identifier: traitmech:000259 label: SEFIR system definition: A phage defense system in which an organism possesses a SEFIR locus represented by a bSEFIR profile that can protect bacteria from bacteriophage infection. definition_source: DOI:10.1016/j.chom.2022.09.017 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: SEFIR synonym_type: EXACT_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md evidence: - reference: DOI:10.1016/j.chom.2022.09.017 snippet: discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments notes: Millman et al. report the computational and experimental cohort that DefenseFinder cites for SEFIR as a bacterial anti-phage system. - reference: DOI:10.1101/2022.05.11.491447 snippet: discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments notes: The bioRxiv version of Millman et al. independently carries the 21-system discovery claim linked from DefenseFinder's SEFIR article registry. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: SEFIR | 10\.1101/2022\.05\.11\.491447 | An expanding arsenal of immune systems that protect bacteria from phages notes: The DefenseFinder model registry maps the named SEFIR system to the Millman et al. antiphage-system discovery preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "SEFIR\tSEFIR\t1\t1\tSEFIR__bSEFIR" notes: The DefenseFinder rules table models SEFIR with a bSEFIR profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: SEFIR__bSEFIR | SEFIR__bSEFIR | SEFIR notes: The DefenseFinder HMM inventory records bSEFIR as a SEFIR profile. causal_graphs: - graph_id: sefir_locus_restricts_phage title: SEFIR loci confer bacterial phage defense description: Conservative system-level sketch linking possession of a SEFIR locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output. scope_status: NONMECHANISTIC scope_notes: The graph captures SEFIR as a named anti-phage system with the required DefenseFinder bSEFIR profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved. nodes: - node_id: sefir_locus label: SEFIR locus node_type: GENETIC_ELEMENT description: A SEFIR anti-phage defense locus satisfying a DefenseFinder rule over the bSEFIR profile. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced propagation of bacteriophage in cells carrying the SEFIR system. - node_id: sefir_system_trait label: SEFIR system node_type: TRAIT grounding: traitmech:000259 description: Possession of a genome-encoded SEFIR phage-defense system. - node_id: phage_defense_system label: phage defense system node_type: TRAIT grounding: traitmech:000209 description: Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection. edges: - subject: sefir_locus predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: DefenseFinder maps SEFIR to a bacterial anti-phage-system discovery preprint and represents SEFIR loci through the bSEFIR component profile. evidence: - reference: DOI:10.1016/j.chom.2022.09.017 snippet: discovery of 21 defense systems that protect bacteria from phages notes: Millman et al. describe the anti-phage discovery cohort that the DefenseFinder SEFIR registry row maps to the SEFIR system. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: SEFIR | 10\.1101/2022\.05\.11\.491447 | An expanding arsenal of immune systems that protect bacteria from phages notes: The DefenseFinder registry maps SEFIR itself to the Millman et al. bacterial antiphage-system discovery preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "SEFIR\tSEFIR\t1\t1\tSEFIR__bSEFIR" notes: The DefenseFinder rules table supports bSEFIR as the required SEFIR system profile. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: sefir_system_trait description: SEFIR-mediated phage restriction realizes the SEFIR system trait. evidence: - reference: DOI:10.1016/j.chom.2022.09.017 snippet: discovery of 21 defense systems that protect bacteria from phages notes: Millman et al. place the SEFIR discovery cohort in the set of bacterial systems that protect against phages. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: SEFIR | 10\.1101/2022\.05\.11\.491447 | An expanding arsenal of immune systems that protect bacteria from phages notes: DefenseFinder records SEFIR as a named system from the Millman et al. antiphage discovery preprint. - subject: sefir_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: SEFIR system possession is a phage-defense-system trait. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: An expanding arsenal of immune systems that protect bacteria from phages notes: DefenseFinder associates SEFIR with the Millman et al. bacterial antiphage-system discovery paper. discussions: - discussion_id: sefir-mechanism-gap prompt: Resolve SEFIR phage triggers and effector outputs before minting narrower SEFIR mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Millman et al. and DefenseFinder support SEFIR as a named anti-phage system with a bSEFIR profile, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait. attaches_to: - causal_graphs#sefir_locus_restricts_phage posed_by: codex posed_date: '2026-09-19' curation_history: - timestamp: '2026-09-19T01:51:02Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted SEFIR system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v136. llm_assisted: true