identifier: traitmech:000566 label: Lamassu-Sir2 system definition: A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Sir2 subtype locus represented by the Lamassu-Sir2 rule row requiring the Lamassu-Fam__LmuA_effector_Sir2 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-Sir2 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv - synonym_text: Lamassu-Fam__LmuA_effector_Sir2 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_Sir2 | Lamassu-Fam__LmuA_effector_Sir2 | Lamassu-Fam | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Sir2 custom profile listed as mandatory by the Lamassu-Sir2 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-Sir2 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-Sir2 rule row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Lamassu-Fam__LmuB_SMC_Sir2 | Lamassu-Fam__LmuB_SMC_Sir2 | Lamassu-Fam | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuB_SMC_Sir2 custom profile that is not the LmuB SMC profile named by the pinned Lamassu-Sir2 rule row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Lamassu-Fam__LmuC_acc_Sir2 | Lamassu-Fam__LmuC_acc_Sir2 | Lamassu-Fam | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuC_acc_Sir2 custom profile that is not the LmuC accessory profile named by the pinned Lamassu-Sir2 rule row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Lamassu-Fam\tLamassu-Sir2\t2\t2\tLamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\t\ Lamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_Cap4_nuclease,\ \ Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, 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_hypothetical\t" notes: The pinned DefenseFinder rules table models Lamassu-Sir2 as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Sir2 and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile. causal_graphs: - graph_id: lamassu_sir2_locus_subtype_defense title: Lamassu-Sir2 is a DefenseFinder Lamassu subtype description: Conservative subtype-level classification linking the DefenseFinder Lamassu-Sir2 rule-row definition to Lamassu-Sir2 system possession and its Lamassu parent. scope_status: NONMECHANISTIC scope_notes: The graph captures Lamassu-Sir2 as a DefenseFinder rule-row subtype of Lamassu system possession without asserting a Lamassu-Sir2-specific antiphage process, exact phage-triggered Sir2 effector activity, viral-DNA trigger, LmuC requirement, native host breadth, cell-death output, or whether every DefenseFinder Lamassu-Sir2 prediction is a complete experimentally active locus. nodes: - node_id: lamassu_sir2_system_trait label: Lamassu-Sir2 system node_type: TRAIT grounding: traitmech:000566 description: Possession of a genome-encoded Lamassu-Sir2 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_sir2_system_trait predicate: is a predicate_id: rdfs:subClassOf object: lamassu_system_trait description: Lamassu-Sir2 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-Sir2\t2\t2" notes: The pinned DefenseFinder rules table places the Lamassu-Sir2 subsystem under the Lamassu-Fam system key with 2 mandatory matches and 2 genes required. discussions: - discussion_id: lamassu-sir2-activity-gap prompt: Resolve Lamassu-Sir2 phage triggers, native hosts, Sir2 effector activity, 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-Sir2 as a Lamassu-Fam subtype whose rule row requires Lamassu-Fam__LmuA_effector_Sir2 and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II. This first-pass record follows the rule row but leaves exact Sir2 effector activity, the rule row's relationship to Sir2-scoped LmuB/LmuC HMM rows, LmuC requirement, native hosts, phage triggers, cell-death output, and profile-to-activity criteria 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_Sir2 | Lamassu-Fam__LmuA_effector_Sir2 | Lamassu-Fam | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records the Lamassu-Fam__LmuA_effector_Sir2 custom profile listed as mandatory by the Lamassu-Sir2 rule row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Lamassu-Fam__LmuB_SMC_Sir2 | Lamassu-Fam__LmuB_SMC_Sir2 | Lamassu-Fam | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuB_SMC_Sir2 custom profile that is not the LmuB SMC profile named by the pinned Lamassu-Sir2 rule row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Lamassu-Fam__LmuC_acc_Sir2 | Lamassu-Fam__LmuC_acc_Sir2 | Lamassu-Fam | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records a Lamassu-Fam__LmuC_acc_Sir2 custom profile that is not the LmuC accessory profile named by the pinned Lamassu-Sir2 rule row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Lamassu-Fam\tLamassu-Sir2\t2\t2\tLamassu-Fam__LmuA_effector_Sir2, Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II\t\ Lamassu-Fam__LmuC_acc_Lipase\tLamassu-Fam__LmuA_effector_Amidase, Lamassu-Fam__LmuA_effector_Cap4_nuclease,\ \ Lamassu-Fam__LmuA_effector_Cap4_nuclease_II, 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_hypothetical\t" notes: The pinned DefenseFinder rules table models Lamassu-Sir2 as a Lamassu-Fam subsystem requiring Lamassu-Fam__LmuA_effector_Sir2 and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II, with Lamassu-Fam__LmuC_acc_Lipase as an accessory profile. attaches_to: - causal_graphs#lamassu_sir2_locus_subtype_defense posed_by: codex posed_date: '2026-10-03' curation_history: - timestamp: '2026-10-03T06:34:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Lamassu-Sir2 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; existing Lamassu-Fam__LmuA_effector_Sir2 mentions were limited to forbidden-profile evidence on neighboring Lamassu-Fam subtypes, their earlier writer scripts, and rendered pages, and the replacement placeholder is reserved in proposals/metpo_traitmech_v443. llm_assisted: true - timestamp: '2026-10-03T06:34:02Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed Lamassu-Sir2 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-Sir2 profiles and experimentally verified endogenous activity. No paid research was used. llm_assisted: true - timestamp: '2026-10-03T06:56:28Z' curator: codex action: EXPANDED_EVIDENCE changes: 'Addressed adversarial review issue #1604 by adding exact evidence for the Sir2-scoped Lamassu-Fam__LmuB_SMC_Sir2 and Lamassu-Fam__LmuC_acc_Sir2 HMM rows so the unresolved relationship between those rows and the generic LmuB/LmuC rows named by the Lamassu-Sir2 rule is auditable on the Lamassu-Sir2 record itself.' llm_assisted: true