TraitMech

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Lamassu-Sir2 system

traitmech:000566 · CLASS · PROPOSED

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.

Trait evidence (8)

Lamassu-Sir2 is a DefenseFinder Lamassu subtype

Conservative subtype-level classification linking the DefenseFinder Lamassu-Sir2 rule-row definition to Lamassu-Sir2 system possession and its Lamassu parent.

NONMECHANISTIC · 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.

Lamassu-Sir2 is a DefenseFinder Lamassu subtype Interactive directed graph showing evidence-backed causal relationships for Lamassu-Sir2 system.

Edge evidence

Provenance

Identifier source
TraitMech local identifier
Definition source
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Parent traits (1)

Synonyms (2)

  • Lamassu-Sir2 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
  • Lamassu-Fam__LmuA_effector_Sir2 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Discussions and Knowledge Gaps (1)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Resolve Lamassu-Sir2 phage triggers, native hosts, Sir2 effector activity, LmuC usage, and profile-to-activity criteria before minting enzyme, trigger, or component children.

KNOWLEDGE GAP OPEN lamassu-sir2-activity-gap · raised by codex · 2026-10-03

Attached to causal_graphs#lamassu_sir2_locus_subtype_defense

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

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    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.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    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.

  3. · EXPANDED_EVIDENCE · codex

    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.