identifier: traitmech:000408 label: NLR-like bNACHT system definition: A phage defense system in which an organism possesses an NLR-related bacterial NACHT locus represented by DefenseFinder as an NLR_like_bNACHT01 or NLR_like_bNACHT09 single-profile model, encoding a NACHT-module STAND-family protein that can restrict bacteriophage production. definition_source: DOI:10.1016/j.cell.2023.04.015 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: NLR synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: bNACHT synonym_type: RELATED_SYNONYM source: DOI:10.1016/j.cell.2023.04.015 - synonym_text: NLR_like_bNACHT01 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv - synonym_text: NLR_like_bNACHT09 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv evidence: - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ snippet: Here we show that proteins containing a NACHT module, the central feature of the animal nucleotide-binding domain and leucine-rich repeat-containing gene family (NLRs), are found in bacteria and defend against phages. notes: Kibby et al. support NACHT-module proteins as bacterial NLR-related proteins that defend against phages. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ snippet: Genome context of bNACHT01, which is located near a CBASS system in Klebsiella pneumoniae MGH 35. notes: Kibby et al. identified a NACHT-module gene in Klebsiella pneumoniae MGH 35 before naming it bNACHT01. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ snippet: We named this gene bacterial NACHT module-containing protein 1 (bNACHT01), and it did not appear to be in an operon with any other genes. notes: Kibby et al. named the selected NACHT-module gene bNACHT01. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ snippet: bNACHT01 conferred over a 100-fold increase in protection against phage T4 and over a 1000-fold increase in protection against phages T5 and T6 notes: bNACHT01 protected against phages T4, T5, and T6 in the E. coli heterologous assay. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ snippet: bacteria expressing bNACHT01 restricted phage virion production and continued growing notes: Kibby et al. observed restricted phage virion production in bacteria expressing bNACHT01. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ snippet: Mutation of R214 to alanine maintained expression of the protein but abrogated phage defense notes: An R214A mutation preserved bNACHT01 expression but abrogated defense, supporting a NACHT-dependent output. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ snippet: Diverse bacterial NACHT proteins from different clades exhibited robust antiphage activity across a wide range of phages notes: Kibby et al. observed antiphage activity across diverse bacterial NACHT proteins. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: NLR | 10\.1101/2022\.07\.19\.500537 | Bacterial NLR-related proteins protect against phage notes: The DefenseFinder article registry maps the NLR family key to the Kibby et al. bNACHT preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "NLR\tNLR_like_bNACHT01\t1\t1\tNLR_like_bNACHT01__NLR_like_bNACHT01\t\t\ \t" notes: The DefenseFinder rules table models NLR_like_bNACHT01 as a one-profile NLR-family subsystem. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "NLR\tNLR_like_bNACHT09\t1\t1\tNLR_like_bNACHT09__NLR_like_bNACHT09\t\t\ \t" notes: The DefenseFinder rules table models NLR_like_bNACHT09 as a one-profile NLR-family subsystem. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| NLR_like_bNACHT01__NLR_like_bNACHT01 | NLR_like_bNACHT01__NLR_like_bNACHT01 | NLR_like_bNACHT01 | Custom | 250 |' notes: The DefenseFinder HMM inventory records the NLR_like_bNACHT01 profile under the same-named model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| NLR_like_bNACHT09__NLR_like_bNACHT09 | NLR_like_bNACHT09__NLR_like_bNACHT09 | NLR_like_bNACHT09 | Custom | 400 |' notes: The DefenseFinder HMM inventory records the NLR_like_bNACHT09 profile under the same-named model namespace. canonical_examples: - taxon_id: NCBITaxon:573 taxon_label: Klebsiella pneumoniae note: Kibby et al. identified the bNACHT01 locus in Klebsiella pneumoniae MGH 35 and found that bNACHT01 expressed from its endogenous promoter in Escherichia coli protected against phages T4, T5, and T6. reference: DOI:10.1016/j.cell.2023.04.015 causal_graphs: - graph_id: nlr_like_bnacht_loci_restrict_phage title: NLR-like bNACHT loci restrict phage production description: Conservative system-level sketch linking NLR-like bNACHT loci to bacteriophage restriction while leaving subtype triggers and effector outputs unresolved. scope_status: NONMECHANISTIC scope_notes: The graph captures DefenseFinder NLR_like_bNACHT01 and NLR_like_bNACHT09 as named bNACHT phage-defense models supported by Kibby et al. bacterial NLR-related protein experiments while leaving natural host breadth, phage triggers, the exact profile-to-bNACHT01 or profile-to-bNACHT09 correspondences, and subtype-specific effector mechanisms unresolved. nodes: - node_id: nlr_like_bnacht_locus label: NLR-like bNACHT locus node_type: GENETIC_ELEMENT description: A bacterial NLR-related phage-defense locus cataloged in DefenseFinder with a bNACHT profile. - node_id: bnacht_phage_restriction label: bNACHT phage restriction node_type: BIOLOGICAL_PROCESS description: Restriction of phage production by a bacterial NACHT-module antiviral protein. - node_id: nlr_like_bnacht_system_trait label: NLR-like bNACHT system node_type: TRAIT grounding: traitmech:000408 description: Possession of a genome-encoded NLR-like bNACHT phage-defense system. - node_id: phage_defense_system label: phage defense system node_type: TRAIT grounding: traitmech:000209 description: Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection. edges: - subject: nlr_like_bnacht_locus predicate: contributes to predicate_id: RO:0002326 object: bnacht_phage_restriction description: Kibby et al. showed that bacterial NACHT proteins can restrict bacteriophages, and DefenseFinder models two NLR_like_bNACHT subtypes. evidence: - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ snippet: Here we show that proteins containing a NACHT module, the central feature of the animal nucleotide-binding domain and leucine-rich repeat-containing gene family (NLRs), are found in bacteria and defend against phages. notes: Kibby et al. support NACHT-module proteins as bacterial NLR-related proteins that defend against phages. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ snippet: bNACHT01 conferred over a 100-fold increase in protection against phage T4 and over a 1000-fold increase in protection against phages T5 and T6 notes: bNACHT01 protected against phages T4, T5, and T6 in the E. coli heterologous assay. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ snippet: bacteria expressing bNACHT01 restricted phage virion production and continued growing notes: Kibby et al. observed restricted phage virion production in bacteria expressing bNACHT01. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "NLR\tNLR_like_bNACHT01\t1\t1\tNLR_like_bNACHT01__NLR_like_bNACHT01\t\ \t\t" notes: The DefenseFinder rules table models NLR_like_bNACHT01 as a one-profile NLR-family subsystem. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "NLR\tNLR_like_bNACHT09\t1\t1\tNLR_like_bNACHT09__NLR_like_bNACHT09\t\ \t\t" notes: The DefenseFinder rules table models NLR_like_bNACHT09 as a one-profile NLR-family subsystem. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| NLR_like_bNACHT01__NLR_like_bNACHT01 | NLR_like_bNACHT01__NLR_like_bNACHT01 | NLR_like_bNACHT01 | Custom | 250 |' notes: The DefenseFinder HMM inventory records the NLR_like_bNACHT01 profile under the same-named model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| NLR_like_bNACHT09__NLR_like_bNACHT09 | NLR_like_bNACHT09__NLR_like_bNACHT09 | NLR_like_bNACHT09 | Custom | 400 |' notes: The DefenseFinder HMM inventory records the NLR_like_bNACHT09 profile under the same-named model namespace. - subject: bnacht_phage_restriction predicate: confers predicate_id: METPO:2007700 object: nlr_like_bnacht_system_trait description: NACHT-module-dependent phage restriction realizes the NLR-like bNACHT system trait. evidence: - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ snippet: bacteria expressing bNACHT01 restricted phage virion production and continued growing notes: Kibby et al. observed restricted phage virion production in bacteria expressing bNACHT01. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ snippet: Mutation of R214 to alanine maintained expression of the protein but abrogated phage defense notes: An R214A mutation preserved bNACHT01 expression but abrogated defense, supporting a NACHT-dependent output. - subject: nlr_like_bnacht_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: NLR-like bNACHT system possession is a phage-defense-system trait. evidence: - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ snippet: Here we show that proteins containing a NACHT module, the central feature of the animal nucleotide-binding domain and leucine-rich repeat-containing gene family (NLRs), are found in bacteria and defend against phages. notes: Kibby et al. support NACHT-module proteins as bacterial NLR-related proteins that defend against phages. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ snippet: Diverse bacterial NACHT proteins from different clades exhibited robust antiphage activity across a wide range of phages notes: Kibby et al. observed antiphage activity across diverse bacterial NACHT proteins. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: NLR | 10\.1101/2022\.07\.19\.500537 | Bacterial NLR-related proteins protect against phage notes: The DefenseFinder article registry maps the NLR family key to the Kibby et al. bNACHT preprint. discussions: - discussion_id: nlr-like-bnacht-mechanism-gap prompt: Resolve the exact mapping between DefenseFinder NLR_like_bNACHT01 and NLR_like_bNACHT09 profiles and the experimentally tested bNACHT proteins, natural host breadth, phage triggers, and bNACHT effector mechanisms before minting narrower bNACHT subtype traits. kind: KNOWLEDGE_GAP status: OPEN rationale: Kibby et al. support bacterial NACHT proteins as NLR-related phage-defense proteins and DefenseFinder models NLR_like_bNACHT01 and NLR_like_bNACHT09 as single-profile NLR-family subsystems. This first system-level record leaves profile-to-assayed-protein correspondence and subtype-specific trigger and effector mechanisms unresolved. evidence: - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ snippet: Here we show that proteins containing a NACHT module, the central feature of the animal nucleotide-binding domain and leucine-rich repeat-containing gene family (NLRs), are found in bacteria and defend against phages. notes: Kibby et al. support NACHT-module proteins as bacterial NLR-related proteins that defend against phages. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ snippet: bNACHT01 conferred over a 100-fold increase in protection against phage T4 and over a 1000-fold increase in protection against phages T5 and T6 notes: bNACHT01 protected against phages T4, T5, and T6 in the E. coli heterologous assay. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "NLR\tNLR_like_bNACHT01\t1\t1\tNLR_like_bNACHT01__NLR_like_bNACHT01\t\ \t\t" notes: The DefenseFinder rules table models NLR_like_bNACHT01 as a one-profile NLR-family subsystem. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "NLR\tNLR_like_bNACHT09\t1\t1\tNLR_like_bNACHT09__NLR_like_bNACHT09\t\ \t\t" notes: The DefenseFinder rules table models NLR_like_bNACHT09 as a one-profile NLR-family subsystem. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| NLR_like_bNACHT01__NLR_like_bNACHT01 | NLR_like_bNACHT01__NLR_like_bNACHT01 | NLR_like_bNACHT01 | Custom | 250 |' notes: The DefenseFinder HMM inventory records the NLR_like_bNACHT01 profile under the same-named model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| NLR_like_bNACHT09__NLR_like_bNACHT09 | NLR_like_bNACHT09__NLR_like_bNACHT09 | NLR_like_bNACHT09 | Custom | 400 |' notes: The DefenseFinder HMM inventory records the NLR_like_bNACHT09 profile under the same-named model namespace. attaches_to: - causal_graphs#nlr_like_bnacht_loci_restrict_phage posed_by: codex posed_date: '2026-09-27' curation_history: - timestamp: '2026-09-27T12:41:08Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted NLR-like bNACHT system as a DOI-, PMID-, and stable-URL-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v285. llm_assisted: true - timestamp: '2026-09-27T12:41:09Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed NLR-like bNACHT system canonical-example evidence and kept the example at the Klebsiella pneumoniae species level because Kibby et al. identified the tested bNACHT01 locus from K. pneumoniae MGH 35 but assayed the endogenous-promoter construct heterologously in Escherichia coli. No paid research was used. llm_assisted: true - timestamp: '2026-09-27T13:11:20Z' curator: codex action: ADDRESS_REVIEW_FINDINGS changes: Corrected the Cell paper attribution from Ofir et al. to Kibby et al. and narrowed the R214A evidence note so it no longer places the residue inside the NACHT module beyond the curated snippet. llm_assisted: true - timestamp: '2026-09-27T13:27:10Z' curator: codex action: ADD_BNACHT01_SOURCE_STRAIN_SNIPPET changes: Added verbatim Kibby et al. evidence that the NACHT-module gene later named bNACHT01 was identified in Klebsiella pneumoniae MGH 35, directly supporting the canonical example taxon. llm_assisted: true