identifier: traitmech:000261 label: Tiamat system definition: A phage defense system in which an organism possesses a Tiamat locus represented by a TmtA profile that can protect bacteria from bacteriophage infection. definition_source: DOI:10.1016/j.chom.2022.09.017 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Tiamat synonym_type: EXACT_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md evidence: - reference: DOI:10.1016/j.chom.2022.09.017 snippet: discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments notes: Millman et al. report the computational and experimental cohort that DefenseFinder cites for Tiamat as a bacterial anti-phage system. - reference: DOI:10.1101/2022.05.11.491447 snippet: discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments notes: The bioRxiv version of Millman et al. independently carries the 21-system discovery claim linked from DefenseFinder's Tiamat article registry. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Tiamat | 10\.1101/2022\.05\.11\.491447 | An expanding arsenal of immune systems that protect bacteria from phages notes: The DefenseFinder model registry maps the named Tiamat system to the Millman et al. antiphage-system discovery preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Tiamat\tTiamat\t1\t1\tTiamat__TmtA" notes: The DefenseFinder rules table models Tiamat with a TmtA profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Tiamat__TmtA | Tiamat__TmtA | Tiamat notes: The DefenseFinder HMM inventory records TmtA in the Tiamat model namespace. causal_graphs: - graph_id: tiamat_locus_restricts_phage title: Tiamat loci confer bacterial phage defense description: Conservative system-level sketch linking possession of a Tiamat locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output. scope_status: NONMECHANISTIC scope_notes: The graph captures Tiamat as a named anti-phage system with the required DefenseFinder TmtA profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved. nodes: - node_id: tiamat_locus label: Tiamat locus node_type: GENETIC_ELEMENT description: A Tiamat anti-phage defense locus satisfying a DefenseFinder rule over the TmtA profile. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced propagation of bacteriophage in cells carrying the Tiamat system. - node_id: tiamat_system_trait label: Tiamat system node_type: TRAIT grounding: traitmech:000261 description: Possession of a genome-encoded Tiamat 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: tiamat_locus predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: DefenseFinder maps Tiamat to a bacterial anti-phage-system discovery preprint and represents Tiamat loci through the TmtA component profile. evidence: - reference: DOI:10.1016/j.chom.2022.09.017 snippet: discovery of 21 defense systems that protect bacteria from phages notes: Millman et al. describe the anti-phage discovery cohort that the DefenseFinder Tiamat registry row maps to the Tiamat system. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Tiamat | 10\.1101/2022\.05\.11\.491447 | An expanding arsenal of immune systems that protect bacteria from phages notes: The DefenseFinder registry maps Tiamat itself to the Millman et al. bacterial antiphage-system discovery preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Tiamat\tTiamat\t1\t1\tTiamat__TmtA" notes: The DefenseFinder rules table supports TmtA as the required Tiamat system profile. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: tiamat_system_trait description: Tiamat-mediated phage restriction realizes the Tiamat system trait. evidence: - reference: DOI:10.1016/j.chom.2022.09.017 snippet: discovery of 21 defense systems that protect bacteria from phages notes: Millman et al. place the Tiamat discovery cohort in the set of bacterial systems that protect against phages. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Tiamat | 10\.1101/2022\.05\.11\.491447 | An expanding arsenal of immune systems that protect bacteria from phages notes: DefenseFinder records Tiamat as a named system from the Millman et al. antiphage discovery preprint. - subject: tiamat_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Tiamat system possession is a phage-defense-system trait. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: An expanding arsenal of immune systems that protect bacteria from phages notes: DefenseFinder associates Tiamat with the Millman et al. bacterial antiphage-system discovery paper. discussions: - discussion_id: tiamat-mechanism-gap prompt: Resolve Tiamat phage triggers and effector outputs before minting narrower Tiamat mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Millman et al. and DefenseFinder support Tiamat as a named anti-phage system with a TmtA 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#tiamat_locus_restricts_phage posed_by: codex posed_date: '2026-09-19' curation_history: - timestamp: '2026-09-19T02:44:11Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Tiamat 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_v138. llm_assisted: true