identifier: traitmech:000380 label: GAPS2 system definition: A phage defense system in which an organism possesses a GMT-encoded GAPS2 locus represented by DefenseFinder as a single-profile model, GAPS2__GAPS2, and experimentally linked to P1-vir and lambda-vir protection when expressed in E. coli. definition_source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: GAPS2 synonym_type: EXACT_SYNONYM source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md - synonym_text: GAPS2__GAPS2 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.1038/s41564-024-01840-5 snippet: We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy notes: Mahata et al. identify four anti-phage defense systems in Gamma-Mobile-Trio islands. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md snippet: The GAPS2 system is composed of a single protein. It was found in Gamma-Mobile-Trio (GMT) protein containing genomic island in Vibrio, and cloned into E. coli K-12 :ref{doi=10.1101/2023.03.28.534373}. The name GAPS derives from the "GMT-encoded Anti-Phage System" acronym. notes: The DefenseFinder wiki describes GAPS2 as a single-protein GMT-encoded system cloned from Vibrio into E. coli K-12. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md snippet: GAPS2 is composed of a single protein with a DNA BRCT domains :ref{doi=10.4161/cc.10.15.16312}. notes: The DefenseFinder wiki reports a DNA BRCT domain in the single GAPS2 protein. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md snippet: As far as we are aware, the molecular mechanism is unknown. notes: The DefenseFinder wiki records the GAPS2 mechanism as unknown. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md snippet: 'The GAPS2 system in *Mannheimia sp. USDA-ARS-USMARC-1261* (GCF_000521605.1, NZ_CP006942) is composed of 1 protein: GAPS2 (WP_025236539.1)' notes: The DefenseFinder wiki illustrates a predicted single-protein GAPS2 locus in RefSeq assembly GCF_000521605.1 on NZ_CP006942. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md snippet: "Mahata_2023[Mahata\ \ et al., 2023] --> Origin_0\n Origin_0[Vibrio parahaemolyticus \nWP_174208646.1]\ \ --> Expressed_0[Escherichia coli]\n Expressed_0[Escherichia coli] ----> P1-vir\ \ & Lambda-vir" notes: The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS2 source locus expressed in E. coli against P1-vir and Lambda-vir. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md snippet: "subgraph Title4[Protects against]\n P1-vir\n Lambda-vir" notes: The DefenseFinder experimental-validation diagram lists P1-vir and Lambda-vir in the GAPS2 protects-against subgraph. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: GAPS2 | 10\.1101/2023\.03\.28\.534373 | Gamma-Mobile-Trio systems define a new class of mobile elements rich in bacterial defensive and offensive tools notes: The DefenseFinder article registry maps the named GAPS2 system to the Mahata et al. preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "GAPS2\tGAPS2\t1\t1\tGAPS2__GAPS2\t\t\t" notes: The DefenseFinder rules table models GAPS2 as a single-profile system requiring GAPS2__GAPS2. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| GAPS2__GAPS2 | GAPS2__GAPS2 | GAPS2 | Custom | 100 |' notes: The DefenseFinder HMM inventory records GAPS2__GAPS2 under the GAPS2 system namespace. causal_graphs: - graph_id: gaps2_locus_restricts_phages title: GAPS2 loci protect against P1-vir and lambda-vir description: Conservative system-level sketch linking GAPS2 locus possession to protection against P1-vir and lambda-vir. scope_status: NONMECHANISTIC scope_notes: The graph captures GAPS2 as a named single-profile DefenseFinder phage-defense system while leaving natural host breadth, the molecular activity of the BRCT-domain GAPS2 component, the phage trigger, and exact GAPS2__GAPS2 profile-to-protein correspondence unresolved. nodes: - node_id: gaps2_locus label: GAPS2 locus node_type: GENETIC_ELEMENT description: A GMT-encoded phage-defense locus represented by the GAPS2__GAPS2 DefenseFinder profile. - node_id: gaps2_listed_phage_protection label: P1-vir and lambda-vir protection node_type: BIOLOGICAL_PROCESS description: Protection against P1-vir and lambda-vir by GAPS2. - node_id: gaps2_system_trait label: GAPS2 system node_type: TRAIT grounding: traitmech:000380 description: Possession of a genome-encoded GAPS2 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: gaps2_locus predicate: contributes to predicate_id: RO:0002326 object: gaps2_listed_phage_protection description: The DefenseFinder wiki links a Vibrio parahaemolyticus GAPS2 locus from Mahata et al. to protection against P1-vir and lambda-vir, and DefenseFinder models GAPS2 through the GAPS2__GAPS2 profile. evidence: - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md snippet: The GAPS2 system is composed of a single protein. It was found in Gamma-Mobile-Trio (GMT) protein containing genomic island in Vibrio, and cloned into E. coli K-12 :ref{doi=10.1101/2023.03.28.534373}. The name GAPS derives from the "GMT-encoded Anti-Phage System" acronym. notes: The DefenseFinder wiki describes GAPS2 as a single-protein GMT-encoded system cloned from Vibrio into E. coli K-12. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md snippet: "Mahata_2023[Mahata\ \ et al., 2023] --> Origin_0\n Origin_0[Vibrio parahaemolyticus \n\ WP_174208646.1]\ \ --> Expressed_0[Escherichia coli]\n Expressed_0[Escherichia coli] ---->\ \ P1-vir & Lambda-vir" notes: The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS2 source locus expressed in E. coli against P1-vir and Lambda-vir. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md snippet: "subgraph Title4[Protects against]\n P1-vir\n Lambda-vir" notes: The DefenseFinder experimental-validation diagram lists P1-vir and Lambda-vir in the GAPS2 protects-against subgraph. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "GAPS2\tGAPS2\t1\t1\tGAPS2__GAPS2\t\t\t" notes: The DefenseFinder rules table models GAPS2 as a single-profile system requiring GAPS2__GAPS2. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| GAPS2__GAPS2 | GAPS2__GAPS2 | GAPS2 | Custom | 100 |' notes: The DefenseFinder HMM inventory records GAPS2__GAPS2 under the GAPS2 system namespace. - subject: gaps2_listed_phage_protection predicate: confers predicate_id: METPO:2007700 object: gaps2_system_trait description: Protection against P1-vir and lambda-vir realizes the GAPS2 system trait. evidence: - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md snippet: "Mahata_2023[Mahata\ \ et al., 2023] --> Origin_0\n Origin_0[Vibrio parahaemolyticus \n\ WP_174208646.1]\ \ --> Expressed_0[Escherichia coli]\n Expressed_0[Escherichia coli] ---->\ \ P1-vir & Lambda-vir" notes: The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS2 source locus expressed in E. coli against P1-vir and Lambda-vir. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md snippet: "subgraph Title4[Protects against]\n P1-vir\n Lambda-vir" notes: The DefenseFinder experimental-validation diagram lists P1-vir and Lambda-vir in the GAPS2 protects-against subgraph. - subject: gaps2_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: GAPS2 system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1038/s41564-024-01840-5 snippet: We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy notes: Mahata et al. identify four anti-phage defense systems in Gamma-Mobile-Trio islands. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: GAPS2 | 10\.1101/2023\.03\.28\.534373 | Gamma-Mobile-Trio systems define a new class of mobile elements rich in bacterial defensive and offensive tools notes: The DefenseFinder article registry maps the named GAPS2 system to the Mahata et al. preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "GAPS2\tGAPS2\t1\t1\tGAPS2__GAPS2\t\t\t" notes: The DefenseFinder rules table models GAPS2 as a single-profile system requiring GAPS2__GAPS2. discussions: - discussion_id: gaps2-mechanism-gap prompt: Resolve GAPS2 natural host breadth, BRCT-domain activity, phage trigger specificity, and exact GAPS2__GAPS2 profile-to-protein correspondence before minting narrower GAPS2 mechanism traits. kind: KNOWLEDGE_GAP status: OPEN rationale: Mahata et al. support GAPS2 as a GMT-encoded anti-phage defense system that protects E. coli against P1-vir and lambda-vir when expressed from a Vibrio parahaemolyticus locus, and DefenseFinder represents GAPS2 as a single-profile system. Natural host breadth, BRCT-domain activity, the phage trigger, and exact profile-to-protein correspondence remain unresolved. evidence: - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md snippet: The GAPS2 system is composed of a single protein. It was found in Gamma-Mobile-Trio (GMT) protein containing genomic island in Vibrio, and cloned into E. coli K-12 :ref{doi=10.1101/2023.03.28.534373}. The name GAPS derives from the "GMT-encoded Anti-Phage System" acronym. notes: The DefenseFinder wiki describes GAPS2 as a single-protein GMT-encoded system cloned from Vibrio into E. coli K-12. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md snippet: GAPS2 is composed of a single protein with a DNA BRCT domains :ref{doi=10.4161/cc.10.15.16312}. notes: The DefenseFinder wiki reports a DNA BRCT domain in the single GAPS2 protein. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md snippet: As far as we are aware, the molecular mechanism is unknown. notes: The DefenseFinder wiki records the GAPS2 mechanism as unknown. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md snippet: "Mahata_2023[Mahata\ \ et al., 2023] --> Origin_0\n Origin_0[Vibrio parahaemolyticus \nWP_174208646.1]\ \ --> Expressed_0[Escherichia coli]\n Expressed_0[Escherichia coli] ---->\ \ P1-vir & Lambda-vir" notes: The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS2 source locus expressed in E. coli against P1-vir and Lambda-vir. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "GAPS2\tGAPS2\t1\t1\tGAPS2__GAPS2\t\t\t" notes: The DefenseFinder rules table models GAPS2 as a single-profile system requiring GAPS2__GAPS2. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| GAPS2__GAPS2 | GAPS2__GAPS2 | GAPS2 | Custom | 100 |' notes: The DefenseFinder HMM inventory records GAPS2__GAPS2 under the GAPS2 system namespace. attaches_to: - causal_graphs#gaps2_locus_restricts_phages posed_by: codex posed_date: '2026-09-26' curation_history: - timestamp: '2026-09-26T11:26:41Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted GAPS2 system as a DOI- and DefenseFinder-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_v257. llm_assisted: true - timestamp: '2026-09-26T11:26:42Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed GAPS2 system canonical_examples and left them empty because the current sources support a Vibrio parahaemolyticus accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Mannheimia sp. example, but not a direct native microbial isolate exemplar with experimentally verified endogenous GAPS2 activity. No paid research was used. llm_assisted: true