CARD-NLR-like system

traitmech:000559 · CLASS · PROPOSED

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.

Trait evidence (7)

https://europepmc.org/article/PPR/PPR668921
Here we show that CARD-like domains are present in defense systems that protect bacteria against phage.

Wein et al. support bacterial CARD-like domains as parts of anti-phage defense systems.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| CARD_NLR | 10\.1101/2023\.05\.28\.542683 | CARD-like domains mediate anti-phage defense in bacterial gasdermin systems |

The pinned DefenseFinder article registry maps the CARD_NLR model namespace to the Wein et al. CARD-like-domain anti-phage defense preprint.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| CARD_NLR__Endonuclease | CARD_NLR__Endonuclease | CARD_NLR | Custom | 500 |

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.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| CARD_NLR__Phospho_Trypsin | CARD_NLR__Phospho_Trypsin | CARD_NLR | Custom | 1000 |

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.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| CARD_NLR__Trypsin_Phospho | CARD_NLR__Trypsin_Phospho | CARD_NLR | Custom | 400 |

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.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
System Subsystem Min_mandatory Minimum_genes Mandatory Accessory Forbidden Neutral

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.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
CARD_NLR CARD_NLR_like 2 4 CARD_NLR__Endonuclease, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase_long_new, CARD_NLR__Trypsin_Phospho CARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin

The pinned DefenseFinder rules table models CARD_NLR_like as a CARD_NLR subsystem requiring two matches from a four-profile candidate effector set.

CARD-NLR-like is a DefenseFinder CARD-NLR subtype

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.

NONMECHANISTIC · 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.

Edge evidence

CARD-NLR-like locus contributes to CARD-like antiphage defense RO:0002326
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.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv System Subsystem Min_mandatory Minimum_genes Mandatory Accessory Forbidden Neutral CARD_NLR CARD_NLR_like 2 4 CARD_NLR__Endonuclease, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase_long_new, CARD_NLR__Trypsin_Phospho CARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin 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.
CARD-like antiphage defense confers CARD-NLR-like system METPO:2007700
The first-pass CARD-NLR-like system trait is realized by a DefenseFinder CARD_NLR_like subtype locus.
- https://europepmc.org/article/PPR/PPR668921 Here we show that CARD-like domains are present in defense systems that protect bacteria against phage. Wein et al. support bacterial CARD-like domains as parts of anti-phage defense systems.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | CARD_NLR | 10\.1101/2023\.05\.28\.542683 | CARD-like domains mediate anti-phage defense in bacterial gasdermin systems | The pinned DefenseFinder article registry maps the CARD_NLR model namespace to the Wein et al. CARD-like-domain anti-phage defense preprint.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv CARD_NLR_like 2 4 CARD_NLR__Endonuclease, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase_long_new, CARD_NLR__Trypsin_Phospho 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.
CARD-NLR-like system is a CARD-NLR system rdfs:subClassOf
CARD-NLR-like system possession is a CARD-NLR-system trait.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | CARD_NLR | 10\.1101/2023\.05\.28\.542683 | CARD-like domains mediate anti-phage defense in bacterial gasdermin systems | The pinned DefenseFinder article registry maps the CARD_NLR model namespace to the Wein et al. CARD-like-domain anti-phage defense preprint.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv System Subsystem Min_mandatory Minimum_genes Mandatory Accessory Forbidden Neutral 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.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv CARD_NLR CARD_NLR_like The pinned DefenseFinder rules table places the CARD_NLR_like subsystem under the CARD_NLR system key.

Provenance

Identifier source: TraitMech local identifier
Definition source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Parent traits (1)

CARD-NLR system traitmech:000337

Synonyms (1)

CARD_NLR_like RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Discussions and Knowledge Gaps (1)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

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.

KNOWLEDGE GAP OPEN card-nlr-like-activity-gap · raised by codex · 2026-10-03

Attached to causal_graphs#card_nlr_like_locus_subtype_defense

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

https://europepmc.org/article/PPR/PPR668921
Here we show that CARD-like domains are present in defense systems that protect bacteria against phage.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| CARD_NLR__Endonuclease | CARD_NLR__Endonuclease | CARD_NLR | Custom | 500 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| CARD_NLR__Phospho_Trypsin | CARD_NLR__Phospho_Trypsin | CARD_NLR | Custom | 1000 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| CARD_NLR__Trypsin_Phospho | CARD_NLR__Trypsin_Phospho | CARD_NLR | Custom | 400 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
System Subsystem Min_mandatory Minimum_genes Mandatory Accessory Forbidden Neutral
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
CARD_NLR CARD_NLR_like 2 4 CARD_NLR__Endonuclease, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase_long_new, CARD_NLR__Trypsin_Phospho CARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin

Curation history

2026-10-03T00:02:50Z · MINTED_TRAITMECH_ID · codex
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.
2026-10-03T00:02:52Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
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.