identifier: traitmech:000465 label: HEC-04 system definition: A phage defense system in which an organism possesses the single-gene HEC-04 Hma-embedded candidate locus, encoding an ABC ATPase fused to a TOPRIM-family nuclease domain, that can reduce bacteriophage plaquing. definition_source: DOI:10.1101/2024.01.29.577857 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: HEC-04 synonym_type: EXACT_SYNONYM source: DOI:10.1101/2024.01.29.577857 - synonym_text: HEC-04__HEC-04 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.1101/2024.01.29.577857 snippet: an ATPase fused to a TOPRIM domain (HEC-04) notes: Payne et al. identify HEC-04 as a Hma-embedded antiviral candidate encoding an ATPase fused to a TOPRIM domain. - reference: DOI:10.1101/2024.01.29.577857 snippet: A quantitative assessment of the remaining systems showed that these were able to reduce the EOP of at least two phages by several orders of magnitude compared to the control notes: Payne et al. support reduced plaquing for the active Hma-embedded candidate systems after excluding inactive HEC-01 and HEC-09 candidates. - reference: DOI:10.1101/2024.01.29.577857 snippet: For HEC-04, mutation of key active site residues in either the ABC ATPase or nuclease domains demonstrated their essential roles in defence notes: Payne et al. show that HEC-04 defense requires intact ABC ATPase and nuclease active-site residues. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| HEC-04 | 10\.1101/2024\.01\.29\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |' notes: The pinned DefenseFinder article registry maps the HEC-04 source key to the Payne et al. Hma-embedded-candidate preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| HEC-04__HEC-04 | | HEC-04 | Custom | 200 |' notes: The pinned DefenseFinder HMM inventory records HEC-04__HEC-04 as a custom HEC-04 profile. causal_graphs: - graph_id: hec_04_locus_reduces_phage_plaquing title: HEC-04 loci reduce bacteriophage plaquing description: Conservative system-level sketch linking the single-gene HEC-04 locus to reduced bacteriophage plaquing and HEC-04 system possession. scope_status: NONMECHANISTIC scope_notes: The graph captures HEC-04 at candidate locus and anti-phage-output level without asserting native host breadth, the direct viral trigger or substrate, exact molecular output, or a DefenseFinder detection rule absent from the pinned rules table. nodes: - node_id: hec_04_locus label: HEC-04 locus node_type: GENETIC_ELEMENT description: A single-gene Hma-embedded candidate locus represented in the pinned DefenseFinder HMM inventory by a HEC-04 custom profile. - node_id: reduced_phage_plaquing label: reduced bacteriophage plaquing node_type: BIOLOGICAL_PROCESS description: Reduced efficiency of plaquing by bacteriophages in cells carrying a complete HEC-04 candidate system. - node_id: hec_04_system_trait label: HEC-04 system node_type: TRAIT grounding: traitmech:000465 description: Possession of a genome-encoded HEC-04 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: hec_04_locus predicate: contributes to predicate_id: RO:0002326 object: reduced_phage_plaquing description: The HEC-04 locus contributes to reduced bacteriophage plaquing when ABC ATPase and nuclease active-site residues are intact. evidence: - reference: DOI:10.1101/2024.01.29.577857 snippet: an ATPase fused to a TOPRIM domain (HEC-04) notes: Payne et al. identify HEC-04 as encoding an ATPase-TOPRIM fused protein. - reference: DOI:10.1101/2024.01.29.577857 snippet: For HEC-04, mutation of key active site residues in either the ABC ATPase or nuclease domains demonstrated their essential roles in defence notes: Payne et al. show that HEC-04 requires intact ATPase and nuclease domains for defense. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| HEC-04__HEC-04 | | HEC-04 | Custom | 200 |' notes: The pinned DefenseFinder HMM inventory records HEC-04__HEC-04 as a custom HEC-04 profile. - subject: reduced_phage_plaquing predicate: confers predicate_id: METPO:2007700 object: hec_04_system_trait description: HEC-04-mediated plaquing reduction realizes the HEC-04 system trait. evidence: - reference: DOI:10.1101/2024.01.29.577857 snippet: A quantitative assessment of the remaining systems showed that these were able to reduce the EOP of at least two phages by several orders of magnitude compared to the control notes: Payne et al. support reduced efficiency of plaquing for the active HEC systems. - reference: DOI:10.1101/2024.01.29.577857 snippet: For HEC-04, mutation of key active site residues in either the ABC ATPase or nuclease domains demonstrated their essential roles in defence notes: Payne et al. support ABC ATPase and nuclease active-site requirements for HEC-04-mediated defense. - subject: hec_04_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: HEC-04 system possession is a phage-defense-system trait. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| HEC-04 | 10\.1101/2024\.01\.29\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |' notes: The pinned DefenseFinder article registry maps the HEC-04 source key to the Payne et al. Hma-embedded-candidate preprint. discussions: - discussion_id: hec-04-defensefinder-model-gap prompt: Resolve HEC-04 native host breadth, sensitive-phage breadth, ATPase-TOPRIM molecular output, and rule-level detection criteria before minting narrower HEC-04 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Payne et al. support HEC-04 as a single-gene Hma-embedded candidate anti-phage system whose ABC ATPase and nuclease domains are both required for defense, and the pinned DefenseFinder HMM inventory records one HEC-04 profile row. The pinned rules table has no HEC-04 row, and the first-pass record does not yet resolve natural host breadth, phage target breadth, or the direct molecular output. evidence: - reference: DOI:10.1101/2024.01.29.577857 snippet: an ATPase fused to a TOPRIM domain (HEC-04) notes: Payne et al. identify HEC-04 as the ATPase-TOPRIM Hma-embedded candidate system. - reference: DOI:10.1101/2024.01.29.577857 snippet: For HEC-04, mutation of key active site residues in either the ABC ATPase or nuclease domains demonstrated their essential roles in defence notes: Payne et al. support HEC-04 domain requirements for defense. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| HEC-04 | 10\.1101/2024\.01\.29\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |' notes: The pinned DefenseFinder article registry maps the HEC-04 source key to the Payne et al. Hma-embedded-candidate preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| HEC-04__HEC-04 | | HEC-04 | Custom | 200 |' notes: The pinned DefenseFinder HMM inventory records HEC-04__HEC-04 as a custom HEC-04 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list HEC-04, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#hec_04_locus_reduces_phage_plaquing posed_by: codex posed_date: '2026-09-29' curation_history: - timestamp: '2026-09-29T14:17:47Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted HEC-04 system as a DOI-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 single-gene candidate-locus level because the pinned DefenseFinder HEC-04 HMM row is not backed by a pinned rules row; the replacement placeholder is reserved in proposals/metpo_traitmech_v342. llm_assisted: true - timestamp: '2026-09-29T14:17:48Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed HEC-04 system during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support heterologous efficiency-of-plaquing assays and a DefenseFinder HEC-04 HMM row, but not a direct named native microbial isolate exemplar with experimentally verified endogenous HEC-04 activity. No paid research was used. llm_assisted: true