identifier: traitmech:000567
label: Lamassu Hydrolase-Protease system
definition: A Lamassu system in which an organism possesses a defense locus encoding
  a protease-domain LmuA effector together with a hydrolase-like protein, an SMC-like
  LmuB sensor, and LmuC.
definition_source: DOI:10.1073/pnas.2519643122
trait_category: GENOMICS
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000572
synonyms:
- synonym_text: Lamassu-Hydrolase_Protease
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
- synonym_text: Lamassu_Hydrolase-Protease
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_Hydrolase-Protease.xml
evidence:
- reference: DOI:10.1073/pnas.2519643122
  snippet: Protease (accompanied by a hydrolase-like protein)
  notes: 'Results, effector-diversity paragraph: the protease branch is paired with
    a hydrolase-like protein in both long and short Lamassu. Figure 1A shows the paired
    architecture with LmuB and LmuC. These annotations do not establish exact effector
    substrates.'
- reference: DOI:10.1073/pnas.2519643122
  snippet: one system from Bacillus cereus B4077, encoding Hydrolase-Protease effectors
  notes: 'Results, LmuB phylogeny paragraph: identifies B4077 as the source of a previously
    validated long-Lamassu system, citing Millman et al. (2022). This supports a strain-qualified
    possession example, not species-wide prevalence or a native-host infection assay.'
- reference: DOI:10.1016/j.chom.2022.09.017
  snippet: Mutation in the effector domains of these systems also abolished defense,
    as well as the deletion of lmuC
  notes: Figure 2C and its Results paragraph report loss of defense after effector
    mutations or lmuC deletion in tested Lamassu systems, including the hydrolase/protease
    construct. The functional tests used heterologous hosts. This does not establish
    a substrate or the biochemical order of activation for the paired proteins.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_Hydrolase-Protease.xml
  snippet: <model inter_gene_max_space="1" min_mandatory_genes_required="4" min_genes_required="4"
    vers="2.0">
  notes: The executable model requires four mandatory components, with at most one
    intervening gene between components.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_Hydrolase-Protease.xml
  snippet: '<gene name="Lamassu__LmuA_Protease" presence="mandatory">

    <exchangeables>

    <gene name="Lamassu__LmuA_Protease_II"/>

    </exchangeables>

    </gene>


    <gene name="Lamassu__LmuA_Hydrolase" presence="mandatory"/>'
  notes: The model requires both protease and hydrolase components; Protease_II can
    substitute for the primary protease profile. Separate mandatory blocks also require
    LmuB_Long (exchangeable with LmuB_Short) and LmuC_Clade_I (with listed alternatives).
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_Hydrolase-Protease.xml
  snippet: <gene name="Lamassu__LmuC_Clade_I" presence="mandatory">
  notes: LmuC is mandatory in this executable model, with alternative LmuC profiles
    listed in its exchangeables block.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
  snippet: "Lamassu-Fam\tLamassu-Hydrolase_Protease\t3\t3"
  notes: The summary TSV places the paired subtype within Lamassu-Fam but gives three
    mandatory matches and three genes. Its mandatory column lists the legacy Hydrolase,
    Protease and Cap4_nuclease_II SMC profiles, and its accessory column lists the
    Lipase LmuC profile. This summary disagrees with the executable XML at the same
    commit and is retained only as provenance for the older label.
canonical_examples:
- taxon_id: NCBITaxon:1396
  taxon_label: Bacillus cereus
  note: Strain B4077 is the source of the experimentally validated long-Lamassu Hydrolase-Protease
    system identified by Haudiquet et al. with reference to Millman et al. (2022).
    The species identifier anchors this strain-qualified example; it does not imply
    that all B. cereus strains possess it.
  reference: DOI:10.1073/pnas.2519643122
discussions:
- discussion_id: lamassu-hydrolase-protease-model-and-mechanism
  prompt: Reconcile model-summary drift and resolve paired effector chemistry.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: The pinned XML uses four mandatory components and newer Lamassu__ profile
    names, but its companion TSV uses three mandatory legacy profiles and accessory
    LmuC. The inventory's Hydrolase_protease LmuB and hydrolase_protease LmuC rows
    also differ from both representations. Model-summary reconciliation is required
    before using that TSV for genotype calls. The definition follows the biological
    paired architecture and executable model, not the table's thresholds. Exact substrates,
    activation order, native-host activity, and accession-level protein examples remain
    unresolved. No causal mechanism graph is asserted without those molecular anchors.
    The single-effector table-defined siblings are not asserted to be parents or equivalents
    of this paired system. The direct parent is now traitmech:000572 Lamassu type
    II system because the biological definition already includes LmuC. The paired
    effector architecture illustrates why type II is not restricted to exactly three
    genes. This refinement does not resolve the legacy detector-summary drift or assign
    the whole trait to one LmuB-length family.
  posed_by: codex
  posed_date: '2026-10-03'
curation_history:
- timestamp: '2026-10-03T09:29:00Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Added the literature-supported paired Lamassu architecture with DOI and
    pinned executable-model evidence, exact snippets, and a B4077 canonical example.
    Ignored-and-hidden searches found only pending parent mentions, not an exact existing
    record or METPO term. Reserved METPO:1052100 in proposals/metpo_traitmech_v444.
    Recorded summary-table drift rather than adopting its constraints.
  llm_assisted: true
- timestamp: '2026-10-03T15:14:27Z'
  curator: codex
  action: ADD_TYPE_II_PARENT
  changes: Linked traitmech:000572 Lamassu type II system using the LmuC-containing
    classification in DOI:10.1093/nar/gkab883. Preserved biological definitions, evidence,
    examples and length-family distinctions. Historical proposal parent axioms remain
    true; v449 documents the additional subclass relations for upstream minting. This
    is not new experimental validation.
  llm_assisted: true