identifier: traitmech:000568
label: Lamassu-HNH system
definition: A Lamassu system in which an organism possesses a locus encoding an HNH-domain
  LmuA effector, a short-form 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:000570
- traitmech:000572
synonyms:
- synonym_text: Lamassu_HNH
  synonym_type: RELATED_SYNONYM
  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_HNH.xml
- synonym_text: Lamassu/Lamassu/Lamassu_HNH
  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. Figure 1A depicts HNH-domain LmuA with short LmuB and LmuC. This establishes
    a recognized architecture, not HNH-specific biochemical or infection-assay validation.'
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_HNH.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_HNH.xml
  snippet: <gene name="Lamassu__LmuA_HNH" presence="mandatory"/>
  notes: HNH-bearing LmuA is mandatory. Other named LmuA effector profiles are forbidden
    by separate blocks; an isolated HNH-profile hit does not establish possession
    of the complete system.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_HNH.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. Its software scope is broader
    than this record's literature-supported short-LmuB architecture, so the model
    key is only a related synonym.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_HNH.xml
  snippet: <gene name="Lamassu__LmuC_Clade_I" presence="mandatory">
  notes: LmuC is mandatory, with Clade II-VII and MC1-MC8 profiles in the exchangeables
    block. There are no accessory components in this XML.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx
  snippet: "ACHA001.0722.00006.C001\tACHA001.0722.00006.C001_03320\tLamassu__LmuB_Short\n\
    ACHA001.0722.00006.C001\tACHA001.0722.00006.C001_03321\tLamassu__LmuC_MC7\nACHA001.0722.00006.C001\t\
    ACHA001.0722.00006.C001_03322\tLamassu__LmuA_HNH"
  notes: Dataset S1, S3_Lamassu_Detection!A121:C123, raw cells in column order. Columns
    E, F, I and M identify one Lamassu/Lamassu/Lamassu_HNH call, ACHA001.0722.00006.C001_Lamassu_HNH_807,
    with sys_wholeness 1.0 and three mandatory hits. The full sheet has 281 unique
    HNH system IDs, each with short LmuB. These are computational genome annotations,
    not experimental antiviral phenotypes.
- reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx
  snippet: "ACHA001.0722.00006.C001\tGCF_009892245.1\tBacteria\tProteobacteria\tAcinetobacter\
    \ haemolyticus\tNZ_CP031972"
  notes: Dataset S1, S2_Genomes!A1159:F1159, raw cells linking the HNH-bearing replicon
    to assembly GCF_009892245.1 and its species. The historical phylum label is quoted
    as source data, not adopted as a taxonomic assertion. This supports a genome-qualified
    possession example.
- reference: https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_009892245.1/dataset_report
  snippet: '"tax_id":29430,"organism_name":"Acinetobacter haemolyticus","infraspecific_names":{"strain":"AN59"}'
  notes: 'NCBI Datasets assembly report, verified 2026-10-03: resolves the study''s
    assembly to species taxon 29430 and strain AN59. This source verifies identity
    only; the published dataset supports the computational system-possession annotation.'
canonical_examples:
- taxon_id: NCBITaxon:29430
  taxon_label: Acinetobacter haemolyticus
  note: 'Computational genomic example: strain AN59, assembly GCF_009892245.1, study
    replicon ACHA001.0722.00006.C001, has a complete three-component HNH-system call
    in Dataset S1 (S3_Lamassu_Detection rows 121-123; S2_Genomes row 1159). NCBI Datasets
    resolves the assembly to this species and strain. This does not establish experimentally
    measured antiviral activity in AN59 or species-wide possession.'
  reference: https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx
discussions:
- discussion_id: lamassu-hnh-function-and-model-scope
  prompt: Validate HNH-system function and reconcile detector scope.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: The paper identifies HNH as a short-Lamassu effector type, and all 281
    HNH calls in Dataset S1 contain short LmuB. The pinned executable XML nevertheless
    permits long LmuB, so the detector name is not an exact biological equivalence.
    At the same commit, the legacy DefenseFinder_rules.tsv and Liste_hmm_system.md
    lack an HNH-system entry even though the executable XML and HNH profile exist.
    Summary-table absence is not model absence. HNH-specific experimental antiviral
    validation, exact substrates, activation order, and accession-level protein anchors
    remain unresolved. Cap4 and Lipase experiments do not establish HNH chemistry
    or its phage spectrum. No protein-resolved causal graph or functional equivalence
    to standalone HNH proteins is asserted. The direct parent is now traitmech:000570
    short Lamassu system, matching the short-form LmuB restriction already present
    in this record's definition. This hierarchy refinement does not narrow the executable
    detector, resolve the functional gaps, or reinterpret computational calls as measured
    antiviral phenotypes. A second direct parent, traitmech:000572 Lamassu type II
    system, now captures the LmuC component already required by this definition. The
    short-family parent is retained because component presence and LmuB-length family
    are separate axes. Neither hierarchy relation experimentally validates HNH antiviral
    activity or narrows the detector's broader scope.
  posed_by: codex
  posed_date: '2026-10-03'
curation_history:
- timestamp: '2026-10-03T10:35:00Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Added the literature-supported short-Lamassu HNH architecture with DOI,
    executable-model, published dataset and NCBI identity evidence and exact snippets.
    Restricted the AN59 example to computational genomic possession. Ignored-and-hidden
    searches found no exact record or METPO term. Reserved METPO:1052200 in proposals/metpo_traitmech_v445;
    retained the detector-scope and HNH-specific functional-validation gaps.
  llm_assisted: true
- timestamp: '2026-10-03T12:33:00Z'
  curator: codex
  action: REPARENT_TO_SHORT_LAMASSU
  changes: Placed the existing short-LmuB HNH architecture below traitmech:000570
    short Lamassu system without changing its definition, evidence, model-scope qualifications
    or example. The v445 broader Lamassu proposal axiom remains true; v447 documents
    the added immediate-parent relation for upstream minting.
  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