identifier: traitmech:000545 label: DRT3 system definition: A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT_3 subtype locus represented by the mandatory DRT_3__drt3a and DRT_3__drt3b profiles. definition_source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000279 synonyms: - synonym_text: DRT_3 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv - synonym_text: DRT_3__drt3a synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: DRT_3__drt3b synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.1126/science.aba0372 snippet: We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems notes: Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems. - reference: DOI:10.1126/science.aba0372 snippet: We named these genes defense-associated RTs (DRTs) notes: Gao et al. coined the defense-associated RT naming that underlies the DRT system family. - reference: DOI:10.1126/science.aba0372 snippet: In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity notes: Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues. - reference: DOI:10.1126/science.aba0372 snippet: the UG3 (drt3a) and UG8 (drt3b) RTs are components of the same defense system (DRT type 3), with both RTs required for defense activity notes: Gao et al. support the two reverse-transcriptase components of the DRT type 3 defense system. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DRT | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ' notes: The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DRT_3__drt3a | DRT_3__drt3a | DRT_3 | Custom | 150 | | DRT_3__drt3b | DRT_3__drt3b | DRT_3 | Custom | 250 | | DRT_3__SLATT | | DRT_3 | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records DRT_3__drt3a, DRT_3__drt3b, and DRT_3__SLATT under the DRT_3 model namespace, with DRT_3__SLATT lacking an emitted HMM name. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "DRT\tDRT_3\t2\t2\tDRT_3__drt3a, DRT_3__drt3b\t\t\t" notes: The pinned DefenseFinder rules table models DRT_3 as a DRT subsystem requiring DRT_3__drt3a and DRT_3__drt3b. causal_graphs: - graph_id: drt3_locus_reverse_transcriptase_defense title: DRT3 loci support DRT antiphage defense description: Conservative system-level sketch linking a DRT3 locus to reverse-transcriptase-dependent DRT phage defense and DRT3 system possession. scope_status: NONMECHANISTIC scope_notes: The graph captures DRT3 at DefenseFinder subtype-locus level without asserting the direct DRT3 reverse-transcriptase products, phage trigger, native host breadth, sensitive phage breadth, non-coding RNA or DRT_3__SLATT partner-feature role, profile-to-activity criteria, or whether every DefenseFinder DRT_3 prediction is a complete experimentally active DRT3 locus. nodes: - node_id: drt3_locus label: DRT3 locus node_type: GENETIC_ELEMENT description: A defense-associated reverse transcriptase subtype III locus represented in DefenseFinder by DRT_3 profiles. - node_id: drt_rt_active_site_activity label: DRT reverse-transcriptase active-site activity node_type: MOLECULAR_FUNCTION description: Reverse-transcriptase active-site-dependent activity of a defense-associated RT antiphage protein. - node_id: drt3_system_trait label: DRT3 system node_type: TRAIT grounding: traitmech:000545 description: Possession of a genome-encoded DRT3 phage-defense system. - node_id: drt_system_trait label: DRT system node_type: TRAIT grounding: traitmech:000279 description: Possession of a genome-encoded defense-associated reverse transcriptase phage-defense system. edges: - subject: drt3_locus predicate: contributes to predicate_id: RO:0002326 object: drt_rt_active_site_activity description: DRT3 loci are represented in DefenseFinder by custom defense-associated reverse transcriptase profiles. evidence: - reference: DOI:10.1126/science.aba0372 snippet: We named these genes defense-associated RTs (DRTs) notes: Gao et al. coined the defense-associated RT naming that underlies the DRT system family. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DRT_3__drt3a | DRT_3__drt3a | DRT_3 | Custom | 150 | | DRT_3__drt3b | DRT_3__drt3b | DRT_3 | Custom | 250 |' notes: The pinned DefenseFinder HMM inventory records DRT_3__drt3a and DRT_3__drt3b under the DRT_3 model namespace. - subject: drt_rt_active_site_activity predicate: confers predicate_id: METPO:2007700 object: drt3_system_trait description: The first-pass DRT3 system trait is realized by a DefenseFinder DRT_3 subtype locus within the reverse-transcriptase-dependent DRT family. evidence: - reference: DOI:10.1126/science.aba0372 snippet: We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems notes: Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems. - reference: DOI:10.1126/science.aba0372 snippet: In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity notes: Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues. - reference: DOI:10.1126/science.aba0372 snippet: the UG3 (drt3a) and UG8 (drt3b) RTs are components of the same defense system (DRT type 3), with both RTs required for defense activity notes: Gao et al. support the two reverse-transcriptase components of the DRT type 3 defense system. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "DRT\tDRT_3\t2\t2\tDRT_3__drt3a, DRT_3__drt3b\t\t\t" notes: The pinned DefenseFinder rules table models DRT_3 as a DRT subsystem requiring DRT_3__drt3a and DRT_3__drt3b. - subject: drt3_system_trait predicate: is a predicate_id: rdfs:subClassOf object: drt_system_trait description: DRT3 system possession is a DRT-system trait. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| DRT | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | ' notes: The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "DRT\tDRT_3\t2\t2\tDRT_3__drt3a, DRT_3__drt3b\t\t\t" notes: The pinned DefenseFinder rules table models DRT_3 as a DRT subsystem requiring DRT_3__drt3a and DRT_3__drt3b. discussions: - discussion_id: drt3-profile-activity-gap prompt: Resolve the DRT3 reverse-transcriptase products, direct phage trigger, host breadth, non-coding RNA or DRT_3__SLATT partner-feature role, and DRT_3 profile-to-activity criteria before minting DRT3 mechanism or component children. kind: KNOWLEDGE_GAP status: OPEN rationale: Gao et al. support defense-associated reverse transcriptases as a broad antiphage-system family and the two RT components of DRT type 3, while the pinned DefenseFinder HMM inventory and rules table support DRT_3 as a two-required-profile DRT subsystem. This first-pass record leaves the exact DRT3 RT products, phage trigger, host breadth, DRT_3__SLATT role, and profile-to-activity requirements unresolved. evidence: - reference: DOI:10.1126/science.aba0372 snippet: We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems notes: Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems. - reference: DOI:10.1126/science.aba0372 snippet: In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity notes: Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues. - reference: DOI:10.1126/science.aba0372 snippet: the UG3 (drt3a) and UG8 (drt3b) RTs are components of the same defense system (DRT type 3), with both RTs required for defense activity notes: Gao et al. support the two reverse-transcriptase components of the DRT type 3 defense system. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| DRT_3__drt3a | DRT_3__drt3a | DRT_3 | Custom | 150 | | DRT_3__drt3b | DRT_3__drt3b | DRT_3 | Custom | 250 | | DRT_3__SLATT | | DRT_3 | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records DRT_3__drt3a, DRT_3__drt3b, and DRT_3__SLATT under the DRT_3 model namespace, with DRT_3__SLATT lacking an emitted HMM name. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "DRT\tDRT_3\t2\t2\tDRT_3__drt3a, DRT_3__drt3b\t\t\t" notes: The pinned DefenseFinder rules table models DRT_3 as a DRT subsystem requiring DRT_3__drt3a and DRT_3__drt3b. attaches_to: - causal_graphs#drt3_locus_reverse_transcriptase_defense posed_by: codex posed_date: '2026-10-02' curation_history: - timestamp: '2026-10-02T12:40:28Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted DRT3 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the DRT system parent after an ignored-and-hidden duplicate review found no exact live DRT3 TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v422. llm_assisted: true - timestamp: '2026-10-02T12:40:29Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed DRT3 system during initial curation and left canonical_examples empty because Gao et al. and the pinned DefenseFinder tables support DRT type 3 and the DRT_3 model namespace but not an accession-backed native microbial taxon exemplar tied to DRT_3__drt3a and DRT_3__drt3b and experimentally verified endogenous DRT3 activity. No paid research was used. llm_assisted: true