TraitMech

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Lamassu type II system

traitmech:000572 · CLASS · PROPOSED

A Lamassu system in which an organism possesses a locus with an additional LmuC component alongside the LmuA effector module and SMC-like LmuB sensor.

Trait evidence (2)

  • DOI:10.1093/nar/gkab883
    Similarly, an additional hypothetical protein (LmuC) was identified in about 10.2% of the Lamassu systems detected (371 systems) (Lamassu type II).

    Results: Payne et al. name the LmuC-containing subtype. The quoted frequency belongs to their RefSeq v201 analysis, not universal prevalence. Methods and Figure 3 identify the DSM 9628 source locus and its heterologous phage-protection assays; these do not establish native-host resistance or universal LmuC essentiality.

  • DOI:10.1038/s41589-025-02102-z
    the type-I Lamassu complex from Bacillus cellulasensis and the type-II Lamassu complex from Vibrio cholerae

    Abstract: Li et al. report cryo-EM structures for these two source-qualified complexes. This independently supports the type-II category, not species-wide possession, equivalence to a long/short family, or transfer of one nuclease mechanism to all LmuC-containing effector architectures.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1093/nar/gkab883

Parent traits (1)

Children (3)

Synonyms (1)

  • Lamassu type II EXACT_SYNONYM · DOI:10.1093/nar/gkab883

kg-microbe context

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

Canonical examples (1)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

  • Janthinobacterium agaricidamnosum NBRC 102515 = DSM 9628 NCBITaxon:1349767 DOI:10.1093/nar/gkab883 Payne et al. amplified the type-II locus from DSM 9628 genomic DNA (source accession NZ_HG322949.1) and tested it in Escherichia coli BL21-AI. NCBI independently resolves that accession and this strain taxon. The example denotes source-strain possession, not native-host antiviral activity or possession by every member of the species.

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 type-II effector diversity and LmuC function without conflating axes.

KNOWLEDGE GAP OPEN lamassu-type-ii-component-and-mechanism-scope · raised by codex · 2026-10-03

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

Type II classifies LmuC-containing Lamassu architecture, not an isolated LmuC hit, a fixed three-gene count, a long-LmuB clade, or a universal LmuC-dependence phenotype. The effector module can include more than one gene. Existing HNH, SMEK and Hydrolase-Protease definitions require LmuC and therefore fall below this class; HNH also retains its short-family parent. This is a definition-based hierarchy inference, not new experimental validation of those children. Legacy detector-defined effector records and the complete long/short families are not reparented merely from model labels or optional LmuC calls. The V. cholerae nuclease mechanism does not establish chemistry for every effector module. Native-host activity, protein accessions and broader mechanistic generalization remain unresolved; no causal mechanism graph is asserted. Type I remains a separate discovery lead. That discovery lead is now represented by traitmech:000573 Lamassu type I system for LmuA/LmuB loci without LmuC. The two component architectures do not establish disjoint organism-level possession classes: one genome could encode both. LmuC absence is not inferred from a missing model hit or a type-II knockout. This record's definition, child classification and unresolved mechanism questions are unchanged.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Added the literature-defined LmuC-containing Lamassu class with two independent DOI sources, exact snippets and an NCBI-resolved DSM 9628 possession example. Kept type II distinct from a length family, fixed gene count and universal biochemical mechanism. Ignored-and-hidden searches found no exact record or METPO term. Reserved METPO:1052600 in proposals/metpo_traitmech_v449 and refined three existing LmuC-containing child definitions' hierarchy.

  2. · TRACK_TYPE_I_CLASS · codex

    Linked traitmech:000573 Lamassu type I system to the existing component-architecture discussion using DOI:10.1073/pnas.2519643122 and DOI:10.1038/s41589-025-02102-z. Preserved all definitions, parents, evidence, examples and prior history. Component absence, LmuB-length family and experimental activity remain separate claims.