identifier: traitmech:000272 label: Damona system definition: A phage defense system in which an organism possesses a Damona locus represented by a VCA0399 profile that can protect bacteria from bacteriophage infection. definition_source: DOI:10.1126/science.ads0768 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Damona synonym_type: EXACT_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: VCA0399 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.1126/science.ads0768 snippet: nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions notes: Darracq et al. support treating the newly discovered Vibrio cholerae SCI antiphage cassettes as bacterial anti-phage systems. - reference: DOI:10.1126/science.ads0768 snippet: Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest notes: Darracq et al. support a conservative system record that does not assert a resolved Damona trigger, effector output, or universal pathway. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Damona | 10\.1126/science\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems notes: The DefenseFinder model registry maps the named Damona system to the Darracq et al. SCI antiphage-system paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Damona__VCA0399 | | Damona notes: The DefenseFinder HMM inventory records VCA0399 in the Damona model namespace. causal_graphs: - graph_id: damona_locus_restricts_phage title: Damona loci confer bacterial phage defense description: Conservative system-level sketch linking possession of a Damona locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output. scope_status: NONMECHANISTIC scope_notes: The graph captures Damona as a named SCI-derived anti-phage system with a VCA0399 DefenseFinder profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved. nodes: - node_id: damona_locus label: Damona locus node_type: GENETIC_ELEMENT description: A Damona anti-phage defense locus represented in DefenseFinder by a VCA0399 profile. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced propagation of bacteriophage in cells carrying the Damona system. - node_id: damona_system_trait label: Damona system node_type: TRAIT grounding: traitmech:000272 description: Possession of a genome-encoded Damona 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: damona_locus predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: DefenseFinder maps Damona to an SCI anti-phage-system discovery paper and represents Damona loci through the VCA0399 component profile. evidence: - reference: DOI:10.1126/science.ads0768 snippet: nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions notes: Darracq et al. describe the newly discovered antiphage-system cohort that the DefenseFinder Damona registry row maps to the Damona system. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Damona__VCA0399 | | Damona notes: The DefenseFinder HMM inventory supports VCA0399 as the Damona component profile. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: damona_system_trait description: Damona-mediated phage restriction realizes the Damona system trait. evidence: - reference: DOI:10.1126/science.ads0768 snippet: Most of these novel systems have little or no similarity to previously known ones notes: Darracq et al. place the Damona discovery cohort in a set of novel bacterial systems that protect against phages. - subject: damona_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Damona system possession is a phage-defense-system trait. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Damona | 10\.1126/science\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems notes: DefenseFinder associates Damona with the Darracq et al. bacterial antiphage-system paper. discussions: - discussion_id: damona-mechanism-gap prompt: Resolve Damona phage triggers and effector outputs before minting narrower Damona mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Darracq et al. and DefenseFinder support Damona as a named anti-phage system with a VCA0399 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#damona_locus_restricts_phage posed_by: codex posed_date: '2026-09-19' curation_history: - timestamp: '2026-09-19T08:24:30Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Damona 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_v149. llm_assisted: true