identifier: traitmech:000569
label: Lamassu-SMEK system
definition: A Lamassu system in which an organism possesses a locus encoding an LmuA
  effector with a SMEK domain, 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_SMEK
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_SMEK.xml
- synonym_text: Lamassu/Lamassu/Lamassu_SMEK
  synonym_type: RELATED_SYNONYM
  source: https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx
evidence:
- reference: DOI:10.1073/pnas.2519643122
  snippet: others are type-specific like the flavin-containing monooxygenase (FMO)
    for long Lamassu, and HNH, SMEK, and Lipase for short Lamassu.
  notes: 'Results, effector-diversity paragraph: ''others'' refers to LmuA effector
    types. The paper recognizes SMEK-bearing Lamassu and describes it as short-specific.
    Dataset S1 nevertheless contains one long-profile SMEK-system call; that annotation
    discrepancy is not resolved by treating the detector as experimental evidence.'
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_SMEK.xml
  snippet: <model inter_gene_max_space="1" min_mandatory_genes_required="3" min_genes_required="3"
    vers="2.0">
  notes: The executable model requires three mandatory components and permits at most
    one intervening gene between components.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_SMEK.xml
  snippet: <gene name="Lamassu__LmuA_SMEK" presence="mandatory"/>
  notes: SMEK-bearing LmuA is mandatory, without an exchangeable effector. Other named
    LmuA effector profiles are forbidden by separate blocks. An isolated SMEK-domain
    or profile hit does not establish this trait.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_SMEK.xml
  snippet: '<gene name="Lamassu__LmuB_Long" presence="mandatory">

    <exchangeables>

    <gene name="Lamassu__LmuB_Short"/>

    </exchangeables>

    </gene>'
  notes: The detector accepts either long or short LmuB. This permissiveness does
    not prove biological function in either clade. The trait definition follows the
    shared architecture without a length restriction.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_SMEK.xml
  snippet: <gene name="Lamassu__LmuC_Clade_I" presence="mandatory">
  notes: LmuC is mandatory, with Clade II-VII and MC1-MC8 exchangeable profiles. There
    are no accessory components in this executable XML.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx
  snippet: "ACJU001.0722.00009.C001\tACJU001.0722.00009.C001_01299\tLamassu__LmuB_Short\n\
    ACJU001.0722.00009.C001\tACJU001.0722.00009.C001_01300\tLamassu__LmuC_Clade_VI\n\
    ACJU001.0722.00009.C001\tACJU001.0722.00009.C001_01301\tLamassu__LmuA_SMEK"
  notes: Dataset S1, S3_Lamassu_Detection!A165:C167, raw cells in column order. Columns
    E, F, I and M identify one Lamassu/Lamassu/Lamassu_SMEK call, ACJU001.0722.00009.C001_Lamassu_SMEK_36,
    with sys_wholeness 1.0 and three mandatory hits. This is computational evidence
    of the complete architecture, not experimental antiviral activity.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx
  snippet: "ACJU001.0722.00009.C001\tGCF_021491935.1\tBacteria\tProteobacteria\tAcinetobacter\
    \ junii\tNZ_CP090890"
  notes: Dataset S1, S2_Genomes!A1383:F1383, raw cells linking the SMEK-system replicon
    to assembly GCF_021491935.1 and its species. The historical phylum name is retained
    only inside this source quote.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx
  snippet: 'Lamassu__LmuB_Long

    Lamassu__LmuC_Clade_VII

    Lamassu__LmuA_SMEK

    Lamassu__LmuB_Long'
  notes: Dataset S1, S3_Lamassu_Detection!C6042:C6045, raw cells for HAAN001.0722.00001.C001_Lamassu_SMEK_499.
    Column F assigns these four rows to one call, including two distinct long-profile
    LmuB hits. Across the sheet, 125 unique SMEK system IDs comprise 124 calls with
    short LmuB and this one call with long LmuB; these sets do not overlap. Component-row
    counts are not system counts. The long-profile call is an annotation exception
    needing review, not a validated biological long-Lamassu SMEK subtype.
- reference: https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_021491935.1/dataset_report
  snippet: '"tax_id":40215,"organism_name":"Acinetobacter junii","infraspecific_names":{"strain":"WCO-9"}'
  notes: 'NCBI Datasets assembly report, verified 2026-10-03: resolves GCF_021491935.1
    to taxon 40215 and strain WCO-9. This source verifies identity only; Dataset S1
    supports system possession.'
canonical_examples:
- taxon_id: NCBITaxon:40215
  taxon_label: Acinetobacter junii
  note: 'Computational genomic example: strain WCO-9, assembly GCF_021491935.1, study
    replicon ACJU001.0722.00009.C001. Dataset S1 S3_Lamassu_Detection rows 165-167
    record a complete short-LmuB, LmuC and SMEK-LmuA call; S2_Genomes row 1383 links
    it to the assembly. NCBI resolves the strain and taxon. This does not establish
    experimentally measured antiviral activity in WCO-9 or species-wide possession.'
  reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx
discussions:
- discussion_id: lamassu-smek-function-and-annotation-scope
  prompt: Resolve the long-profile exception and validate SMEK-system function.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: The paper describes SMEK as short-Lamassu-specific, while Dataset S1
    has 124 short-profile calls and one long-profile call with two distinct LmuB hits.
    The pinned model accepts both lengths. Reconcile that exceptional call with phylogeny
    and locus context before claiming a biological long-LmuB subtype or short-only
    distribution. The definition therefore captures architecture without a length
    restriction. The pinned legacy summary TSV and HMM inventory lack SMEK entries
    although the executable model and SMEK profile exist. This whole-system trait
    is not equivalent to DS-27 (traitmech:000451), whose existing definition denotes
    a single-gene transcriptional unit with the working label SMEK. No DS-27 assay
    phenotype or exact synonym is transferred. SMEK-specific Lamassu antiviral validation,
    substrates, activation order, domain-name expansion and accession-level protein
    mechanisms remain unresolved. Cap4 and Lipase experiments do not establish SMEK
    chemistry. No causal graph is asserted from these computational architecture calls
    alone. The direct parent is now traitmech:000572 Lamassu type II system because
    this definition already includes LmuC. This component-based refinement neither
    resolves the long-profile exception nor restricts the trait to short Lamassu,
    and does not confer experimental validation on the computational calls.
  posed_by: codex
  posed_date: '2026-10-03'
curation_history:
- timestamp: '2026-10-03T11:15:00Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Added the literature-recognized Lamassu-SMEK architecture using DOI, pinned
    executable-model, Dataset S1 and NCBI identity evidence with exact snippets. Distinguished
    125 system calls from 377 component rows and recorded the long-profile exception.
    Kept the WCO-9 example computational and rejected equivalence to DS-27. Ignored-and-hidden
    searches found no exact record or METPO term. Reserved METPO:1052300 in proposals/metpo_traitmech_v446.
  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