CARD-NLR phospho system

traitmech:000551 · CLASS · PROPOSED

A CARD-NLR system in which an organism possesses a genome-encoded DefenseFinder CARD_NLR_Phospho subtype locus represented by the CARD_NLR__Trypsin_Phospho 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__Trypsin_Phospho | CARD_NLR__Trypsin_Phospho | CARD_NLR | Custom | 400 |

The pinned DefenseFinder HMM inventory records CARD_NLR__Trypsin_Phospho as a custom CARD_NLR profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
CARD_NLR CARD_NLR_Phospho 1 3 CARD_NLR__Trypsin_Phospho CARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin CARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsine_Endonuclease_new, GasderMIN__bGSDM

The pinned DefenseFinder rules table models CARD_NLR_Phospho as a CARD_NLR subsystem requiring the CARD_NLR__Trypsin_Phospho profile with CARD_Protease, NLR_new, and Trypsin accessory profiles.

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

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

NONMECHANISTIC · The graph captures the CARD_NLR_Phospho subtype at DefenseFinder rule-row level without asserting the exact phosphorylated substrate, phage trigger, native host breadth, CARD-to-effector activation sequence, or whether every DefenseFinder CARD_NLR_Phospho prediction is a complete experimentally active locus.

Edge evidence

CARD-NLR phospho locus contributes to CARD-like antiphage defense RO:0002326
CARD_NLR_Phospho loci are represented in DefenseFinder by a CARD_NLR__Trypsin_Phospho mandatory profile plus CARD_NLR accessory profiles.
- 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 CARD_NLR__Trypsin_Phospho as a custom CARD_NLR profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv CARD_NLR CARD_NLR_Phospho 1 3 CARD_NLR__Trypsin_Phospho CARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin CARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsine_Endonuclease_new, GasderMIN__bGSDM The pinned DefenseFinder rules table models CARD_NLR_Phospho as a CARD_NLR subsystem requiring the CARD_NLR__Trypsin_Phospho profile with CARD_Protease, NLR_new, and Trypsin accessory profiles.
CARD-like antiphage defense confers CARD-NLR phospho system METPO:2007700
The first-pass CARD-NLR phospho system trait is realized by a DefenseFinder CARD_NLR_Phospho 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__Trypsin_Phospho | CARD_NLR__Trypsin_Phospho | CARD_NLR | Custom | 400 | The pinned DefenseFinder HMM inventory records CARD_NLR__Trypsin_Phospho as a custom CARD_NLR profile.
CARD-NLR phospho system is a CARD-NLR system rdfs:subClassOf
CARD-NLR phospho 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_Phospho 1 3 CARD_NLR__Trypsin_Phospho CARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin CARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsine_Endonuclease_new, GasderMIN__bGSDM The pinned DefenseFinder rules table models CARD_NLR_Phospho as a CARD_NLR subsystem requiring the CARD_NLR__Trypsin_Phospho 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_Phospho RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
CARD_NLR__Trypsin_Phospho 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_Phospho phage triggers, native hosts, phosphorylated substrate, CARD-to-effector activation sequence, and profile-to-activity criteria before minting enzyme, trigger, or component children.

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

Attached to causal_graphs#card_nlr_phospho_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_Phospho as a subtype with a CARD_NLR__Trypsin_Phospho mandatory profile. This first-pass record leaves exact phage triggers, native hosts, accessory-profile requirements, phosphorylated substrate, and CARD-to-phospho-effector 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__Trypsin_Phospho | CARD_NLR__Trypsin_Phospho | CARD_NLR | Custom | 400 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
CARD_NLR CARD_NLR_Phospho 1 3 CARD_NLR__Trypsin_Phospho CARD_NLR__CARD_Protease, CARD_NLR__NLR_new, CARD_NLR__Trypsin CARD_NLR__Endonuclease, CARD_NLR__Endonuclease_new, CARD_NLR__Subtilase, CARD_NLR__Subtilase_long_new, CARD_NLR__Subtilase_small_new, CARD_NLR__Trypsine_Endonuclease_new, GasderMIN__bGSDM

Curation history

2026-10-02T17:23:11Z · MINTED_TRAITMECH_ID · codex
Minted CARD-NLR phospho 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_v428.
2026-10-02T17:23:12Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed CARD-NLR phospho 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_Phospho model namespace but not an accession-backed native microbial taxon exemplar tied to CARD_NLR_Phospho profiles and experimentally verified endogenous CARD-NLR phospho activity. No paid research was used.