CARD-NLR endonuclease system

traitmech:000550 · CLASS · PROPOSED

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.

Trait evidence (4)

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 CARD_NLR__Endonuclease as a custom CARD_NLR profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
CARD_NLR CARD_NLR_Endonuclease 1 3 CARD_NLR__Endonuclease CARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin CARD_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

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.

CARD-NLR endonuclease loci mark a CARD-NLR antiphage subtype

Conservative subtype-level sketch linking a DefenseFinder CARD_NLR_Endonuclease locus to CARD-like anti-phage defense and CARD-NLR endonuclease system possession.

NONMECHANISTIC · 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.

Edge evidence

CARD-NLR endonuclease locus contributes to CARD-like antiphage defense RO:0002326
CARD_NLR_Endonuclease loci are represented in DefenseFinder by a CARD_NLR__Endonuclease mandatory profile plus CARD_NLR accessory profiles.
- 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 CARD_NLR__Endonuclease as a custom CARD_NLR profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv CARD_NLR CARD_NLR_Endonuclease 1 3 CARD_NLR__Endonuclease CARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin CARD_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 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.
CARD-like antiphage defense confers CARD-NLR endonuclease system METPO:2007700
The first-pass CARD-NLR endonuclease system trait is realized by a DefenseFinder CARD_NLR_Endonuclease 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/Liste_hmm_system.md | CARD_NLR__Endonuclease | CARD_NLR__Endonuclease | CARD_NLR | Custom | 500 | The pinned DefenseFinder HMM inventory records CARD_NLR__Endonuclease as a custom CARD_NLR profile.
CARD-NLR endonuclease system is a CARD-NLR system rdfs:subClassOf
CARD-NLR endonuclease 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 CARD_NLR CARD_NLR_Endonuclease 1 3 CARD_NLR__Endonuclease CARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin CARD_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 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.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1101/2023.05.28.542683

Parent traits (1)

CARD-NLR system traitmech:000337

Synonyms (5)

CARD_NLR_Endonuclease RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
CARD_NLR__Endonuclease RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
CARD_NLR__CARD_Protease RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
CARD_NLR__NLR_new RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
CARD_NLR__Trypsin 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_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.

KNOWLEDGE GAP OPEN card-nlr-endonuclease-activity-gap · raised by codex · 2026-10-02

Attached to causal_graphs#card_nlr_endonuclease_locus_subtype_defense

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

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/DefenseFinder_rules.tsv
CARD_NLR CARD_NLR_Endonuclease 1 3 CARD_NLR__Endonuclease CARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin CARD_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

Curation history

2026-10-02T16:57:23Z · MINTED_TRAITMECH_ID · codex
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.
2026-10-02T16:57:24Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
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.