Lamassu-SMEK system

traitmech:000569 · CLASS · PROPOSED

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.

Trait evidence (9)

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

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

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

LmuC is mandatory, with Clade II-VII and MC1-MC8 exchangeable profiles. There are no accessory components in this executable XML.
https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx
ACJU001.0722.00009.C001 ACJU001.0722.00009.C001_01299 Lamassu__LmuB_Short ACJU001.0722.00009.C001 ACJU001.0722.00009.C001_01300 Lamassu__LmuC_Clade_VI ACJU001.0722.00009.C001 ACJU001.0722.00009.C001_01301 Lamassu__LmuA_SMEK

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.
https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx
ACJU001.0722.00009.C001 GCF_021491935.1 Bacteria Proteobacteria Acinetobacter junii NZ_CP090890

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.
https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx
Lamassu__LmuB_Long Lamassu__LmuC_Clade_VII Lamassu__LmuA_SMEK Lamassu__LmuB_Long

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.
https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_021491935.1/dataset_report
"tax_id":40215,"organism_name":"Acinetobacter junii","infraspecific_names":{"strain":"WCO-9"}

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.

Provenance

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

Parent traits (1)

Lamassu type II system traitmech:000572

Synonyms (2)

Lamassu_SMEK RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Lamassu-Fam/Lamassu_SMEK.xml
Lamassu/Lamassu/Lamassu_SMEK 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 junii NCBITaxon:40215 https://pmc-oa-opendata.s3.amazonaws.com/PMC12663957.1/pnas.2519643122.sd01.xlsx 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.

Discussions and Knowledge Gaps (1)

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

Resolve the long-profile exception and validate SMEK-system function.

KNOWLEDGE GAP OPEN lamassu-smek-function-and-annotation-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 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.

Curation history

2026-10-03T11:15:00Z · MINTED_TRAITMECH_ID · codex
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.
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.