identifier: traitmech:000486 label: VP1796 system definition: A phage defense system in which an organism possesses a VP1796-family locus represented by the DefenseFinder VP1796__VP1796 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1796 cassette is expressed from a VSV105 plasmid. definition_source: DOI:10.1038/s41564-025-01927-7 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: VP1796 synonym_type: EXACT_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: Vp1796 synonym_type: RELATED_SYNONYM source: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx - synonym_text: VP1796__VP1796 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.1038/s41564-025-01927-7 snippet: Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence. notes: Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx snippet: "VP_RS08620\tVp1796\tY\tWP_005477844.1 \tHypothetical Protein" notes: Supplementary Table 8 lists VP_RS08620/Vp1796 as a cloned RIMD 2210633 integron cassette with protein accession WP_005477844.1. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx snippet: "VSV105-vp1796\tVSV105 carrying gene vp1796 behind the lac promoter, cloned\ \ into KpnI by In-Fusion\tThis Study" notes: Supplementary Table 12 records the VSV105-vp1796 lac-expression plasmid used to express vp1796 behind the lac promoter. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx snippet: "VP1796\tLL1\t0" notes: Supplementary Table 9 identifies the VP1796/LL1 phage-plating readout as a Fold Change value of 0. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx snippet: "VP1796\tVp1\t3.33e-09" notes: Supplementary Table 9 identifies the VP1796/Vp1 phage-plating readout as a Fold Change value of 3.33e-09. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx snippet: '>WP_005477844.1 hypothetical protein [Vibrio parahaemolyticus]' notes: Supplementary Data 1's VP1796 worksheet labels WP_005477844.1 from Vibrio parahaemolyticus as the PSI-BLAST query protein. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx snippet: "Scientific Name\tQuery Cover\tE value\tPer. ident\tAcc. Len\tAccession\ \ \nVibrio parahaemolyticus\t1\t6e-141\t100\t283\tWP_257878370.1" notes: Supplementary Data 1's VP1796 worksheet records a full-length 100% PSI-BLAST hit from the WP_005477844.1 query to the separate Vibrio parahaemolyticus homolog WP_257878370.1. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| VP1796 | 10\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ' notes: The pinned DefenseFinder article registry maps the VP1796 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| VP1796__VP1796 | | VP1796 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records VP1796__VP1796 as a custom VP1796 profile. causal_graphs: - graph_id: vp1796_locus_reduces_bacteriophage_plaquing title: VP1796 loci reduce bacteriophage plaquing description: Conservative system-level sketch linking VP1796-family locus possession to reduced bacteriophage plaquing without resolving VP1796 component function or molecular output. scope_status: NONMECHANISTIC scope_notes: The graph captures VP1796 as a RIMD 2210633 integron cassette with cloned phage-plating readouts, a PSI-BLAST homolog lead, one pinned DefenseFinder custom HMM-profile row, and no pinned DefenseFinder rule row. It does not assert native host breadth, exact profile-to-protein correspondence, molecular activity, phage trigger, substrate, complete homolog boundary, endogenous activity, or rule-level DefenseFinder detection criteria. nodes: - node_id: vp1796_locus label: VP1796 locus node_type: GENETIC_ELEMENT description: A VP1796-like integron cassette locus represented in the pinned DefenseFinder HMM inventory by the VP1796__VP1796 custom profile. - node_id: reduced_bacteriophage_plaquing label: reduced bacteriophage plaquing node_type: BIOLOGICAL_PROCESS description: Reduced plaquing of bacteriophages in cells expressing cloned vp1796. - node_id: vp1796_system_trait label: VP1796 system node_type: TRAIT grounding: traitmech:000486 description: Possession of a genome-encoded VP1796 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: vp1796_locus predicate: contributes to predicate_id: RO:0002326 object: reduced_bacteriophage_plaquing description: The cloned V. parahaemolyticus vp1796 integron cassette contributes to reduced bacteriophage plaquing in VSV105 plasmid-expression assays, and DefenseFinder represents the VP1796 family with one custom HMM profile. evidence: - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx snippet: "VP_RS08620\tVp1796\tY\tWP_005477844.1 \tHypothetical Protein" notes: Supplementary Table 8 lists VP_RS08620/Vp1796 as a cloned RIMD 2210633 integron cassette with protein accession WP_005477844.1. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx snippet: "VSV105-vp1796\tVSV105 carrying gene vp1796 behind the lac promoter,\ \ cloned into KpnI by In-Fusion\tThis Study" notes: Supplementary Table 12 records the VSV105-vp1796 lac-expression plasmid used to express vp1796 behind the lac promoter. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx snippet: "VP1796\tLL1\t0" notes: Supplementary Table 9 identifies the VP1796/LL1 phage-plating readout as a Fold Change value of 0. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx snippet: "VP1796\tVp1\t3.33e-09" notes: Supplementary Table 9 identifies the VP1796/Vp1 phage-plating readout as a Fold Change value of 3.33e-09. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx snippet: '>WP_005477844.1 hypothetical protein [Vibrio parahaemolyticus]' notes: Supplementary Data 1's VP1796 worksheet labels WP_005477844.1 from Vibrio parahaemolyticus as the PSI-BLAST query protein. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx snippet: "Scientific Name\tQuery Cover\tE value\tPer. ident\tAcc. Len\tAccession\ \ \nVibrio parahaemolyticus\t1\t6e-141\t100\t283\tWP_257878370.1" notes: Supplementary Data 1's VP1796 worksheet records a full-length 100% PSI-BLAST hit from the WP_005477844.1 query to the separate Vibrio parahaemolyticus homolog WP_257878370.1. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| VP1796__VP1796 | | VP1796 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records VP1796__VP1796 as a custom VP1796 profile. - subject: reduced_bacteriophage_plaquing predicate: confers predicate_id: METPO:2007700 object: vp1796_system_trait description: VP1796-mediated bacteriophage plaquing reduction realizes the VP1796 system trait. evidence: - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx snippet: "VP1796\tLL1\t0" notes: Supplementary Table 9 identifies the VP1796/LL1 phage-plating readout as a Fold Change value of 0. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx snippet: "VP1796\tVp1\t3.33e-09" notes: Supplementary Table 9 identifies the VP1796/Vp1 phage-plating readout as a Fold Change value of 3.33e-09. - subject: vp1796_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: VP1796 system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1038/s41564-025-01927-7 snippet: Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence. notes: Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| VP1796 | 10\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ' notes: The pinned DefenseFinder article registry maps the VP1796 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper. discussions: - discussion_id: vp1796-defensefinder-model-gap prompt: Resolve VP1796 native host breadth, exact single-component activity, profile-to-protein mapping, homolog boundary, full phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower VP1796 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Getz et al. support VP1796 as one of nine RIMD 2210633 integron-encoded cassettes whose cloned expression reduced phage plaquing, Supplementary Tables 8, 9, and 12 map VP1796 to VP_RS08620/Vp1796, WP_005477844.1, VSV105-vp1796, and phage-plating fold changes, and Supplementary Data 1 reports PSI-BLAST homologs. The pinned DefenseFinder HMM inventory records one VP1796 custom profile row. The pinned rules table has no VP1796 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, molecular output, or endogenous activity. evidence: - reference: DOI:10.1038/s41564-025-01927-7 snippet: Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence. notes: Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx snippet: "VP_RS08620\tVp1796\tY\tWP_005477844.1 \tHypothetical Protein" notes: Supplementary Table 8 lists VP_RS08620/Vp1796 as a cloned RIMD 2210633 integron cassette with protein accession WP_005477844.1. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx snippet: "VSV105-vp1796\tVSV105 carrying gene vp1796 behind the lac promoter,\ \ cloned into KpnI by In-Fusion\tThis Study" notes: Supplementary Table 12 records the VSV105-vp1796 lac-expression plasmid used to express vp1796 behind the lac promoter. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx snippet: "VP1796\tLL1\t0" notes: Supplementary Table 9 identifies the VP1796/LL1 phage-plating readout as a Fold Change value of 0. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx snippet: '>WP_005477844.1 hypothetical protein [Vibrio parahaemolyticus]' notes: Supplementary Data 1's VP1796 worksheet labels WP_005477844.1 from Vibrio parahaemolyticus as the PSI-BLAST query protein. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx snippet: "Scientific Name\tQuery Cover\tE value\tPer. ident\tAcc. Len\tAccession\ \ \nVibrio parahaemolyticus\t1\t6e-141\t100\t283\tWP_257878370.1" notes: Supplementary Data 1's VP1796 worksheet records a full-length 100% PSI-BLAST hit from the WP_005477844.1 query to the separate Vibrio parahaemolyticus homolog WP_257878370.1. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| VP1796 | 10\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ' notes: The pinned DefenseFinder article registry maps the VP1796 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| VP1796__VP1796 | | VP1796 | Custom | 50 |' notes: The pinned DefenseFinder HMM inventory records VP1796__VP1796 as a custom VP1796 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list VP1796, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#vp1796_locus_reduces_bacteriophage_plaquing posed_by: codex posed_date: '2026-09-30' curation_history: - timestamp: '2026-09-30T07:47:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted VP1796 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned integron-cassette level because molecular output, native activity, and rule rows remain unresolved; proposals/metpo_traitmech_v363 reserves the replacement placeholder. llm_assisted: true - timestamp: '2026-09-30T07:47:01Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed VP1796 system canonical_examples and left them empty because Getz et al. directly support cloned VP1796 VSV105-plasmid assays, PSI-BLAST homologs, and a DefenseFinder VP1796 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous VP1796 activity. No paid research was used. llm_assisted: true