Lamassu-HNH system

traitmech:000568 · CLASS · PROPOSED

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.

Trait evidence (8)

DOI:10.1073/pnas.2519643122
others are type-specific like the flavin-containing monooxygenase (FMO) for long Lamassu, and HNH, SMEK, and Lipase for short Lamassu.

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.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_HNH.xml
<model inter_gene_max_space="1" min_mandatory_genes_required="3" min_genes_required="3" vers="2.0">

The executable model requires three mandatory components and permits at most one intervening gene between components.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_HNH.xml
<gene name="Lamassu__LmuA_HNH" presence="mandatory"/>

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.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_HNH.xml
<gene name="Lamassu__LmuB_Long" presence="mandatory"> <exchangeables> <gene name="Lamassu__LmuB_Short"/> </exchangeables> </gene>

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.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_HNH.xml
<gene name="Lamassu__LmuC_Clade_I" presence="mandatory">

LmuC is mandatory, with Clade II-VII and MC1-MC8 profiles in the exchangeables block. There are no accessory components in this XML.
https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx
ACHA001.0722.00006.C001 ACHA001.0722.00006.C001_03320 Lamassu__LmuB_Short ACHA001.0722.00006.C001 ACHA001.0722.00006.C001_03321 Lamassu__LmuC_MC7 ACHA001.0722.00006.C001 ACHA001.0722.00006.C001_03322 Lamassu__LmuA_HNH

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.
https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx
ACHA001.0722.00006.C001 GCF_009892245.1 Bacteria Proteobacteria Acinetobacter haemolyticus NZ_CP031972

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.
https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_009892245.1/dataset_report
"tax_id":29430,"organism_name":"Acinetobacter haemolyticus","infraspecific_names":{"strain":"AN59"}

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.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1073/pnas.2519643122

Parent traits (2)

Synonyms (2)

Lamassu_HNH RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_HNH.xml
Lamassu/Lamassu/Lamassu_HNH RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Canonical examples (1)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

Acinetobacter haemolyticus NCBITaxon:29430 https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx 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.

Discussions and Knowledge Gaps (1)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Validate HNH-system function and reconcile detector scope.

KNOWLEDGE GAP OPEN lamassu-hnh-function-and-model-scope · raised by codex · 2026-10-03

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

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.

Curation history

2026-10-03T10:35:00Z · MINTED_TRAITMECH_ID · codex
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.
2026-10-03T12:33:00Z · REPARENT_TO_SHORT_LAMASSU · codex
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.
2026-10-03T15:14:27Z · ADD_TYPE_II_PARENT · codex
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.