identifier: traitmech:000559 label: CARD-NLR-like system definition: A CARD-NLR system in which an organism possesses a genome-encoded DefenseFinder CARD_NLR_like subtype locus represented by the CARD_NLR_like rule row requiring two matches from the CARD_NLR__Endonuclease, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase_long_new, and CARD_NLR__Trypsin_Phospho effector-profile set and four genes overall after considering CARD_NLR__CARD_Protease, CARD_NLR__NLR_new, and CARD_NLR__Trypsin accessory profiles. definition_source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000337 synonyms: - synonym_text: CARD_NLR_like 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 the CARD_NLR__Endonuclease custom profile listed among the candidate effector profiles by the CARD_NLR_like rule row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| CARD_NLR__Phospho_Trypsin | CARD_NLR__Phospho_Trypsin | CARD_NLR | Custom | 1000 |' notes: The pinned DefenseFinder HMM inventory records the CARD_NLR__Phospho_Trypsin custom profile listed among the candidate effector profiles by the CARD_NLR_like rule row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| CARD_NLR__Trypsin_Phospho | CARD_NLR__Trypsin_Phospho | CARD_NLR | Custom | 400 |' notes: The pinned DefenseFinder HMM inventory records the CARD_NLR__Trypsin_Phospho custom profile listed among the candidate effector profiles by the CARD_NLR_like rule row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "System\tSubsystem\tMin_mandatory\tMinimum_genes\tMandatory\tAccessory\t\ Forbidden\tNeutral" notes: The pinned DefenseFinder rules header identifies the second, third, fourth, fifth, and sixth CARD_NLR_like row fields as Subsystem, Min_mandatory, Minimum_genes, Mandatory, and Accessory, respectively. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "CARD_NLR\tCARD_NLR_like\t2\t4\tCARD_NLR__Endonuclease, CARD_NLR__Phospho_Trypsin,\ \ CARD_NLR__Subtilase_long_new, CARD_NLR__Trypsin_Phospho\tCARD_NLR__CARD_Protease,\ \ CARD_NLR__NLR_new, CARD_NLR__Trypsin\t\t" notes: The pinned DefenseFinder rules table models CARD_NLR_like as a CARD_NLR subsystem requiring two matches from a four-profile candidate effector set. causal_graphs: - graph_id: card_nlr_like_locus_subtype_defense title: CARD-NLR-like is a DefenseFinder CARD-NLR subtype description: Conservative subtype-level sketch linking a DefenseFinder CARD_NLR_like locus to CARD-like anti-phage defense, CARD-NLR-like system possession, and its CARD-NLR parent. scope_status: NONMECHANISTIC scope_notes: The graph captures the CARD_NLR_like subtype at DefenseFinder rule-row level without expanding candidate effector-profile names, selecting which two of the four candidate effector profiles realize activity, resolving the absent CARD_NLR__Subtilase_long_new HMM inventory row, or resolving exact phage triggers, native host breadth, CARD-to-effector activation sequence, cell-death output, or whether every DefenseFinder CARD_NLR_like prediction is a complete experimentally active locus. nodes: - node_id: card_nlr_like_locus label: CARD-NLR-like locus node_type: GENETIC_ELEMENT description: A DefenseFinder CARD_NLR_like subtype locus represented by at least two of four candidate CARD_NLR effector profiles 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_like_system_trait label: CARD-NLR-like system node_type: TRAIT grounding: traitmech:000559 description: Possession of a genome-encoded CARD-NLR-like 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_like_locus predicate: contributes to predicate_id: RO:0002326 object: card_like_antiphage_defense description: CARD_NLR_like loci are represented in DefenseFinder by at least two matches from four candidate CARD_NLR effector profiles plus CARD_NLR accessory profiles. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "System\tSubsystem\tMin_mandatory\tMinimum_genes\tMandatory\tAccessory\t\ Forbidden\tNeutral\nCARD_NLR\tCARD_NLR_like\t2\t4\tCARD_NLR__Endonuclease,\ \ CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase_long_new, CARD_NLR__Trypsin_Phospho\t\ CARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin\t\t" notes: The pinned DefenseFinder rules header and CARD_NLR_like row identify CARD_NLR_like as a CARD_NLR subsystem with Min_mandatory=2, Minimum_genes=4, four candidate Mandatory effector profiles, and three Accessory profiles. - subject: card_like_antiphage_defense predicate: confers predicate_id: METPO:2007700 object: card_nlr_like_system_trait description: The first-pass CARD-NLR-like system trait is realized by a DefenseFinder CARD_NLR_like 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/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_like\t2\t4\tCARD_NLR__Endonuclease, CARD_NLR__Phospho_Trypsin,\ \ CARD_NLR__Subtilase_long_new, CARD_NLR__Trypsin_Phospho" notes: The pinned DefenseFinder rules table models CARD_NLR_like with two required matches from Endonuclease, Phospho_Trypsin, Subtilase_long_new, and Trypsin_Phospho candidate effector profiles. - subject: card_nlr_like_system_trait predicate: is a predicate_id: rdfs:subClassOf object: card_nlr_system_trait description: CARD-NLR-like 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: "System\tSubsystem\tMin_mandatory\tMinimum_genes\tMandatory\tAccessory\t\ Forbidden\tNeutral" notes: The pinned DefenseFinder rules header identifies the second, third, fourth, fifth, and sixth CARD_NLR_like row fields as Subsystem, Min_mandatory, Minimum_genes, Mandatory, and Accessory, respectively. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "CARD_NLR\tCARD_NLR_like" notes: The pinned DefenseFinder rules table places the CARD_NLR_like subsystem under the CARD_NLR system key. discussions: - discussion_id: card-nlr-like-activity-gap prompt: Resolve the CARD_NLR_like phage triggers, native hosts, four-profile effector-combination semantics, CARD_NLR__Subtilase_long_new HMM inventory gap, and profile-to-activity criteria before minting effector or trigger children. kind: KNOWLEDGE_GAP status: OPEN rationale: Wein et al. support CARD-like anti-phage defense, and the pinned DefenseFinder HMM inventory and rules table support CARD_NLR_like as a CARD_NLR subsystem requiring two matches from a four-profile Endonuclease, Phospho_Trypsin, Subtilase_long_new, and Trypsin_Phospho candidate effector set. This first-pass record follows the rule row but leaves exact phage triggers, native hosts, how the two-of-four effector profile combinations map to activity, how CARD_NLR__Subtilase_long_new maps to the pinned HMM inventory, and whether every DefenseFinder CARD_NLR_like prediction is a complete experimentally active 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 the CARD_NLR__Endonuclease custom profile listed among the candidate effector profiles by the CARD_NLR_like rule row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| CARD_NLR__Phospho_Trypsin | CARD_NLR__Phospho_Trypsin | CARD_NLR | Custom | 1000 |' notes: The pinned DefenseFinder HMM inventory records the CARD_NLR__Phospho_Trypsin custom profile listed among the candidate effector profiles by the CARD_NLR_like rule row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| CARD_NLR__Trypsin_Phospho | CARD_NLR__Trypsin_Phospho | CARD_NLR | Custom | 400 |' notes: The pinned DefenseFinder HMM inventory records the CARD_NLR__Trypsin_Phospho custom profile listed among the candidate effector profiles by the CARD_NLR_like rule row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "System\tSubsystem\tMin_mandatory\tMinimum_genes\tMandatory\tAccessory\t\ Forbidden\tNeutral" notes: The pinned DefenseFinder rules header identifies the second, third, fourth, fifth, and sixth CARD_NLR_like row fields as Subsystem, Min_mandatory, Minimum_genes, Mandatory, and Accessory, respectively. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "CARD_NLR\tCARD_NLR_like\t2\t4\tCARD_NLR__Endonuclease, CARD_NLR__Phospho_Trypsin,\ \ CARD_NLR__Subtilase_long_new, CARD_NLR__Trypsin_Phospho\tCARD_NLR__CARD_Protease,\ \ CARD_NLR__NLR_new, CARD_NLR__Trypsin\t\t" notes: The pinned DefenseFinder rules table models CARD_NLR_like as a CARD_NLR subsystem requiring two matches from a four-profile candidate effector set. attaches_to: - causal_graphs#card_nlr_like_locus_subtype_defense posed_by: codex posed_date: '2026-10-03' curation_history: - timestamp: '2026-10-03T00:02:50Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted CARD-NLR-like 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_like mentions were scoped to the CARD-NLR parent, not an exact child TraitRecord, and the replacement placeholder is reserved in proposals/metpo_traitmech_v436. llm_assisted: true - timestamp: '2026-10-03T00:02:52Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed CARD-NLR-like system during initial curation and left canonical_examples empty because Wein et al. and the pinned DefenseFinder tables support CARD-like anti-phage systems and the CARD_NLR_like rule row but not an accession-backed native microbial taxon exemplar tied to CARD_NLR_like profiles and experimentally verified endogenous activity. No paid research was used. llm_assisted: true