identifier: traitmech:000477 label: ARMADA system definition: 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. definition_source: DOI:10.1016/j.chom.2026.05.015 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: ARMADA synonym_type: EXACT_SYNONYM source: DOI:10.1016/j.chom.2026.05.015 - synonym_text: Armada synonym_type: EXACT_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: disARM-related antiviral defense array synonym_type: EXACT_SYNONYM source: DOI:10.1016/j.chom.2026.05.015 evidence: - reference: DOI:10.1016/j.chom.2026.05.015 snippet: 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). notes: Bell et al. define ARMADA as a broad YprA-like helicase defense-system class. - reference: DOI:10.1016/j.chom.2026.05.015 snippet: We show experimentally that ARMADA protects bacteria against a broad range of phages via a direct, non-abortive mechanism. notes: Bell et al. summarize experimental support that ARMADA protects bacteria against a broad range of phages. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/ snippet: 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 notes: The preprint full text describes ARMADA operons as carrying YprA homologs plus BrxHII-like and PglX-like components shared with DISARM Class I systems. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/ snippet: The ARMADA clade splits into two well-separated, strongly supported subclades which we denote Type I and Type II. notes: The preprint full text separates the broad ARMADA clade into Type I and Type II subclades. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/ snippet: Log-protection (reduction in phage titer) conferred by ARMADA, expressed from plasmid pBeloBAC11 in BL21-AI, against a panel of 80 phages notes: 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. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/ snippet: 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. notes: 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. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Armada | 10\.1101/2025\.09\.15\.676423 | YprA family helicases provide the missing link between diverse prokaryotic immune systems notes: 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. canonical_examples: - taxon_id: NCBITaxon:562 taxon_label: Escherichia coli note: 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. reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/ causal_graphs: - graph_id: armada_locus_phage_protection title: ARMADA loci protect against broad phage panels description: Conservative system-level sketch linking an ARMADA YprA-like-helicase locus to experimentally measured anti-phage protection and ARMADA system possession. scope_status: NONMECHANISTIC scope_notes: 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. nodes: - node_id: armada_locus label: ARMADA locus node_type: GENETIC_ELEMENT description: A YprA-like-helicase ARMADA antiphage locus from a Type I or Type II ARMADA clade. - node_id: armada_broad_phage_protection label: ARMADA broad phage protection node_type: BIOLOGICAL_PROCESS description: Experimentally measured reduction in bacteriophage growth or plaque formation by tested ARMADA Type II systems. - node_id: armada_system_trait label: ARMADA system node_type: TRAIT grounding: traitmech:000477 description: Possession of a genome-encoded ARMADA phage-defense system. - node_id: phage_defense_system label: phage defense system node_type: TRAIT grounding: traitmech:000209 description: Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection. edges: - subject: armada_locus predicate: contributes to predicate_id: RO:0002326 object: armada_broad_phage_protection description: ARMADA Type II loci from E. coli NCTC 12900 and ATCC 8739 provided experimentally measured anti-phage protection. evidence: - reference: DOI:10.1016/j.chom.2026.05.015 snippet: We show experimentally that ARMADA protects bacteria against a broad range of phages via a direct, non-abortive mechanism. notes: Bell et al. summarize broad, direct, non-abortive ARMADA anti-phage protection. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/ snippet: 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. notes: Precise ARMADA and Druantia deletions in E. coli ATCC 8739 resolved native ARMADA-associated phage immunity. - subject: armada_broad_phage_protection predicate: confers predicate_id: METPO:2007700 object: armada_system_trait description: Broad phage protection realizes the ARMADA system possession trait. evidence: - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/ snippet: Log-protection (reduction in phage titer) conferred by ARMADA, expressed from plasmid pBeloBAC11 in BL21-AI, against a panel of 80 phages notes: The cloned NCTC 12900 ARMADA Type II locus was tested in BL21-AI against a broad phage panel. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/ snippet: 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. notes: The native ATCC 8739 ARMADA Type II system protected against a broader tested phage panel than its co-located Druantia Type III system. - subject: armada_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: ARMADA system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1016/j.chom.2026.05.015 snippet: 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). notes: Bell et al. define ARMADA among YprA-family prokaryotic immune systems. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Armada | 10\.1101/2025\.09\.15\.676423 | YprA family helicases provide the missing link between diverse prokaryotic immune systems notes: 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. discussions: - discussion_id: armada-subtype-model-and-mechanism-gap prompt: 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. kind: KNOWLEDGE_GAP status: OPEN rationale: 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: - reference: DOI:10.1016/j.chom.2026.05.015 snippet: 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). notes: Bell et al. define ARMADA as a broad YprA-like helicase defense-system class. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/ snippet: The ARMADA clade splits into two well-separated, strongly supported subclades which we denote Type I and Type II. notes: The broad ARMADA clade is split into Type I and Type II subclades. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC12458937/ snippet: Druantia Type III and ARMADA Type II systems showed clear evidence of synergizing to confer phage defense in their native host notes: The ATCC 8739 native-host experiments support ARMADA Type II and Druantia Type III interaction while leaving their coupling mechanism unresolved. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Armada | 10\.1101/2025\.09\.15\.676423 | YprA family helicases provide the missing link between diverse prokaryotic immune systems notes: 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. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md notes: No Armada or ARMADA HMM inventory row was present in the pinned DefenseFinder model file. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: No Armada or ARMADA rule row was present in the pinned DefenseFinder rules table. attaches_to: - causal_graphs#armada_locus_phage_protection posed_by: codex posed_date: '2026-09-30' curation_history: - timestamp: '2026-09-30T00:00:29Z' curator: codex action: MINTED_TRAITMECH_ID changes: 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. llm_assisted: true