identifier: traitmech:000292 label: Ukko system definition: A phage defense system in which an organism possesses a Ukko locus that can protect bacteria from bacteriophage infection. definition_source: DOI:10.1101/2025.01.08.631966 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Ukko synonym_type: EXACT_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: UkkA1 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: UkkA2 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: UkkB1 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: UkkB2 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: UkkC1 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: UkkC2 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: UkkD1 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: UkkD2 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.1101/2025.01.08.631966 snippet: Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun). notes: Mordret et al. directly name Ukko among six Streptomyces systems that increased resistance to at least one phage. - reference: DOI:10.1101/2025.01.08.631966 snippet: The bacterial pangenome encodes an immense array of antiphage systems, yet much of their diversity remains uncharted notes: Mordret et al. motivate a conservative system-level record that does not assert a resolved Ukko trigger, effector output, or universal pathway. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Ukko | 10\.1101/2025\.01\.08\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses notes: The DefenseFinder model registry maps the named Ukko system to the Mordret et al. antiphage-system discovery preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Ukko__UkkA1 | | Ukko notes: The DefenseFinder HMM inventory records UkkA1 in the Ukko model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Ukko__UkkA2 | | Ukko notes: The DefenseFinder HMM inventory records UkkA2 in the Ukko model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Ukko__UkkB1 | | Ukko notes: The DefenseFinder HMM inventory records UkkB1 in the Ukko model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Ukko__UkkB2 | | Ukko notes: The DefenseFinder HMM inventory records UkkB2 in the Ukko model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Ukko__UkkC1 | | Ukko notes: The DefenseFinder HMM inventory records UkkC1 in the Ukko model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Ukko__UkkC2 | | Ukko notes: The DefenseFinder HMM inventory records UkkC2 in the Ukko model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Ukko__UkkD1 | | Ukko notes: The DefenseFinder HMM inventory records UkkD1 in the Ukko model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Ukko__UkkD2 | | Ukko notes: The DefenseFinder HMM inventory records UkkD2 in the Ukko model namespace. causal_graphs: - graph_id: ukko_locus_restricts_phage title: Ukko loci confer bacterial phage defense description: Conservative system-level sketch linking possession of a Ukko locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output. scope_status: NONMECHANISTIC scope_notes: The graph captures Ukko as a named anti-phage system with UkkA1, UkkA2, UkkB1, UkkB2, UkkC1, UkkC2, UkkD1, and UkkD2 DefenseFinder HMM profile entries while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved. nodes: - node_id: ukko_locus label: Ukko locus node_type: GENETIC_ELEMENT description: A Ukko anti-phage defense locus cataloged in DefenseFinder with UkkA1, UkkA2, UkkB1, UkkB2, UkkC1, UkkC2, UkkD1, and UkkD2 HMM profile entries. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced propagation of bacteriophage in cells carrying the Ukko system. - node_id: ukko_system_trait label: Ukko system node_type: TRAIT grounding: traitmech:000292 description: Possession of a genome-encoded Ukko 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: ukko_locus predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: DefenseFinder maps Ukko to a protein- and genomic-language-model antiphage-system discovery preprint and catalogs UkkA1, UkkA2, UkkB1, UkkB2, UkkC1, UkkC2, UkkD1, and UkkD2 HMM profile entries in the Ukko model namespace. evidence: - reference: DOI:10.1101/2025.01.08.631966 snippet: Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun). notes: Mordret et al. directly name Ukko among six Streptomyces systems that restricted at least one phage. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Ukko | 10\.1101/2025\.01\.08\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses notes: The DefenseFinder registry maps Ukko itself to the Mordret et al. bacterial antiphage-system discovery preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Ukko__UkkA1 | | Ukko notes: The DefenseFinder HMM inventory records UkkA1 in the Ukko model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Ukko__UkkA2 | | Ukko notes: The DefenseFinder HMM inventory records UkkA2 in the Ukko model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Ukko__UkkB1 | | Ukko notes: The DefenseFinder HMM inventory records UkkB1 in the Ukko model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Ukko__UkkB2 | | Ukko notes: The DefenseFinder HMM inventory records UkkB2 in the Ukko model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Ukko__UkkC1 | | Ukko notes: The DefenseFinder HMM inventory records UkkC1 in the Ukko model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Ukko__UkkC2 | | Ukko notes: The DefenseFinder HMM inventory records UkkC2 in the Ukko model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Ukko__UkkD1 | | Ukko notes: The DefenseFinder HMM inventory records UkkD1 in the Ukko model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Ukko__UkkD2 | | Ukko notes: The DefenseFinder HMM inventory records UkkD2 in the Ukko model namespace. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: ukko_system_trait description: Ukko-mediated phage restriction realizes the Ukko system trait. evidence: - reference: DOI:10.1101/2025.01.08.631966 snippet: Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun). notes: Mordret et al. directly name Ukko among six systems that increased resistance to at least one phage. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Ukko | 10\.1101/2025\.01\.08\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses notes: DefenseFinder records Ukko as a named system from the Mordret et al. antiphage discovery preprint. - subject: ukko_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Ukko system possession is a phage-defense-system trait. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| Ukko | 10\.1101/2025\.01\.08\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses |' notes: DefenseFinder associates Ukko with the Mordret et al. bacterial antiphage-system discovery preprint. discussions: - discussion_id: ukko-mechanism-gap prompt: Resolve Ukko phage triggers and effector outputs before minting narrower Ukko mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Mordret et al. and DefenseFinder support Ukko as a named anti-phage system with UkkA1, UkkA2, UkkB1, UkkB2, UkkC1, UkkC2, UkkD1, and UkkD2 HMM profile entries, 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#ukko_locus_restricts_phage posed_by: codex posed_date: '2026-09-19' curation_history: - timestamp: '2026-09-19T20:26:31Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Ukko 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_v169. llm_assisted: true