notes: The DefenseFinder HMM inventory records Pif__PifA under Pif. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Pif__PifC | Pif__PifC | Pif | Custom | 20 |' notes: The DefenseFinder HMM inventory records Pif__PifC under Pif. causal_graphs: - graph_id: pif_locus_specifies_t7_abortive_infection title: Pif locus specifies T7 abortive infection description: Conservative system-level sketch linking an F-plasmid pif-family locus to T7 abortive infection and Pif-system possession without asserting the direct phage trigger, host-cell output, or PifA/PifC molecular targets. scope_status: NONMECHANISTIC scope_notes: The graph captures Pif as a named DefenseFinder two-profile abortive-infection system whose F-plasmid prototype specifies T7 abortive infection. It leaves the direct T7 trigger, PifA and PifC molecular functions, host-cell output, and phage escape route unresolved. nodes: - node_id: pif_locus label: pif locus node_type: GENETIC_ELEMENT description: An F-plasmid pif-family abortive-infection locus represented by the DefenseFinder Pif__PifA and Pif__PifC profiles. - node_id: t7_abortive_infection label: T7 abortive infection node_type: BIOLOGICAL_PROCESS description: Abortive infection of T7 phage specified by an F-plasmid pif region. - node_id: pif_system_trait label: Pif system node_type: TRAIT grounding: traitmech:000323 description: Possession of a genome-encoded Pif abortive-infection phage-defense system. edges: - subject: pif_locus predicate: contributes to predicate_id: RO:0002326 object: t7_abortive_infection description: The F-plasmid pif region specifies T7 abortive infection, and DefenseFinder represents Pif with required PifA and PifC profiles. evidence: - reference: PMID:6096670 snippet: Molecular analysis of F plasmid pif region specifying abortive infection of T7 phage. notes: Cram et al. frame the F-plasmid pif region as specifying T7 abortive infection. - reference: DOI:10.1007/BF00327934 snippet: the region specifies at least two proteins of molecular weights 80,000 and 40,000 notes: Cram et al. observed two pif-region polypeptides in maxicells. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Pif\tPif\t2\t2\tPif__PifA, Pif__PifC" notes: The DefenseFinder rules table models Pif as a two-component system requiring both the Pif__PifA and Pif__PifC profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Pif__PifA | Pif__PifA | Pif | Custom | 20 |' notes: The DefenseFinder HMM inventory records Pif__PifA under Pif. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Pif__PifC | Pif__PifC | Pif | Custom | 20 |' notes: The DefenseFinder HMM inventory records Pif__PifC under Pif. - subject: t7_abortive_infection predicate: confers predicate_id: METPO:2007700 object: pif_system_trait description: F-plasmid-pif-specified T7 abortive infection realizes the Pif system trait. evidence: - reference: PMID:6096670 snippet: Molecular analysis of F plasmid pif region specifying abortive infection of T7 phage. notes: Cram et al. support T7 abortive infection as the pif-region output. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Pif | 10\.1007/BF00327934 | Molecular analysis of F plasmid pif region specifying abortive infection of T7 phage notes: The DefenseFinder article registry maps the named Pif model namespace to the F-plasmid pif-region molecular analysis paper. discussions: - discussion_id: pif-output-gap prompt: Resolve the direct T7 trigger, PifA and PifC molecular functions, host-cell output, and phage escape routes before minting narrower Pif mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Cram et al. support an F-plasmid pif-region abortive-infection system that maps to a two-profile DefenseFinder model, but the direct T7 trigger, the molecular functions of PifA and PifC, the host-cell growth-arrest or cell-death output, and phage escape routes remain unresolved. attaches_to: - causal_graphs#pif_locus_specifies_t7_abortive_infection posed_by: codex posed_date: '2026-09-21' curation_history: - timestamp: '2026-09-21T01:30:12Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Pif system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent 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_v200. llm_assisted: true - timestamp: '2026-09-21T01:30:13Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: 'Reviewed canonical example evidence while minting Pif system and left canonical_examples empty: the Cram et al. prototype supports an F-plasmid pif region that specifies T7 abortive infection and the pinned DefenseFinder registry maps a two-profile Pif namespace, but the available curation sources do not identify a natural organism instance with a directly observed Pif locus. No paid research was used.' llm_assisted: true