identifier: traitmech:000409 label: Gao-Her system definition: A phage defense system in which an organism possesses a Gao_Her locus represented by DefenseFinder as either a Gao_Her_DUF or Gao_Her_SIR two-profile subsystem. definition_source: DOI:10.1126/science.aba0372 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Gao_Her synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md evidence: - reference: PMID:32855333 snippet: By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages. notes: Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Gao_Her | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes notes: The DefenseFinder article registry maps Gao_Her to the Gao et al. prokaryotic antiviral-immunity paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Gao_Her\tGao_Her_DUF\t2\t2\tGao_Her_DUF__DUF4297, Gao_Her_DUF__HerA_DUF" notes: The DefenseFinder rules table models Gao_Her_DUF as a two-profile Gao_Her subsystem requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Gao_Her\tGao_Her_SIR\t2\t2\tGao_Her_SIR__HerA_SIR2, Gao_Her_SIR__SIR2" notes: The DefenseFinder rules table models Gao_Her_SIR as a two-profile Gao_Her subsystem requiring Gao_Her_SIR__HerA_SIR2 and Gao_Her_SIR__SIR2. causal_graphs: - graph_id: gao_her_locus_restricts_phage title: Gao-Her loci confer bacterial phage defense description: Conservative family-level sketch linking Gao_Her loci to Gao et al. antiviral cassette defense without asserting the unresolved Her-DUF or Her-SIR component activities. scope_status: NONMECHANISTIC scope_notes: The graph captures Gao-Her as the DefenseFinder Gao_Her family containing Gao_Her_DUF and Gao_Her_SIR subsystems while leaving natural hosts, subtype-specific phage triggers, and DUF4297, HerA_DUF, HerA_SIR2, and SIR2 molecular functions unresolved. nodes: - node_id: gao_her_locus label: Gao_Her locus node_type: GENETIC_ELEMENT description: A DefenseFinder Gao_Her phage-defense locus represented as a Gao_Her_DUF or Gao_Her_SIR two-profile subsystem. - node_id: gao_2020_antiviral_cassette_defense label: Gao 2020 antiviral cassette defense node_type: BIOLOGICAL_PROCESS description: Bacteriophage protection by one of the antiviral gene cassettes described in the Gao et al. systematic defense-gene discovery campaign. - node_id: gao_her_system_trait label: Gao-Her system node_type: TRAIT grounding: traitmech:000409 description: Possession of a genome-encoded Gao-Her 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: gao_her_locus predicate: contributes to predicate_id: RO:0002326 object: gao_2020_antiviral_cassette_defense description: DefenseFinder maps Gao_Her to the Gao et al. systematic antiphage-system discovery paper and models two Gao_Her subsystems, Gao_Her_DUF and Gao_Her_SIR. evidence: - reference: PMID:32855333 snippet: By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages. notes: Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Gao_Her | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes notes: The DefenseFinder article registry maps Gao_Her to the Gao et al. prokaryotic antiviral-immunity paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Gao_Her\tGao_Her_DUF\t2\t2\tGao_Her_DUF__DUF4297, Gao_Her_DUF__HerA_DUF" notes: The DefenseFinder rules table models Gao_Her_DUF as a two-profile Gao_Her subsystem requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Gao_Her\tGao_Her_SIR\t2\t2\tGao_Her_SIR__HerA_SIR2, Gao_Her_SIR__SIR2" notes: The DefenseFinder rules table models Gao_Her_SIR as a two-profile Gao_Her subsystem requiring Gao_Her_SIR__HerA_SIR2 and Gao_Her_SIR__SIR2. - subject: gao_2020_antiviral_cassette_defense predicate: confers predicate_id: METPO:2007700 object: gao_her_system_trait description: Gao_Her-associated antiviral cassette defense realizes the Gao-Her system trait. evidence: - reference: PMID:32855333 snippet: By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages. notes: Gao et al. support a systematic defense-gene prediction and heterologous reconstitution campaign that discovered widespread antiviral gene cassettes. - subject: gao_her_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Gao-Her system possession is a phage-defense-system trait. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Gao_Her | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes notes: The DefenseFinder article registry maps Gao_Her to the Gao et al. prokaryotic antiviral-immunity paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Gao_Her\tGao_Her_DUF\t2\t2\tGao_Her_DUF__DUF4297, Gao_Her_DUF__HerA_DUF" notes: The DefenseFinder rules table models Gao_Her_DUF as a two-profile Gao_Her subsystem requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Gao_Her\tGao_Her_SIR\t2\t2\tGao_Her_SIR__HerA_SIR2, Gao_Her_SIR__SIR2" notes: The DefenseFinder rules table models Gao_Her_SIR as a two-profile Gao_Her subsystem requiring Gao_Her_SIR__HerA_SIR2 and Gao_Her_SIR__SIR2. discussions: - discussion_id: gao-her-family-mechanism-gap prompt: Resolve Gao_Her natural host breadth, subtype boundaries, phage triggers, and the effector outputs of Gao_Her_DUF and Gao_Her_SIR before minting narrower Gao-Her mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Gao et al. support bacteriophage protection by widespread antiviral gene cassettes, and DefenseFinder models Gao_Her_DUF and Gao_Her_SIR as two-profile subsystems under the Gao_Her family key. This first parent record captures the Gao_Her family while leaving subtype-specific triggers, natural host breadth, and direct effector activities unresolved. attaches_to: - causal_graphs#gao_her_locus_restricts_phage posed_by: codex posed_date: '2026-09-27' curation_history: - timestamp: '2026-09-27T13:51:19Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Gao-Her 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_v286. llm_assisted: true - timestamp: '2026-09-27T13:56:56Z' curator: codex action: EDIT changes: Removed a repeated DefenseFinder article-row citation from the Gao-Her confers edge so no graph reuses the same snippet more than twice. llm_assisted: true