identifier: traitmech:000361 label: Gao-Her-DUF system definition: A phage defense system in which an organism possesses a Gao_Her_DUF locus represented by DefenseFinder as a two-profile model requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF. definition_source: DOI:10.1126/science.aba0372 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000409 synonyms: - synonym_text: Gao_Her_DUF synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv - synonym_text: Gao_Her_DUF__DUF4297 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: Gao_Her_DUF__HerA_DUF synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.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 the broader Gao_Her family key 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 system requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Gao_Her_DUF__DUF4297 | Gao_Her_DUF__DUF4297 | Gao_Her_DUF | Custom | 20 |' notes: The DefenseFinder HMM inventory records Gao_Her_DUF__DUF4297 under Gao_Her_DUF. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Gao_Her_DUF__HerA_DUF | Gao_Her_DUF__HerA_DUF | Gao_Her_DUF | Custom | 20 |' notes: The DefenseFinder HMM inventory records Gao_Her_DUF__HerA_DUF under Gao_Her_DUF. causal_graphs: - graph_id: gao_her_duf_locus_restricts_phage title: Gao-Her-DUF loci confer bacterial phage defense description: Conservative system-level sketch linking possession of a Gao_Her_DUF locus to Gao et al. antiviral cassette defense without asserting the unresolved Her-DUF component activities. scope_status: NONMECHANISTIC scope_notes: The graph captures Gao-Her-DUF as a named DefenseFinder two-profile Gao-family system while leaving natural hosts, DUF4297/HerA_DUF protein functions, phage triggers, and direct effector activity unresolved. nodes: - node_id: gao_her_duf_locus label: Gao_Her_DUF locus node_type: GENETIC_ELEMENT description: A DefenseFinder Gao_Her_DUF phage-defense locus represented by custom DUF4297 and HerA_DUF profiles. - 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_duf_system_trait label: Gao-Her-DUF system node_type: TRAIT grounding: traitmech:000361 description: Possession of a genome-encoded Gao-Her-DUF phage-defense system. - node_id: gao_her_system label: Gao-Her system node_type: TRAIT grounding: traitmech:000409 description: Possession of a genome-encoded Gao-Her phage-defense system. edges: - subject: gao_her_duf_locus predicate: contributes to predicate_id: RO:0002326 object: gao_2020_antiviral_cassette_defense description: DefenseFinder maps the broader Gao_Her family key to the Gao et al. systematic antiphage-system discovery paper and models Gao_Her_DUF as a two-profile system requiring DUF4297 and HerA_DUF. 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 bacteriophage protection by 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 the broader Gao_Her family key 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 system requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Gao_Her_DUF__DUF4297 | Gao_Her_DUF__DUF4297 | Gao_Her_DUF | Custom | 20 |' notes: The DefenseFinder HMM inventory records Gao_Her_DUF__DUF4297 under Gao_Her_DUF. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Gao_Her_DUF__HerA_DUF | Gao_Her_DUF__HerA_DUF | Gao_Her_DUF | Custom | 20 |' notes: The DefenseFinder HMM inventory records Gao_Her_DUF__HerA_DUF under Gao_Her_DUF. - subject: gao_2020_antiviral_cassette_defense predicate: confers predicate_id: METPO:2007700 object: gao_her_duf_system_trait description: Gao_Her_DUF-associated antiviral cassette defense realizes the Gao-Her-DUF 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 bacteriophage protection by widespread antiviral gene cassettes. - subject: gao_her_duf_system_trait predicate: is a predicate_id: rdfs:subClassOf object: gao_her_system description: Gao-Her-DUF system possession is a Gao-Her family phage-defense-system trait. evidence: - 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. discussions: - discussion_id: gao-her-duf-mechanism-gap prompt: Resolve Gao_Her_DUF natural hosts, DUF4297/HerA_DUF component functions, phage triggers, and effector activity before minting narrower Gao_Her_DUF mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Gao et al. support widespread antiviral gene cassettes that mediate protection against specific bacteriophages, and DefenseFinder models Gao_Her_DUF as a two-profile system under the Gao_Her family key. The exact natural host breadth, DUF4297/HerA_DUF component identities, phage trigger, and profile-to-activity mapping remain unresolved. attaches_to: - causal_graphs#gao_her_duf_locus_restricts_phage posed_by: codex posed_date: '2026-09-22' curation_history: - timestamp: '2026-09-22T09:33:34Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Gao-Her-DUF system as a DOI-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_v238. llm_assisted: true - timestamp: '2026-09-27T13:51:19Z' curator: codex action: EDIT changes: Reparented the record under traitmech:000409 Gao-Her system and added a Gao-Her parent node plus subclass edge to the causal graph. llm_assisted: true - timestamp: '2026-09-27T13:56:56Z' curator: codex action: EDIT changes: Removed the redundant Gao-Her-to-phage subclass edge from the child graph; the Gao-Her parent record now carries that edge. llm_assisted: true