identifier: traitmech:000570 label: short Lamassu system definition: 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. definition_source: DOI:10.1073/pnas.2519643122 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000232 synonyms: - synonym_text: short Lamassu synonym_type: EXACT_SYNONYM source: DOI:10.1073/pnas.2519643122 evidence: - reference: DOI:10.1073/pnas.2519643122 snippet: two major clades, which were mainly distinguished by the length of coiled-coil regions notes: '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.' - reference: DOI:10.1073/pnas.2519643122 snippet: short Lamassus, selecting the experimentally validated Cap4 system from V. cholerae notes: '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.' - reference: https://data.rcsb.org/rest/v1/core/polymer_entity/9NY5/3 snippet: '"rcsb_sample_sequence_length":653' notes: '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.' - reference: https://data.rcsb.org/rest/v1/core/polymer_entity/9NY5/3 snippet: '"pdbx_gene_src_ncbi_taxonomy_id":"666","pdbx_gene_src_scientific_name":"Vibrio cholerae"' notes: '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.' - reference: https://data.rcsb.org/rest/v1/core/polymer_entity/9NY5/3 snippet: '"pdbx_host_org_ncbi_taxonomy_id":"562","pdbx_host_org_scientific_name":"Escherichia coli"' notes: PDB entity_src_gen explicitly identifies the separate expression host. This does not establish natural E. coli possession of the Vc-Cap4 locus. canonical_examples: - taxon_id: NCBITaxon:666 taxon_label: Vibrio cholerae reference: DOI:10.1073/pnas.2519643122 note: 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: - discussion_id: short-lamassu-classification-and-mechanism-scope prompt: Resolve family-wide mechanisms and classify borderline loci. kind: KNOWLEDGE_GAP status: OPEN rationale: 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. posed_by: codex posed_date: '2026-10-03' curation_history: - timestamp: '2026-10-03T12:33:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: 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. llm_assisted: true - timestamp: '2026-10-03T13:17:37Z' curator: codex action: STRENGTHEN_TAXON_IDENTITY_SNIPPET changes: 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. llm_assisted: true - timestamp: '2026-10-03T13:41:34Z' curator: codex action: REFINE_SYNONYM_AND_EVIDENCE_SCOPE changes: 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. llm_assisted: true - timestamp: '2026-10-03T13:57:07Z' curator: codex action: CLARIFY_HISTORICAL_SNIPPET_VERIFICATION changes: '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 (for references in articles please use ncbitaxon:666)
. The lowercase form is quoted source text, not a curated CURIE. Current evidence and taxon grounding are unchanged; earlier events remain preserved.' llm_assisted: true - timestamp: '2026-10-03T15:57:07Z' curator: codex action: TRACK_TYPE_I_CLASS changes: 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. llm_assisted: true