identifier: traitmech:000550 label: CARD-NLR endonuclease system definition: A CARD-NLR system in which an organism possesses a genome-encoded DefenseFinder CARD_NLR_Endonuclease subtype locus represented by the CARD_NLR__Endonuclease mandatory rule profile. definition_source: DOI:10.1101/2023.05.28.542683 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000337 synonyms: - synonym_text: CARD_NLR_Endonuclease synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv - synonym_text: CARD_NLR__Endonuclease synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: CARD_NLR__CARD_Protease synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv - synonym_text: CARD_NLR__NLR_new synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv - synonym_text: CARD_NLR__Trypsin synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv evidence: - reference: https://europepmc.org/article/PPR/PPR668921 snippet: Here we show that CARD-like domains are present in defense systems that protect bacteria against phage. notes: Wein et al. support bacterial CARD-like domains as parts of anti-phage defense systems. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| CARD_NLR | 10\.1101/2023\.05\.28\.542683 | CARD-like domains mediate anti-phage defense in bacterial gasdermin systems | ' notes: The pinned DefenseFinder article registry maps the CARD_NLR model namespace to the Wein et al. CARD-like-domain anti-phage defense preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| CARD_NLR__Endonuclease | CARD_NLR__Endonuclease | CARD_NLR | Custom | 500 |' notes: The pinned DefenseFinder HMM inventory records CARD_NLR__Endonuclease as a custom CARD_NLR profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "CARD_NLR\tCARD_NLR_Endonuclease\t1\t3\tCARD_NLR__Endonuclease\tCARD_NLR__CARD_Protease,\ \ CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin,\ \ CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new,\ \ CARD_NLR__Trypsin_Phospho, GasderMIN__bGSDM\t" notes: The pinned DefenseFinder rules table models CARD_NLR_Endonuclease as a CARD_NLR subsystem requiring the CARD_NLR__Endonuclease profile with CARD_Protease, NLR_new, and Trypsin accessory profiles. causal_graphs: - graph_id: card_nlr_endonuclease_locus_subtype_defense title: CARD-NLR endonuclease loci mark a CARD-NLR antiphage subtype description: Conservative subtype-level sketch linking a DefenseFinder CARD_NLR_Endonuclease locus to CARD-like anti-phage defense and CARD-NLR endonuclease system possession. scope_status: NONMECHANISTIC scope_notes: The graph captures the CARD_NLR_Endonuclease subtype at DefenseFinder rule-row level without asserting the exact endonuclease effector substrate, phage trigger, native host breadth, CARD-to-effector activation sequence, or whether every DefenseFinder CARD_NLR_Endonuclease prediction is a complete experimentally active locus. nodes: - node_id: card_nlr_endonuclease_locus label: CARD-NLR endonuclease locus node_type: GENETIC_ELEMENT description: A DefenseFinder CARD_NLR_Endonuclease subtype locus represented by the mandatory CARD_NLR__Endonuclease profile and generic CARD_NLR accessory profiles. - node_id: card_like_antiphage_defense label: CARD-like antiphage defense node_type: BIOLOGICAL_PROCESS description: Anti-phage defense mediated by a bacterial CARD-like defense system. - node_id: card_nlr_endonuclease_system_trait label: CARD-NLR endonuclease system node_type: TRAIT grounding: traitmech:000550 description: Possession of a genome-encoded CARD-NLR endonuclease phage-defense system. - node_id: card_nlr_system_trait label: CARD-NLR system node_type: TRAIT grounding: traitmech:000337 description: Possession of a genome-encoded CARD-NLR phage-defense system. edges: - subject: card_nlr_endonuclease_locus predicate: contributes to predicate_id: RO:0002326 object: card_like_antiphage_defense description: CARD_NLR_Endonuclease loci are represented in DefenseFinder by a CARD_NLR__Endonuclease mandatory profile plus CARD_NLR accessory profiles. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| CARD_NLR__Endonuclease | CARD_NLR__Endonuclease | CARD_NLR | Custom | 500 |' notes: The pinned DefenseFinder HMM inventory records CARD_NLR__Endonuclease as a custom CARD_NLR profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "CARD_NLR\tCARD_NLR_Endonuclease\t1\t3\tCARD_NLR__Endonuclease\tCARD_NLR__CARD_Protease,\ \ CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin,\ \ CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new,\ \ CARD_NLR__Trypsin_Phospho, GasderMIN__bGSDM\t" notes: The pinned DefenseFinder rules table models CARD_NLR_Endonuclease as a CARD_NLR subsystem requiring the CARD_NLR__Endonuclease profile with CARD_Protease, NLR_new, and Trypsin accessory profiles. - subject: card_like_antiphage_defense predicate: confers predicate_id: METPO:2007700 object: card_nlr_endonuclease_system_trait description: The first-pass CARD-NLR endonuclease system trait is realized by a DefenseFinder CARD_NLR_Endonuclease subtype locus. evidence: - reference: https://europepmc.org/article/PPR/PPR668921 snippet: Here we show that CARD-like domains are present in defense systems that protect bacteria against phage. notes: Wein et al. support bacterial CARD-like domains as parts of anti-phage defense systems. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| CARD_NLR__Endonuclease | CARD_NLR__Endonuclease | CARD_NLR | Custom | 500 |' notes: The pinned DefenseFinder HMM inventory records CARD_NLR__Endonuclease as a custom CARD_NLR profile. - subject: card_nlr_endonuclease_system_trait predicate: is a predicate_id: rdfs:subClassOf object: card_nlr_system_trait description: CARD-NLR endonuclease system possession is a CARD-NLR-system trait. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| CARD_NLR | 10\.1101/2023\.05\.28\.542683 | CARD-like domains mediate anti-phage defense in bacterial gasdermin systems | ' notes: The pinned DefenseFinder article registry maps the CARD_NLR model namespace to the Wein et al. CARD-like-domain anti-phage defense preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "CARD_NLR\tCARD_NLR_Endonuclease\t1\t3\tCARD_NLR__Endonuclease\tCARD_NLR__CARD_Protease,\ \ CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin,\ \ CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new,\ \ CARD_NLR__Trypsin_Phospho, GasderMIN__bGSDM\t" notes: The pinned DefenseFinder rules table models CARD_NLR_Endonuclease as a CARD_NLR subsystem requiring the CARD_NLR__Endonuclease profile with CARD_Protease, NLR_new, and Trypsin accessory profiles. discussions: - discussion_id: card-nlr-endonuclease-activity-gap prompt: Resolve the CARD_NLR_Endonuclease phage triggers, native hosts, endonuclease effector substrate, CARD-to-effector activation sequence, and profile-to-activity criteria before minting enzyme, trigger, or component children. kind: KNOWLEDGE_GAP status: OPEN rationale: Wein et al. support CARD-like anti-phage defense systems, and the pinned DefenseFinder HMM inventory and rules table support CARD_NLR_Endonuclease as a subtype with a CARD_NLR__Endonuclease mandatory profile. This first-pass record leaves exact phage triggers, native hosts, accessory-profile requirements, nuclease substrate, and CARD-to-endonuclease activation unresolved. evidence: - reference: https://europepmc.org/article/PPR/PPR668921 snippet: Here we show that CARD-like domains are present in defense systems that protect bacteria against phage. notes: Wein et al. support bacterial CARD-like domains as parts of anti-phage defense systems. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| CARD_NLR__Endonuclease | CARD_NLR__Endonuclease | CARD_NLR | Custom | 500 |' notes: The pinned DefenseFinder HMM inventory records CARD_NLR__Endonuclease as a custom CARD_NLR profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "CARD_NLR\tCARD_NLR_Endonuclease\t1\t3\tCARD_NLR__Endonuclease\tCARD_NLR__CARD_Protease,\ \ CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin,\ \ CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new,\ \ CARD_NLR__Trypsin_Phospho, GasderMIN__bGSDM\t" notes: The pinned DefenseFinder rules table models CARD_NLR_Endonuclease as a CARD_NLR subsystem requiring the CARD_NLR__Endonuclease profile with CARD_Protease, NLR_new, and Trypsin accessory profiles. attaches_to: - causal_graphs#card_nlr_endonuclease_locus_subtype_defense posed_by: codex posed_date: '2026-10-02' curation_history: - timestamp: '2026-10-02T16:57:23Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted CARD-NLR endonuclease system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the CARD-NLR system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record for the target local ID, placeholder METPO ID, proposal cohort, record slug, or human label; the replacement placeholder is reserved in proposals/metpo_traitmech_v427. llm_assisted: true - timestamp: '2026-10-02T16:57:24Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed CARD-NLR endonuclease system during initial curation and left canonical_examples empty because Wein et al. and the pinned DefenseFinder tables support CARD-like anti-phage defense and the CARD_NLR_Endonuclease model namespace but not an accession-backed native microbial taxon exemplar tied to CARD_NLR_Endonuclease profiles and experimentally verified endogenous CARD-NLR endonuclease activity. No paid research was used. llm_assisted: true