identifier: traitmech:000533 label: Hma system definition: A phage defense system in which an organism possesses a genome-encoded Hma locus with predicted HmaA helicase, HmaB m5c methyltransferase, and HmaC ATPase components. definition_source: DOI:10.1093/nar/gkab883 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Hma synonym_type: EXACT_SYNONYM source: DOI:10.1093/nar/gkab883 - synonym_text: Hma__HmaA synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: Hma__HmaB synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: Hma__HmaC synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.1093/nar/gkab883 snippet: We designated this as a new candidate defence system named Hma, as it encodes three proteins with predicted helicase (HmaA), m5c methyltransferase (HmaB) and ATPase (HmaC) domains. notes: Payne et al. define Hma as a predicted three-gene antiviral defense system with HmaA, HmaB, and HmaC components. - reference: DOI:10.1093/nar/gkab883 snippet: The putative Hma system was very widespread, present in 26 phyla, surpassed only by CBASS type I, Gabija and Septu type I. notes: Payne et al. report that the predicted Hma system occurs across many bacterial and archaeal phyla. - reference: DOI:10.1111/1751-7915.14524 snippet: we characterized a new defence system, Hma notes: Liu et al. experimentally studied Hma in coral-associated Halomonas meridiana. - reference: DOI:10.1111/1751-7915.14524 snippet: Mutation analysis revealed the nickase activity of the nuclease domain (belonging to PDD/EXK superfamily) of HmaA is essential in phage defence. notes: Liu et al. connect HmaA nuclease activity to anti-phage defense against Escherichia phage T4. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| Hma | 10\.1093/nar/gkac400 | PADLOC: a web server for the identification of antiviral defence systems in microbial genomes | ' notes: The pinned DefenseFinder article registry maps the Hma source key to the PADLOC web-server paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Hma__HmaA | | Hma | Custom | 400 |' notes: The pinned DefenseFinder HMM inventory records Hma__HmaA under the Hma model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Hma__HmaB | | Hma | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records Hma__HmaB under the Hma model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Hma__HmaC | | Hma | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records Hma__HmaC under the Hma model namespace. causal_graphs: - graph_id: hma_locus_phage_defense title: Hma loci support helicase-associated phage defense description: Conservative system-level sketch linking a three-gene Hma locus to HmaA-dependent phage defense and Hma system possession. scope_status: NONMECHANISTIC scope_notes: The graph captures Hma at locus and HmaA antiviral-output level without asserting HmaB or HmaC regulation, HmaB/HmaC effector activity, complete HmaABC phage breadth, natural host activity, accessory systems inserted in the hma region, or rule-level DefenseFinder detection criteria. nodes: - node_id: hma_locus label: Hma locus node_type: GENETIC_ELEMENT description: A candidate antiviral Hma locus encoding HmaA, HmaB, and HmaC components. - node_id: hmaA_phage_defense label: HmaA phage defense node_type: BIOLOGICAL_PROCESS description: HmaA helicase/nickase-associated inhibition of bacteriophage infection. - node_id: hma_system_trait label: Hma system node_type: TRAIT grounding: traitmech:000533 description: Possession of a genome-encoded Hma 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: hma_locus predicate: contributes to predicate_id: RO:0002326 object: hmaA_phage_defense description: Hma loci encode HmaA, and HmaA nickase activity is required for the characterized anti-phage activity. evidence: - reference: DOI:10.1093/nar/gkab883 snippet: We designated this as a new candidate defence system named Hma, as it encodes three proteins with predicted helicase (HmaA), m5c methyltransferase (HmaB) and ATPase (HmaC) domains. notes: Payne et al. define Hma as a predicted three-gene antiviral defense system with HmaA, HmaB, and HmaC components. - reference: DOI:10.1111/1751-7915.14524 snippet: Mutation analysis revealed the nickase activity of the nuclease domain (belonging to PDD/EXK superfamily) of HmaA is essential in phage defence. notes: Liu et al. connect HmaA nuclease activity to anti-phage defense against Escherichia phage T4. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Hma__HmaA | | Hma | Custom | 400 |' notes: The pinned DefenseFinder HMM inventory records Hma__HmaA under the Hma model namespace. - subject: hmaA_phage_defense predicate: confers predicate_id: METPO:2007700 object: hma_system_trait description: HmaA-dependent anti-phage activity realizes the first-pass organism-level Hma system trait. evidence: - reference: DOI:10.1111/1751-7915.14524 snippet: we characterized a new defence system, Hma notes: Liu et al. experimentally studied Hma in coral-associated Halomonas meridiana. - reference: DOI:10.1111/1751-7915.14524 snippet: Mutation analysis revealed the nickase activity of the nuclease domain (belonging to PDD/EXK superfamily) of HmaA is essential in phage defence. notes: Liu et al. connect HmaA nuclease activity to anti-phage defense against Escherichia phage T4. - subject: hma_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Hma system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1093/nar/gkab883 snippet: We designated this as a new candidate defence system named Hma, as it encodes three proteins with predicted helicase (HmaA), m5c methyltransferase (HmaB) and ATPase (HmaC) domains. notes: Payne et al. define Hma as a predicted three-gene antiviral defense system with HmaA, HmaB, and HmaC components. - reference: DOI:10.1093/nar/gkab883 snippet: The putative Hma system was very widespread, present in 26 phyla, surpassed only by CBASS type I, Gabija and Septu type I. notes: Payne et al. report that the predicted Hma system occurs across many bacterial and archaeal phyla. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| Hma | 10\.1093/nar/gkac400 | PADLOC: a web server for the identification of antiviral defence systems in microbial genomes | ' notes: The pinned DefenseFinder article registry maps the Hma source key to the PADLOC web-server paper. discussions: - discussion_id: hma-defensefinder-rule-and-component-gap prompt: Resolve HmaB/HmaC contributions, complete HmaABC system requirements, hma-region accessory systems, sensitive-phage breadth, native host breadth, and DefenseFinder rule-level criteria before minting Hma mechanism or component children. kind: KNOWLEDGE_GAP status: OPEN rationale: Payne et al. predicted Hma as a three-gene candidate defense system, Liu et al. showed that the HmaA nuclease domain is essential for T4 phage defense, and the pinned DefenseFinder HMM inventory records HmaA, HmaB, and HmaC profiles. However, Liu et al. state that HmaB/HmaC regulation of HmaA was not known, and the pinned DefenseFinder rules table lacks an Hma row. This first-pass record therefore does not resolve exact HmaB or HmaC activities, complete-system genetic requirements, accessory defense systems inserted near hma, full sensitive-phage breadth, endogenous native-host activity, or reusable rule-level detection criteria. evidence: - reference: DOI:10.1093/nar/gkab883 snippet: We designated this as a new candidate defence system named Hma, as it encodes three proteins with predicted helicase (HmaA), m5c methyltransferase (HmaB) and ATPase (HmaC) domains. notes: Payne et al. define Hma as a predicted three-gene antiviral defense system with HmaA, HmaB, and HmaC components. - reference: DOI:10.1111/1751-7915.14524 snippet: we characterized a new defence system, Hma notes: Liu et al. experimentally studied Hma in coral-associated Halomonas meridiana. - reference: DOI:10.1111/1751-7915.14524 snippet: Mutation analysis revealed the nickase activity of the nuclease domain (belonging to PDD/EXK superfamily) of HmaA is essential in phage defence. notes: Liu et al. connect HmaA nuclease activity to anti-phage defense against Escherichia phage T4. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Hma__HmaA | | Hma | Custom | 400 |' notes: The pinned DefenseFinder HMM inventory records Hma__HmaA under the Hma model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Hma__HmaB | | Hma | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records Hma__HmaB under the Hma model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Hma__HmaC | | Hma | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records Hma__HmaC under the Hma model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: A structured first-pass search of the pinned DefenseFinder rules table found no exact Hma system row. attaches_to: - causal_graphs#hma_locus_phage_defense posed_by: codex posed_date: '2026-10-02' curation_history: - timestamp: '2026-10-02T03:38:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Hma system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the phage defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v410. llm_assisted: true - timestamp: '2026-10-02T03:38:01Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed Hma system during initial curation and left canonical_examples empty because the sources support the three-gene Hma system namespace, Hma HMM profiles, and HmaA-dependent activity but not an accession-backed native microbial taxon exemplar with experimentally verified endogenous HmaABC activity. No paid research was used. llm_assisted: true