identifier: traitmech:000557 label: Lamassu-Cap4 nuclease system definition: A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Cap4_nuclease subtype locus represented by the Lamassu-Cap4_nuclease rule row requiring the Lamassu-Fam__LmuA_effector_Cap4_nuclease_II and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II 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:000232 synonyms: - synonym_text: Lamassu-Cap4_nuclease synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv - synonym_text: Lamassu-Fam__LmuA_effector_Cap4_nuclease_II synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: Lamassu-Fam__LmuC_acc_Lipase synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.1073/pnas.2519643122 snippet: a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor notes: Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| Lamassu-Fam | 10\.1101/2022\.05\.11\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | ' notes: The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Lamassu-Fam__LmuA_effector_Cap4_nuclease_II | Lamassu-Fam__LmuA_effector_Cap4_nuclease_II | Lamassu-Fam | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Cap4_nuclease_II custom profile listed as mandatory by the Lamassu-Cap4_nuclease rule row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II | Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II | Lamassu-Fam | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II custom profile listed as mandatory by the Lamassu-Cap4_nuclease rule row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Lamassu-Fam__LmuC_acc_Lipase | Lamassu-Fam__LmuC_acc_Lipase | Lamassu-Fam | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuC_acc_Lipase custom profile listed as accessory by the Lamassu-Cap4_nuclease rule row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Lamassu-Fam\tLamassu-Cap4_nuclease\t2\t2\tLamassu-Fam__LmuA_effector_Cap4_nuclease_II,\ \ Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase,\ \ Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase,\ \ Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease,\ \ Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t" notes: The pinned DefenseFinder rules table models Lamassu-Cap4_nuclease as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Cap4_nuclease_II and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile. causal_graphs: - graph_id: lamassu_cap4_nuclease_locus_subtype_defense title: Lamassu-Cap4 nuclease loci mark a Lamassu antiphage subtype description: Conservative subtype-level sketch linking a DefenseFinder Lamassu-Cap4_nuclease locus to Lamassu antiphage activity and Lamassu-Cap4 nuclease system possession. scope_status: NONMECHANISTIC scope_notes: The graph captures the Lamassu-Cap4_nuclease subtype at DefenseFinder rule-row level without asserting exact phage-triggered substrate chemistry, viral-DNA trigger, LmuC requirement, native host breadth, cell-death output, or whether every DefenseFinder Lamassu-Cap4_nuclease prediction is a complete experimentally active locus. nodes: - node_id: lamassu_cap4_nuclease_locus label: Lamassu-Cap4 nuclease locus node_type: GENETIC_ELEMENT description: A DefenseFinder Lamassu-Cap4_nuclease subtype locus represented by LmuA Cap4 nuclease and LmuB SMC mandatory profiles. - node_id: lamassu_subtype_antiphage_activity label: Lamassu subtype antiphage activity node_type: BIOLOGICAL_PROCESS description: Antiphage activity of a Lamassu-Fam subtype locus with a specific LmuA effector profile. - node_id: lamassu_cap4_nuclease_system_trait label: Lamassu-Cap4 nuclease system node_type: TRAIT grounding: traitmech:000557 description: Possession of a genome-encoded Lamassu-Cap4 nuclease phage-defense system. - node_id: lamassu_system_trait label: Lamassu system node_type: TRAIT grounding: traitmech:000232 description: Possession of a genome-encoded Lamassu phage-defense system. edges: - subject: lamassu_cap4_nuclease_locus predicate: contributes to predicate_id: RO:0002326 object: lamassu_subtype_antiphage_activity description: Lamassu-Cap4 nuclease loci are modeled in DefenseFinder by LmuA Cap4 nuclease and LmuB SMC mandatory profiles plus an LmuC accessory profile. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Lamassu-Fam__LmuA_effector_Cap4_nuclease_II | Lamassu-Fam__LmuA_effector_Cap4_nuclease_II | Lamassu-Fam | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Cap4_nuclease_II custom profile listed as mandatory by the Lamassu-Cap4_nuclease rule row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II | Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II | Lamassu-Fam | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II custom profile listed as mandatory by the Lamassu-Cap4_nuclease rule row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Lamassu-Fam__LmuC_acc_Lipase | Lamassu-Fam__LmuC_acc_Lipase | Lamassu-Fam | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuC_acc_Lipase custom profile listed as accessory by the Lamassu-Cap4_nuclease rule row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Lamassu-Fam\tLamassu-Cap4_nuclease\t2\t2\tLamassu-Fam__LmuA_effector_Cap4_nuclease_II,\ \ Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase,\ \ Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase,\ \ Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease,\ \ Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t" notes: The pinned DefenseFinder rules table models Lamassu-Cap4_nuclease as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Cap4_nuclease_II and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile. - subject: lamassu_subtype_antiphage_activity predicate: confers predicate_id: METPO:2007700 object: lamassu_cap4_nuclease_system_trait description: The first-pass Lamassu-Cap4 nuclease system trait is realized by a DefenseFinder Lamassu-Cap4_nuclease subtype locus. evidence: - reference: DOI:10.1073/pnas.2519643122 snippet: a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor notes: Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Lamassu-Cap4_nuclease\t2\t2\tLamassu-Fam__LmuA_effector_Cap4_nuclease_II,\ \ Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase" notes: The pinned DefenseFinder rules table models Lamassu-Cap4_nuclease as requiring LmuA Cap4 nuclease and LmuB SMC profiles with LmuC as an accessory profile. - subject: lamassu_cap4_nuclease_system_trait predicate: is a predicate_id: rdfs:subClassOf object: lamassu_system_trait description: Lamassu-Cap4 nuclease system possession is a Lamassu-system trait. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| Lamassu-Fam | 10\.1101/2022\.05\.11\.491447 | An expanding arsenal of immune systems that protect bacteria from phages | ' notes: The pinned DefenseFinder article registry maps the Lamassu-Fam model namespace to a bacterial immune-systems preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Lamassu-Fam\tLamassu-Cap4_nuclease\t2\t2" notes: The pinned DefenseFinder rules table places the Lamassu-Cap4_nuclease subsystem under the Lamassu-Fam system key with 2 mandatory matches and 2 genes required. discussions: - discussion_id: lamassu-cap4-nuclease-activity-gap prompt: Resolve Lamassu-Cap4 nuclease phage triggers, native hosts, Cap4 nuclease substrates, LmuC usage, and profile-to-activity criteria before minting enzyme, trigger, or component children. kind: KNOWLEDGE_GAP status: OPEN rationale: Haudiquet et al. support a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor, and the pinned DefenseFinder HMM inventory and rules table support Lamassu-Cap4_nuclease as a Lamassu-Fam subtype whose rule row requires Lamassu-Fam__LmuA_effector_Cap4_nuclease_II and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II. This first-pass record leaves exact Cap4 nuclease substrates, LmuC requirement, native hosts, phage triggers, cell-death output, profile-to-activity criteria, and the relationship between the DefenseFinder _II row and the structurally characterized Lamassu Vc-Cap4 branch unresolved. evidence: - reference: DOI:10.1073/pnas.2519643122 snippet: a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor notes: Haudiquet et al. support placing Lamassu subtypes under a Lamassu family with diverse LmuA effectors and a conserved SMC-like sensor. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Lamassu-Fam__LmuA_effector_Cap4_nuclease_II | Lamassu-Fam__LmuA_effector_Cap4_nuclease_II | Lamassu-Fam | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Cap4_nuclease_II custom profile listed as mandatory by the Lamassu-Cap4_nuclease rule row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Lamassu-Fam\tLamassu-Cap4_nuclease\t2\t2\tLamassu-Fam__LmuA_effector_Cap4_nuclease_II,\ \ Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\tLamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase,\ \ Lamassu-Fam__LmuA_effector_FMO, Lamassu-Fam__LmuA_effector_Hydrolase, Lamassu-Fam__LmuA_effector_Lipase,\ \ Lamassu-Fam__LmuA_effector_Mrr, Lamassu-Fam__LmuA_effector_PDDEXK, Lamassu-Fam__LmuA_effector_Protease,\ \ Lamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuA_effector_hypothetical\t" notes: The pinned DefenseFinder rules table models Lamassu-Cap4_nuclease as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Cap4_nuclease_II and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile. attaches_to: - causal_graphs#lamassu_cap4_nuclease_locus_subtype_defense posed_by: codex posed_date: '2026-10-02' curation_history: - timestamp: '2026-10-02T22:16:24Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Lamassu-Cap4 nuclease system as a DefenseFinder-backed GENOMICS TraitRecord under the Lamassu system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record for the target local ID, placeholder METPO ID, proposal cohort, record slug, human label, or DefenseFinder subsystem; the replacement placeholder is reserved in proposals/metpo_traitmech_v434. Exact Cap4 effector profile hits were limited to evidence and forbidden-profile strings on the neighboring Lamassu-Amidase record. llm_assisted: true - timestamp: '2026-10-02T22:16:26Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed Lamassu-Cap4 nuclease system during initial curation and left canonical_examples empty because the pinned DefenseFinder tables support a rule-row subtype but not an accession-backed native microbial taxon exemplar tied to the Lamassu-Cap4_nuclease profiles and experimentally verified endogenous activity. No paid research was used. llm_assisted: true