identifier: traitmech:000358 label: Gao-Upx system definition: A phage defense system in which an organism possesses a Gao_Upx locus represented by DefenseFinder as a single-profile model requiring Gao_Upx__UpxA. definition_source: DOI:10.1126/science.aba0372 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Gao_Upx synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: Gao_Upx__UpxA 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_Upx | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes notes: The DefenseFinder article registry maps the named Gao_Upx system to the Gao et al. prokaryotic antiviral-immunity paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Gao_Upx\tGao_Upx\t1\t1\tGao_Upx__UpxA" notes: The DefenseFinder rules table models Gao_Upx as a single-mandatory-profile system with the Gao_Upx__UpxA profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Gao_Upx__UpxA | Gao_Upx__UpxA | Gao_Upx | Custom | 250 |' notes: The DefenseFinder HMM inventory records Gao_Upx__UpxA under Gao_Upx. causal_graphs: - graph_id: gao_upx_locus_restricts_phage title: Gao-Upx loci confer bacterial phage defense description: Conservative system-level sketch linking possession of a Gao_Upx locus to Gao et al. antiviral cassette defense without asserting the unresolved UpxA component activity. scope_status: NONMECHANISTIC scope_notes: The graph captures Gao-Upx as a named DefenseFinder single-profile Gao-family system while leaving natural hosts, UpxA protein function, phage triggers, and direct effector activity unresolved. nodes: - node_id: gao_upx_locus label: Gao_Upx locus node_type: GENETIC_ELEMENT description: A DefenseFinder Gao_Upx phage-defense locus represented by a custom UpxA profile. - 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_upx_system_trait label: Gao-Upx system node_type: TRAIT grounding: traitmech:000358 description: Possession of a genome-encoded Gao-Upx 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_upx_locus predicate: contributes to predicate_id: RO:0002326 object: gao_2020_antiviral_cassette_defense description: DefenseFinder maps Gao_Upx to the Gao et al. systematic antiphage-system discovery paper and models it as a single-profile system requiring UpxA. 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_Upx | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes notes: The DefenseFinder article registry maps the named Gao_Upx system to the Gao et al. prokaryotic antiviral-immunity paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Gao_Upx\tGao_Upx\t1\t1\tGao_Upx__UpxA" notes: The DefenseFinder rules table models Gao_Upx as a single-mandatory-profile system with the Gao_Upx__UpxA profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Gao_Upx__UpxA | Gao_Upx__UpxA | Gao_Upx | Custom | 250 |' notes: The DefenseFinder HMM inventory records Gao_Upx__UpxA under Gao_Upx. - subject: gao_2020_antiviral_cassette_defense predicate: confers predicate_id: METPO:2007700 object: gao_upx_system_trait description: Gao_Upx-associated antiviral cassette defense realizes the Gao-Upx 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_upx_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Gao-Upx 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_Upx | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes notes: The DefenseFinder article registry maps the named Gao_Upx system to the Gao et al. prokaryotic antiviral-immunity paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Gao_Upx\tGao_Upx\t1\t1\tGao_Upx__UpxA" notes: The DefenseFinder rules table models Gao_Upx as a single-mandatory-profile system with the Gao_Upx__UpxA profile. discussions: - discussion_id: gao-upx-mechanism-gap prompt: Resolve Gao_Upx natural hosts, UpxA component function, phage triggers, and effector activity before minting narrower Gao_Upx 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_Upx as a single-profile system. The exact natural host breadth, UpxA component identity, phage trigger, and profile-to-activity mapping remain unresolved. attaches_to: - causal_graphs#gao_upx_locus_restricts_phage posed_by: codex posed_date: '2026-09-22' curation_history: - timestamp: '2026-09-22T07:33:14Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Gao-Upx 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_v235. llm_assisted: true