identifier: traitmech:000553 label: CARD-NLR subtilase system definition: A CARD-NLR system in which an organism possesses a genome-encoded DefenseFinder CARD_NLR_Subtilase subtype locus represented by the CARD_NLR_Subtilase rule row requiring the CARD_NLR__Subtilase_long_new 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_Subtilase synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv - synonym_text: CARD_NLR__Subtilase_long_new synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv - 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__Subtilase | CARD_NLR__Subtilase | CARD_NLR | Custom | 500 | | CARD_NLR__Subtilase_small_new | CARD_NLR__Subtilase_small_new | CARD_NLR | Custom | 500 |' notes: The pinned DefenseFinder HMM inventory records two custom CARD_NLR subtilase-family profile rows, while the exact CARD_NLR__Subtilase_long_new rule profile was not present under the CARD_NLR model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "CARD_NLR\tCARD_NLR_Subtilase\t1\t3\tCARD_NLR__Subtilase_long_new\tCARD_NLR__CARD_Protease,\ \ CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new,\ \ CARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin, CARD_NLR__Trypsin_Phospho, CARD_NLR__Trypsine_Endonuclease_new,\ \ GasderMIN__bGSDM\t" notes: The pinned DefenseFinder rules table models CARD_NLR_Subtilase as a CARD_NLR subsystem requiring the CARD_NLR__Subtilase_long_new rule profile with CARD_Protease, NLR_new, and Trypsin accessory profiles. causal_graphs: - graph_id: card_nlr_subtilase_locus_subtype_defense title: CARD-NLR subtilase loci mark a CARD-NLR antiphage subtype description: Conservative subtype-level sketch linking a DefenseFinder CARD_NLR_Subtilase locus to CARD-like anti-phage defense and CARD-NLR subtilase system possession. scope_status: NONMECHANISTIC scope_notes: The graph captures the CARD_NLR_Subtilase subtype at DefenseFinder rule-row level without asserting the exact subtilase substrate, phage trigger, native host breadth, CARD-to-effector activation sequence, how the missing CARD_NLR__Subtilase_long_new HMM row maps to the listed CARD_NLR subtilase profiles, or whether every DefenseFinder CARD_NLR_Subtilase prediction is a complete experimentally active locus. nodes: - node_id: card_nlr_subtilase_locus label: CARD-NLR subtilase locus node_type: GENETIC_ELEMENT description: A DefenseFinder CARD_NLR_Subtilase subtype locus represented by the CARD_NLR__Subtilase_long_new rule 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_subtilase_system_trait label: CARD-NLR subtilase system node_type: TRAIT grounding: traitmech:000553 description: Possession of a genome-encoded CARD-NLR subtilase 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_subtilase_locus predicate: contributes to predicate_id: RO:0002326 object: card_like_antiphage_defense description: CARD_NLR_Subtilase loci are represented in DefenseFinder by a CARD_NLR__Subtilase_long_new rule profile plus CARD_NLR accessory profiles. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "CARD_NLR\tCARD_NLR_Subtilase\t1\t3\tCARD_NLR__Subtilase_long_new\t\ CARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Endonuclease,\ \ CARD_NLR__Endonuclease_new, CARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin,\ \ CARD_NLR__Trypsin_Phospho, CARD_NLR__Trypsine_Endonuclease_new, GasderMIN__bGSDM\t" notes: The pinned DefenseFinder rules table models CARD_NLR_Subtilase as a CARD_NLR subsystem requiring the CARD_NLR__Subtilase_long_new rule profile with CARD_Protease, NLR_new, and Trypsin accessory profiles. - subject: card_like_antiphage_defense predicate: confers predicate_id: METPO:2007700 object: card_nlr_subtilase_system_trait description: The first-pass CARD-NLR subtilase system trait is realized by a DefenseFinder CARD_NLR_Subtilase 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/DefenseFinder_rules.tsv snippet: "CARD_NLR_Subtilase\t1\t3\tCARD_NLR__Subtilase_long_new\tCARD_NLR__CARD_Protease,\ \ CARD_NLR__NLR_new, CARD_NLR__Trypsin" notes: The pinned DefenseFinder rules table models CARD_NLR_Subtilase as a CARD_NLR subsystem requiring the CARD_NLR__Subtilase_long_new rule profile with CARD_Protease, NLR_new, and Trypsin accessory profiles. - subject: card_nlr_subtilase_system_trait predicate: is a predicate_id: rdfs:subClassOf object: card_nlr_system_trait description: CARD-NLR subtilase 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_Subtilase\t1\t3\tCARD_NLR__Subtilase_long_new" notes: The pinned DefenseFinder rules table places the CARD_NLR_Subtilase subsystem under the CARD_NLR system key and requires CARD_NLR__Subtilase_long_new. discussions: - discussion_id: card-nlr-subtilase-activity-gap prompt: Resolve the CARD_NLR_Subtilase phage triggers, native hosts, CARD_NLR__Subtilase_long_new HMM inventory coverage, subtilase 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 rules table supports CARD_NLR_Subtilase as a rule-row subtype with a CARD_NLR__Subtilase_long_new rule profile. This first-pass record leaves exact phage triggers, native hosts, accessory-profile requirements, subtilase substrates, CARD-to-subtilase activation, and exact HMM profile coverage unresolved because the pinned HMM inventory lists CARD_NLR__Subtilase and CARD_NLR__Subtilase_small_new but not CARD_NLR__Subtilase_long_new. 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__Subtilase | CARD_NLR__Subtilase | CARD_NLR | Custom | 500 | | CARD_NLR__Subtilase_small_new | CARD_NLR__Subtilase_small_new | CARD_NLR | Custom | 500 |' notes: The pinned DefenseFinder HMM inventory records two custom CARD_NLR subtilase-family profile rows, while the exact CARD_NLR__Subtilase_long_new rule profile was not present under the CARD_NLR model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "CARD_NLR\tCARD_NLR_Subtilase\t1\t3\tCARD_NLR__Subtilase_long_new\tCARD_NLR__CARD_Protease,\ \ CARD_NLR__NLR_new, CARD_NLR__Trypsin\tCARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new,\ \ CARD_NLR__Phospho, CARD_NLR__Phospho_Trypsin, CARD_NLR__Trypsin_Phospho, CARD_NLR__Trypsine_Endonuclease_new,\ \ GasderMIN__bGSDM\t" notes: The pinned DefenseFinder rules table models CARD_NLR_Subtilase as a CARD_NLR subsystem requiring the CARD_NLR__Subtilase_long_new rule profile with CARD_Protease, NLR_new, and Trypsin accessory profiles. attaches_to: - causal_graphs#card_nlr_subtilase_locus_subtype_defense posed_by: codex posed_date: '2026-10-02' curation_history: - timestamp: '2026-10-02T19:23:10Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted CARD-NLR subtilase 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; existing CARD_NLR_Subtilase mentions were scoped to CARD-NLR parent evidence, not an exact child TraitRecord, and the replacement placeholder is reserved in proposals/metpo_traitmech_v430. llm_assisted: true - timestamp: '2026-10-02T19:23:12Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed CARD-NLR subtilase 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_Subtilase rule row but not an accession-backed native microbial taxon exemplar tied to CARD_NLR_Subtilase profiles and experimentally verified endogenous CARD-NLR subtilase activity. No paid research was used. llm_assisted: true