identifier: traitmech:000418 label: HEC-03 system definition: A phage defense system in which an organism possesses the two-gene HEC-03 Hma-embedded candidate locus, encoding an ABC ATPase and an associated PilT N-terminal domain protein, 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-03 synonym_type: EXACT_SYNONYM source: DOI:10.1101/2024.01.29.577857 evidence: - reference: DOI:10.1101/2024.01.29.577857 snippet: The candidate systems encoded diverse protein families, including three ATPases associated with either a topoisomerase-primase (TOPRIM) (HEC-01), nuclease-related (NERD) (HEC-02), or PilT N-terminal (PIN) (HEC-03) domain-containing protein notes: Payne et al. identify HEC-03 as a candidate two-gene Hma-embedded antiviral system pairing an ATPase with a PilT N-terminal-domain protein. - 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 the two-gene systems HEC-02 and HEC-03, both genes were required for defence notes: Payne et al. show that both genes in the two-gene HEC-03 candidate system were required for defense. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| HEC-03 | 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-03 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-03__HEC-03A | | HEC-03 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records HEC-03__HEC-03A as a custom HEC-03 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| HEC-03__HEC-03B | | HEC-03 | Custom | 150 |' notes: The pinned DefenseFinder HMM inventory records HEC-03__HEC-03B as a custom HEC-03 profile. causal_graphs: - graph_id: hec_03_locus_reduces_phage_plaquing title: HEC-03 loci reduce bacteriophage plaquing description: Conservative system-level sketch linking the two-gene HEC-03 locus to reduced bacteriophage plaquing and HEC-03 system possession. scope_status: NONMECHANISTIC scope_notes: The graph captures HEC-03 at candidate locus and anti-phage-output level without asserting native host breadth, exact profile-to-component mapping, the direct viral trigger or substrate, exact molecular output, or a DefenseFinder detection rule absent from the pinned rules table. nodes: - node_id: hec_03_locus label: HEC-03 locus node_type: GENETIC_ELEMENT description: A two-gene Hma-embedded candidate locus represented in the pinned DefenseFinder HMM inventory by HEC-03A and HEC-03B custom profiles. - 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-03 candidate system. - node_id: hec_03_system_trait label: HEC-03 system node_type: TRAIT grounding: traitmech:000418 description: Possession of a genome-encoded HEC-03 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_03_locus predicate: contributes to predicate_id: RO:0002326 object: reduced_phage_plaquing description: The two-gene HEC-03 locus contributes to reduced bacteriophage plaquing when both HEC-03 genes are present. evidence: - reference: DOI:10.1101/2024.01.29.577857 snippet: The candidate systems encoded diverse protein families, including three ATPases associated with either a topoisomerase-primase (TOPRIM) (HEC-01), nuclease-related (NERD) (HEC-02), or PilT N-terminal (PIN) (HEC-03) domain-containing protein notes: Payne et al. identify HEC-03 as pairing an ATPase with a PilT N-terminal-domain protein. - reference: DOI:10.1101/2024.01.29.577857 snippet: For the two-gene systems HEC-02 and HEC-03, both genes were required for defence notes: Payne et al. show that HEC-03 requires both genes for defense. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| HEC-03__HEC-03A | | HEC-03 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records HEC-03__HEC-03A as a custom HEC-03 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| HEC-03__HEC-03B | | HEC-03 | Custom | 150 |' notes: The pinned DefenseFinder HMM inventory records HEC-03__HEC-03B as a custom HEC-03 profile. - subject: reduced_phage_plaquing predicate: confers predicate_id: METPO:2007700 object: hec_03_system_trait description: HEC-03-mediated plaquing reduction realizes the HEC-03 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 the two-gene systems HEC-02 and HEC-03, both genes were required for defence notes: Payne et al. show that complete HEC-03 requires both genes for defense. - subject: hec_03_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: HEC-03 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-03 | 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-03 source key to the Payne et al. Hma-embedded-candidate preprint. discussions: - discussion_id: hec-03-defensefinder-model-gap prompt: Resolve HEC-03 native host breadth, exact HEC-03A/HEC-03B component functions, sensitive-phage breadth, molecular output, and rule-level detection criteria before minting narrower HEC-03 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Payne et al. support HEC-03 as an Hma-embedded candidate anti-phage system whose two genes are both required for defense, and the pinned DefenseFinder HMM inventory records HEC-03A and HEC-03B profile rows. The pinned rules table has no HEC-03 row, and the first-pass record does not yet resolve natural host breadth, HEC-03 profile-to-component mapping, phage target breadth, or the direct molecular output. evidence: - reference: DOI:10.1101/2024.01.29.577857 snippet: The candidate systems encoded diverse protein families, including three ATPases associated with either a topoisomerase-primase (TOPRIM) (HEC-01), nuclease-related (NERD) (HEC-02), or PilT N-terminal (PIN) (HEC-03) domain-containing protein notes: Payne et al. identify HEC-03 as one of the ATPase-associated Hma-embedded candidate systems. - reference: DOI:10.1101/2024.01.29.577857 snippet: For the two-gene systems HEC-02 and HEC-03, both genes were required for defence notes: Payne et al. support two-gene requirement for HEC-03-mediated defense. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| HEC-03 | 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-03 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-03__HEC-03A | | HEC-03 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records HEC-03__HEC-03A as a custom HEC-03 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| HEC-03__HEC-03B | | HEC-03 | Custom | 150 |' notes: The pinned DefenseFinder HMM inventory records HEC-03__HEC-03B as a custom HEC-03 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list HEC-03, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#hec_03_locus_reduces_phage_plaquing posed_by: codex posed_date: '2026-09-27' curation_history: - timestamp: '2026-09-27T21:21:54Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted HEC-03 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 two-gene candidate-locus level because the pinned DefenseFinder HEC-03 HMM rows are not backed by pinned rules rows; the replacement placeholder is reserved in proposals/metpo_traitmech_v295. llm_assisted: true - timestamp: '2026-09-27T21:21:55Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed HEC-03 system during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support heterologous efficiency-of-plaquing assays and DefenseFinder HEC-03 HMM rows, but not a direct named native microbial isolate exemplar with experimentally verified endogenous HEC-03 activity. No paid research was used. llm_assisted: true