Hachiman type II system

traitmech:000574 · CLASS · PROPOSED

A Hachiman system in which an organism possesses a locus encoding HamA and HamB together with an additional HamC (DUF3223) component.

Trait evidence (4)

DOI:10.1093/nar/gkab883
a gene encoding a DUF3223 protein (HamC) either upstream or downstream of hamAB

Results, new-subtype classification: Payne et al. name this HamC-associated Hachiman architecture type II. Methods and Figure 3 identify the DSM 14551 source locus and show antiphage activity after expression in E. coli BL21-AI. The natural source and engineered assay host are distinct. The paper does not establish native-host resistance, a universal phage spectrum, HamC essentiality or HamC chemistry.
DOI:10.1038/s41467-025-57851-1
Hachiman systems that include HamA, HamB, and HamC (DUF3223) were referred to as type II

Introduction: Cui et al. retain the HamABC classification and attribute it to Payne et al.; this is corroborating terminology, not an independent type-II experiment. Their biochemical experiments on type I-A/I-B do not establish DNA-damage sensing, DNA cleavage or HamC function in type II.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Hachiman/Hachiman_II.xml
<gene name="Hachiman_II__HamC" presence="mandatory"/>

Pinned DefenseFinder XML, retrieved 2026-10-03: HamA (HamA_1 with HamA_2 exchangeable), HamB and HamC are marked mandatory, but both minimum gene counts are 2 and the inter-gene maximum space is 5. Thus the model does not require all three marked components in every accepted call; a raw Hachiman_II call alone is insufficient to establish the complete biological architecture. This is a detector constraint, not an experiment or a trait synonym.
https://raw.githubusercontent.com/padlocbio/padloc-db/9e380165633a8d6aef93b5a164cea0f3359bd33f/sys/hachiman_type_II.yaml
minimum_core: 3 minimum_total: 3 core_genes: - HamA2 - HamB2 - HamC2

Pinned PADLOC rule, retrieved 2026-10-03: all three core components are required, maximum_separation is 0 and force_strand is FALSE. This differs from DefenseFinder's two-gene minimum; neither detector proves functional defense or experimental necessity of each component.

Provenance

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

Parent traits (1)

Hachiman system traitmech:000219

Synonyms (1)

Hachiman type II 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.

Sphingopyxis witflariensis NCBITaxon:173675 DOI:10.1093/nar/gkab883 DSM 14551 is the natural source of the type-II locus amplified from genomic DNA by Payne et al. (NZ_NISJ01000011.1). The NCBI GenBank source feature independently identifies DSM 14551 and taxon 173675. This example denotes possession in this source strain, not all members of the species or native-host resistance. The reported defense assays used engineered E. coli BL21-AI.

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 HamC function and type-II mechanisms beyond heterologous defense assays.

KNOWLEDGE GAP OPEN hachiman-type-ii-component-and-mechanism-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 II denotes the HamABC locus architecture, not a HamC hit alone, a source database row or a fixed phage-protection phenotype. Type-I DNA-damage sensing and DNA-cleavage mechanisms are not generalized to this class; HamC's biochemical role and necessity remain unresolved by these sources. No causal mechanism graph or unverified protein accession is asserted. Native-host assays and accession-resolved functional evidence remain desirable. DefenseFinder and PADLOC have different component-count rules; inspect complete locus context before converting calls into trait assertions. Component absence cannot be inferred from a failed hit or incomplete assembly. Type I remains a separate discovery lead, and coexisting loci would not make organism-level type-I and type-II possession traits disjoint. The type-I lead is now represented by traitmech:000575 Hachiman type I system for the literature-defined HamC-lacking HamAB architecture. This does not imply organism-level disjointness, turn missing detector hits into absence evidence, or transfer type-I chemistry to type II. HamC function and type-II mechanisms remain unresolved.

Curation history

2026-10-03T18:08:00Z · MINTED_TRAITMECH_ID · codex
Added the literature-defined HamABC possession class with two DOI sources, exact snippets, pinned detector rules and the NCBI-resolved DSM 14551 example. Searches included ignored and hidden files and found no exact live record or METPO class. Reserved METPO:1052801 in v451; METPO:1052800 replaces the broad parent's v96 proposal. Kept natural source, heterologous activity and type-I chemistry distinct.
2026-10-03T18:37:00Z · TRACK_HACHIMAN_TYPE_I_CLASS · codex
Linked traitmech:000575 Hachiman type I system using the component classification in DOI:10.1093/nar/gkab883 and DOI:10.1038/s41467-025-57851-1. Kept definitions, hierarchy, examples, evidence and graphs unchanged; mechanism questions remain open. No absence assertion is inferred from detector output.