TraitMech

TraitMech › GENOMICS

Hma system

traitmech:000533 · CLASS · PROPOSED

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.

Trait evidence (8)

Hma loci support helicase-associated phage defense

Conservative system-level sketch linking a three-gene Hma locus to HmaA-dependent phage defense and Hma system possession.

NONMECHANISTIC · 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.

Hma loci support helicase-associated phage defense Interactive directed graph showing evidence-backed causal relationships for Hma system.

Edge evidence

  • Hma locus contributes to HmaA phage defense RO:0002326

    Hma loci encode HmaA, and HmaA nickase activity is required for the characterized anti-phage activity.

  • HmaA phage defense confers Hma system METPO:2007700

    HmaA-dependent anti-phage activity realizes the first-pass organism-level Hma system trait.

    • DOI:10.1111/1751-7915.14524 we characterized a new defence system, Hma Liu et al. experimentally studied Hma in coral-associated Halomonas meridiana.
    • DOI:10.1111/1751-7915.14524 Mutation analysis revealed the nickase activity of the nuclease domain (belonging to PDD/EXK superfamily) of HmaA is essential in phage defence. Liu et al. connect HmaA nuclease activity to anti-phage defense against Escherichia phage T4.
  • Hma system is a phage defense system rdfs:subClassOf

    Hma system possession is a phage-defense-system trait.

    • DOI:10.1093/nar/gkab883 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. Payne et al. define Hma as a predicted three-gene antiviral defense system with HmaA, HmaB, and HmaC components.
    • DOI:10.1093/nar/gkab883 The putative Hma system was very widespread, present in 26 phyla, surpassed only by CBASS type I, Gabija and Septu type I. Payne et al. report that the predicted Hma system occurs across many bacterial and archaeal phyla.
    • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | Hma | 10\.1093/nar/gkac400 | PADLOC: a web server for the identification of antiviral defence systems in microbial genomes | The pinned DefenseFinder article registry maps the Hma source key to the PADLOC web-server paper.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1093/nar/gkab883

Parent traits (1)

Synonyms (4)

  • Hma EXACT_SYNONYM · DOI:10.1093/nar/gkab883
  • Hma__HmaA RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  • Hma__HmaB RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  • Hma__HmaC RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md

kg-microbe context

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

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 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.

KNOWLEDGE GAP OPEN hma-defensefinder-rule-and-component-gap · raised by codex · 2026-10-02

Attached to causal_graphs#hma_locus_phage_defense

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

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    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.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    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.