identifier: traitmech:000571
label: long Lamassu system
definition: A Lamassu system in which an organism possesses a locus from the long-LmuB
  family, characterized by longer coiled-coil regions in its SMC-like LmuB sensor
  than in short 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: long 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 long family is distinguished
    from short Lamassu by phylogeny and structure. The approximate 800-residue total
    LmuB length is descriptive, not a membership cutoff.'
- reference: DOI:10.1073/pnas.2519643122
  snippet: one system from Bacillus cereus B4077, encoding Hydrolase-Protease effectors
  notes: The same paragraph explicitly identifies B4077 as the long-clade exception
    among previously validated systems. This supports strain-qualified possession,
    not species-wide distribution or a native-host phage-resistance measurement.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx
  snippet: "ACCA003.0722.00003.C001\tACCA003.0722.00003.C001_02431\tLamassu__LmuB_Long\n\
    ACCA003.0722.00003.C001\tACCA003.0722.00003.C001_02432\tLamassu__LmuC_Clade_VII\n\
    ACCA003.0722.00003.C001\tACCA003.0722.00003.C001_02433\tLamassu__LmuA_Cap4_III"
  notes: Dataset S1, S3_Lamassu_Detection!A58:C60, raw cells in column order. Column
    F assigns these rows to one ACCA003.0722.00003.C001_Lamassu_Cap4_321 call; column
    I reports sys_wholeness 1.0. Column C (gene_name) identifies the actual long-LmuB
    hit, unlike column L (hit_gene_ref), which can name the long model slot for short
    hits. These are computational locus observations, not an experimental antiviral
    phenotype or a family-membership rule.
canonical_examples:
- taxon_id: NCBITaxon:1396
  taxon_label: Bacillus cereus
  reference: DOI:10.1073/pnas.2519643122
  note: Strain B4077 is the source of the Hydrolase-Protease system assigned to the
    long family by Haudiquet et al. The species identifier anchors this strain-qualified
    example; no genome assembly, universal species possession, or native-host phage-resistance
    phenotype is inferred.
discussions:
- discussion_id: long-lamassu-classification-and-mechanism-scope
  prompt: Resolve borderline loci and long-family activation mechanisms.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: Long denotes a phylogenetic and structural family, not an isolated protein,
    a fixed amino-acid threshold, an effector name, or the component-number type II
    category. A raw long-profile hit alone does not settle membership of an ambiguous
    locus. The published detection sheet uses gene_name for actual hits and hit_gene_ref
    for potentially exchangeable model slots; these fields must not be conflated.
    Hydrolase-Protease spans both length families; the legacy FMO record's detector-defined
    scope and SMEK's long-profile exception need separate reconciliation before reparenting.
    No universal effector chemistry, LmuC requirement, zinc-hook count, or stoichiometry
    is imposed. The experimentally resolved short Vc-Cap4 activation mechanism is
    not transferred to this family. Native-host activity, accession-level protein
    anchors and family-wide activation remain open, so no causal mechanism graph is
    asserted.
  posed_by: codex
  posed_date: '2026-10-03'
curation_history:
- timestamp: '2026-10-03T14:29:24Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Added the literature-defined long Lamassu family with exact primary paper
    and dataset snippets and a strain-qualified B4077 example. Distinguished actual
    profile hits from model slots without adopting a length cutoff or transferring
    short-family mechanisms. Ignored-and-hidden searches found no exact record or
    METPO term. Reserved METPO:1052500 in proposals/metpo_traitmech_v448; left sibling
    hierarchies unchanged pending their own scope reconciliation.
  llm_assisted: true