ARMADA system

traitmech:000477 · CLASS · PROPOSED

A phage defense system in which an organism possesses an ARMADA YprA-like-helicase locus whose Type I and Type II operons share BrxHII-like and PglX-like components with DISARM Class I systems and whose experimentally tested Type II forms protect against a broad range of phages.

Trait evidence (7)

DOI:10.1016/j.chom.2026.05.015
Through comprehensive phylogenetic and structural analyses of YprA-like helicases, we identify several major clades, which define distinct defense systems including a broad class we call ARMADA (disARM-related antiviral defense array).

Bell et al. define ARMADA as a broad YprA-like helicase defense-system class.
DOI:10.1016/j.chom.2026.05.015
We show experimentally that ARMADA protects bacteria against a broad range of phages via a direct, non-abortive mechanism.

Bell et al. summarize experimental support that ARMADA protects bacteria against a broad range of phages.
https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/
The two largest uncharacterized YprA-like clades encompass a distinct set of related operons that, in addition to the YprA homologs, share two other genes with DISARM Class I systems

The preprint full text describes ARMADA operons as carrying YprA homologs plus BrxHII-like and PglX-like components shared with DISARM Class I systems.
https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/
The ARMADA clade splits into two well-separated, strongly supported subclades which we denote Type I and Type II.

The preprint full text separates the broad ARMADA clade into Type I and Type II subclades.
https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/
Log-protection (reduction in phage titer) conferred by ARMADA, expressed from plasmid pBeloBAC11 in BL21-AI, against a panel of 80 phages

A cloned E. coli NCTC 12900 ARMADA Type II cluster was tested for protection against a broad phage panel in a heterologous BL21-AI assay.
https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/
Screening 66 phages that could form plaques on the double-deletion strain showed that the strain carrying only Druantia III exhibited at least modest protection (<0.01 EOP or <0.5 SFC) against 3 phages, whereas the strain carrying ARMADA Type II exhibited a much broader range of immunity, with at least modest protection observed against 30 phages.

Precise system deletions in E. coli ATCC 8739 supported native ARMADA Type II protection across a broader tested phage set than the co-located Druantia Type III system.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
Armada | 10\.1101/2025\.09\.15\.676423 | YprA family helicases provide the missing link between diverse prokaryotic immune systems

The pinned DefenseFinder article registry maps the named Armada system to the Bell et al. YprA-family helicase preprint. The pinned HMM inventory and rules table do not list Armada, so this row is name-to-paper evidence rather than model-component evidence.

ARMADA loci protect against broad phage panels

Conservative system-level sketch linking an ARMADA YprA-like-helicase locus to experimentally measured anti-phage protection and ARMADA system possession.

NONMECHANISTIC · The graph captures ARMADA as a named YprA-like-helicase phage-defense system with Type I and Type II subclades while leaving direct phage triggers or effectors, native host breadth, exact Type I and Type II boundaries, profile-to-component mapping, and DefenseFinder HMM/rules detection criteria unresolved.

Edge evidence

ARMADA locus contributes to ARMADA broad phage protection RO:0002326
ARMADA Type II loci from E. coli NCTC 12900 and ATCC 8739 provided experimentally measured anti-phage protection.
- DOI:10.1016/j.chom.2026.05.015 We show experimentally that ARMADA protects bacteria against a broad range of phages via a direct, non-abortive mechanism. Bell et al. summarize broad, direct, non-abortive ARMADA anti-phage protection.
- https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/ Screening 66 phages that could form plaques on the double-deletion strain showed that the strain carrying only Druantia III exhibited at least modest protection (<0.01 EOP or <0.5 SFC) against 3 phages, whereas the strain carrying ARMADA Type II exhibited a much broader range of immunity, with at least modest protection observed against 30 phages. Precise ARMADA and Druantia deletions in E. coli ATCC 8739 resolved native ARMADA-associated phage immunity.
ARMADA broad phage protection confers ARMADA system METPO:2007700
Broad phage protection realizes the ARMADA system possession trait.
- https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/ Log-protection (reduction in phage titer) conferred by ARMADA, expressed from plasmid pBeloBAC11 in BL21-AI, against a panel of 80 phages The cloned NCTC 12900 ARMADA Type II locus was tested in BL21-AI against a broad phage panel.
- https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/ Screening 66 phages that could form plaques on the double-deletion strain showed that the strain carrying only Druantia III exhibited at least modest protection (<0.01 EOP or <0.5 SFC) against 3 phages, whereas the strain carrying ARMADA Type II exhibited a much broader range of immunity, with at least modest protection observed against 30 phages. The native ATCC 8739 ARMADA Type II system protected against a broader tested phage panel than its co-located Druantia Type III system.
ARMADA system is a phage defense system rdfs:subClassOf
ARMADA system possession is a phage-defense-system trait.
- DOI:10.1016/j.chom.2026.05.015 Through comprehensive phylogenetic and structural analyses of YprA-like helicases, we identify several major clades, which define distinct defense systems including a broad class we call ARMADA (disARM-related antiviral defense array). Bell et al. define ARMADA among YprA-family prokaryotic immune systems.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Armada | 10\.1101/2025\.09\.15\.676423 | YprA family helicases provide the missing link between diverse prokaryotic immune systems The pinned DefenseFinder article registry maps the named Armada system to the Bell et al. YprA-family helicase preprint. The pinned HMM inventory and rules table do not list Armada, so this row is name-to-paper evidence rather than model-component evidence.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1016/j.chom.2026.05.015

Parent traits (1)

phage defense system traitmech:000209

Synonyms (3)

ARMADA EXACT_SYNONYM · DOI:10.1016/j.chom.2026.05.015
Armada EXACT_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
disARM-related antiviral defense array EXACT_SYNONYM · DOI:10.1016/j.chom.2026.05.015

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.

Escherichia coli NCBITaxon:562 https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/ Bell et al. generated precise armABCD deletions in E. coli strain ATCC 8739 and showed that its native ARMADA Type II system provided broader phage protection than the co-located Druantia Type III system.

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 exact ARMADA Type I and Type II boundaries, DefenseFinder HMM/rules coverage, profile-to-component mapping, direct phage triggers or outputs, and native host breadth before minting narrower ARMADA mechanism, subtype, or protein-component traits.

KNOWLEDGE GAP OPEN armada-subtype-model-and-mechanism-gap · raised by codex · 2026-09-30

Attached to causal_graphs#armada_locus_phage_protection

Bell et al. support ARMADA as a broad YprA-like-helicase system family that shares BrxHII-like and PglX-like components with DISARM Class I systems and splits into Type I and Type II subclades, and the article experimentally validates Type II protection from E. coli NCTC 12900 and ATCC 8739 loci. The pinned DefenseFinder article registry names Armada and maps it to the Bell et al. preprint, but the pinned HMM inventory and rules table do not contain Armada rows, leaving profile coverage and detection criteria unresolved.

Evidence

DOI:10.1016/j.chom.2026.05.015
Through comprehensive phylogenetic and structural analyses of YprA-like helicases, we identify several major clades, which define distinct defense systems including a broad class we call ARMADA (disARM-related antiviral defense array).
https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/
The ARMADA clade splits into two well-separated, strongly supported subclades which we denote Type I and Type II.
https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/
Druantia Type III and ARMADA Type II systems showed clear evidence of synergizing to confer phage defense in their native host
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
Armada | 10\.1101/2025\.09\.15\.676423 | YprA family helicases provide the missing link between diverse prokaryotic immune systems
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-30T00:00:29Z · MINTED_TRAITMECH_ID · codex
Minted ARMADA system as a final-DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at broad YprA-like-helicase system level because the pinned DefenseFinder article row is not backed by pinned HMM or rules rows; the replacement placeholder is reserved in proposals/metpo_traitmech_v354.