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short Lamassu system

traitmech:000570 · CLASS · PROPOSED

A Lamassu system in which an organism possesses a locus from the short-LmuB family, characterized by shorter coiled-coil regions in its SMC-like LmuB sensor than in long Lamassu systems.

Trait evidence (5)

  • DOI:10.1073/pnas.2519643122
    two major clades, which were mainly distinguished by the length of coiled-coil regions

    Results, LmuB phylogeny paragraph and Figure 1: the authors distinguish short and long families using phylogeny and structure. Their approximate 600-residue short-family average is not a membership cutoff.

  • DOI:10.1073/pnas.2519643122
    short Lamassus, selecting the experimentally validated Cap4 system from V. cholerae

    Results, paragraph introducing structural work: identifies Vc-Cap4 as a short-family exemplar. Figure 2A shows its 653-residue LmuB. Antiphage assays here used the natural operon expressed in E. coli, not a species-wide native-host assay.

  • https://data.rcsb.org/rest/v1/core/polymer_entity/9NY5/3
    "rcsb_sample_sequence_length":653

    PDB 9NY5, entity 3, entity_poly: deposited LmuB sequence length, consistent with paper Figure 2A. This is not the number of modeled residues or a length threshold for the family.

  • https://data.rcsb.org/rest/v1/core/polymer_entity/9NY5/3
    "pdbx_gene_src_ncbi_taxonomy_id":"666","pdbx_gene_src_scientific_name":"Vibrio cholerae"

    PDB entity_src_gen: source organism of the deposited LmuB, not the recombinant expression host. No strain or genome assembly is inferred from the species-level deposition.

  • https://data.rcsb.org/rest/v1/core/polymer_entity/9NY5/3
    "pdbx_host_org_ncbi_taxonomy_id":"562","pdbx_host_org_scientific_name":"Escherichia coli"

    PDB entity_src_gen explicitly identifies the separate expression host. This does not establish natural E. coli possession of the Vc-Cap4 locus.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1073/pnas.2519643122

Parent traits (1)

Children (1)

Synonyms (1)

  • short Lamassu EXACT_SYNONYM · DOI:10.1073/pnas.2519643122

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.

  • Vibrio cholerae NCBITaxon:666 DOI:10.1073/pnas.2519643122 The source organism of the Vc-Cap4 system explicitly selected as a short-Lamassu exemplar. PDB 9NY5 entity 3 independently records a 653-residue LmuB from taxon 666, expressed in E. coli. The cited antiphage assays use a heterologous E. coli host. This does not assert species-wide possession, a specific strain or assembly, or native V. cholerae phage resistance.

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 family-wide mechanisms and classify borderline loci.

KNOWLEDGE GAP OPEN short-lamassu-classification-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.

Short denotes the phylogenetic and structural LmuB family, not an arbitrary amino-acid cutoff or an isolated short protein. LmuC-loss clade S and effector-domain-loss clade O preclude requiring one universal three-component effector architecture. Type I/II component classifications and effector names are not exact synonyms for this family. HNH's explicitly short-form definition supports its new parent; SMEK's unresolved long-profile call prevents the same inference. Other table-defined subtypes require their own scope review before reparenting. The Vc-Cap4 mechanism already described on the Lamassu parent is not assumed universal across short-family effectors, so no duplicate or universal mechanism graph is asserted here. A registry Hypothetical label must not be equated with clade O's effector-domain loss without explicit evidence. The LmuC-loss architecture is now represented separately by traitmech:000573 Lamassu type I system. The paper identifies clade S as type I; clade O's effector-domain loss remains a distinct question. The new component class is not treated as a synonym for this whole length family, and its broader phylogenetic distribution is left open rather than inferred from one clade. Existing hierarchy and mechanism scope are unchanged.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Added the literature-defined short Lamassu family with exact paper, PDB and NCBI snippets, a qualified Vc-Cap4 source-organism example, and no artificial protein-length cutoff. Ignored-and-hidden searches found no exact record or METPO term. Reserved METPO:1052400 in proposals/metpo_traitmech_v447 and refined the HNH child's parent.

  2. · STRENGTHEN_TAXON_IDENTITY_SNIPPET · codex

    Replaced the verbatim ID-only NCBI snippet with a contiguous species-name-and-ID span supporting the identity notes (#1617). Fresh source checks confirmed the earlier citation form was also verbatim; this change improves claim support, not taxon grounding.

  3. · REFINE_SYNONYM_AND_EVIDENCE_SCOPE · codex

    Used the source-attested family name as the exact synonym and aligned the v447 template (#1618). Removed the redundant NCBI evidence row to avoid a quote spanning HTML blocks (#1619). The paper, five exact paper/PDB snippets, PDB source metadata and verified canonical-example taxon retain the substantive support. Earlier curation history is preserved.

  4. · CLARIFY_HISTORICAL_SNIPPET_VERIFICATION · codex

    Correction to the 13:17:37Z event (#1620): withdraw the description of the removed species-name-and-ID quote as contiguous. That check joined text across HTML blocks and did not establish a contiguous source span. The distinct earlier citation-form verification is supported by these exact inline raw HTML bytes from https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=666&mode=Info: Taxonomy ID: 666 <small>(for references in articles please use ncbitaxon:666)</small><br>. The lowercase form is quoted source text, not a curated CURIE. Current evidence and taxon grounding are unchanged; earlier events remain preserved.

  5. · 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.