TraitMech

TraitMech › GENOMICS

Hachiman type I system

traitmech:000575 · CLASS · PROPOSED

A Hachiman system in which an organism possesses a HamA/HamB locus without a HamC component.

Trait evidence (4)

  • DOI:10.1093/nar/gkab883
    We refer to the new Hachiman systems as type II, and the original Hachiman systems as type I.

    Results, new-subtype classification: Payne et al. distinguish the original HamAB architecture from the newly identified HamC-associated systems. Figure 2C depicts the component contrast. These names classify system architecture, not individual proteins or organism-level disjoint classes.

  • DOI:10.1038/s41467-025-57851-1
    Payne et al. classified the Hachiman systems that contain only HamA and HamB as type I

    Introduction: Cui et al. explicitly retain the HamAB-only classification, citing Payne rather than independently originating the name. Their own experiments characterize type I-A and I-B. Methods identify the type-I-B source as K-12, U00096.3 positions 2761204-2765368. Defense assays used plasmid-borne HamAB in a hamAB-deleted MG1655 host; these are not measurements of unmodified native-locus activity. The subtype results do not establish a universal type-I effector domain, activation trigger or phage spectrum.

  • https://raw.githubusercontent.com/padlocbio/padloc-db/9e380165633a8d6aef93b5a164cea0f3359bd33f/sys/hachiman_type_I.yaml
    prohibited_genes: - HamC2

    Pinned PADLOC rule, retrieved 2026-10-03: the core is HamA1 plus HamB1, minimum_core and minimum_total are 2, maximum_separation is 0, and force_strand is FALSE. HamC2 is prohibited in the detected system. This is a profile constraint, not proof that a biological locus lacks every divergent HamC homolog or that the whole genome lacks HamC.

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Hachiman/Hachiman.xml
    <gene name="Hachiman__HamB" presence="mandatory"/>

    Pinned DefenseFinder XML, retrieved 2026-10-03: HamA_1 (exchangeable with HamA_2) and HamB are mandatory, both minimum counts are 2, and inter_gene_max_space is 5. The model has no forbidden HamC component. A raw Hachiman call therefore does not establish the type-I absence condition; complete biological locus context must be reviewed. The model name is not added as a type-I exact synonym.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1038/s41467-025-57851-1

Parent traits (1)

Synonyms (1)

  • Hachiman type I EXACT_SYNONYM · DOI:10.1093/nar/gkab883

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 str. K-12 substr. MG1655 NCBITaxon:511145 DOI:10.1038/s41467-025-57851-1 Cui et al. identify the type-I-B source locus at U00096.3 positions 2761204-2765368. NCBI independently resolves that accession to K-12 MG1655, taxon 511145; the source region contains abpA (HamA) and abpB (HamB). This example denotes natural source-strain possession, not all E. coli strains or native-locus protection measured without manipulation. Their defense assays complemented a hamAB-deleted MG1655 host with plasmid-borne HamAB, and protein expression used BL21(DE3). The type-I assignment comes from the paper, not an inference of HamC absence from the retrieved sequence interval alone.

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 type-I subtype mechanisms without equating missing hits with component absence.

KNOWLEDGE GAP OPEN hachiman-type-i-absence-and-subtype-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.

Type I denotes the literature-defined HamAB architecture without HamC, not an isolated HamA/HamB hit, an incomplete assembly, a purified-complex omission or automatic reclassification of a type-II HamC knockout. A genome may possess both type-I and type-II loci, so these possession traits are not disjoint. Cui et al. separate four HamA-domain subtypes within type I; experimental support for I-A/I-B does not validate every predicted subtype or establish one universal nuclease domain, DNA substrate, trigger or antiviral spectrum. Subtype classes remain discovery leads requiring separate source review. The broader Hachiman record already retains source-qualified I-A/I-B mechanism evidence; no duplicate or universal causal graph is added here. Native-locus activity and broader accession-resolved functional generalization remain open.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Added the literature-defined HamC-lacking HamAB possession class with two DOI sources, exact snippets, pinned detector constraints and an NCBI-resolved MG1655 source-locus example. Novelty and allocation searches included ignored and hidden files; the fresh METPO seed has no exact class. Reserved METPO:1052900 in v452. Kept natural source, engineered assays and subtype chemistry distinct.