identifier: traitmech:000450 label: VP1840 system definition: A phage defense system in which an organism possesses a VP1840-family locus represented by the DefenseFinder VP1840__VP1840 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1840 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: VP1840 synonym_type: EXACT_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: Vp1840 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: VP1840__VP1840 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_RS08920\tVp1840\tY\tWP_005483293.1 \tHypothetical Protein" notes: Supplementary Table 8 lists VP_RS08920/Vp1840 as a cloned RIMD 2210633 integron cassette with protein accession WP_005483293.1. - 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-vp1840\tVSV105 carrying gene vp1840 behind the lac promoter, cloned\ \ into KpnI by In-Fusion\tThis Study" notes: Supplementary Table 12 records the VSV105-vp1840 lac-expression plasmid used to express vp1840 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: "VP1840\tBas21\t2e-09" notes: Supplementary Table 9 identifies the VP1840/Bas21 phage-plating readout as a Fold Change value of 2e-09. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx snippet: "VP1840\tLL1\t0" notes: Supplementary Table 9 identifies the VP1840/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: '>BAC60103.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]' notes: Supplementary Data 1's VP1840 worksheet labels BAC60103.1 from Vibrio parahaemolyticus RIMD 2210633 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\tAccession \nVibrio\ \ parahaemolyticus\t1\t3e-121\t100\tWP_229652597.1" notes: Supplementary Data 1's VP1840 worksheet records a full-length 100% PSI-BLAST hit from the BAC60103.1 query to the separate Vibrio parahaemolyticus homolog WP_229652597.1. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| VP1840 | 10\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ' notes: The pinned DefenseFinder article registry maps the VP1840 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: '| VP1840__VP1840 | | VP1840 | Custom | 75 |' notes: The pinned DefenseFinder HMM inventory records VP1840__VP1840 as a custom VP1840 profile. causal_graphs: - graph_id: vp1840_locus_reduces_bacteriophage_plaquing title: VP1840 loci reduce bacteriophage plaquing description: Conservative system-level sketch linking VP1840-family locus possession to reduced bacteriophage plaquing without resolving VP1840 component function or molecular output. scope_status: NONMECHANISTIC scope_notes: The graph captures VP1840 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: vp1840_locus label: VP1840 locus node_type: GENETIC_ELEMENT description: A Vp1840-like integron cassette locus represented in the pinned DefenseFinder HMM inventory by the VP1840__VP1840 custom profile. - node_id: reduced_bacteriophage_plaquing label: reduced bacteriophage plaquing node_type: BIOLOGICAL_PROCESS description: Reduced plaquing of bacteriophages in cells expressing cloned vp1840. - node_id: vp1840_system_trait label: VP1840 system node_type: TRAIT grounding: traitmech:000450 description: Possession of a genome-encoded VP1840 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: vp1840_locus predicate: contributes to predicate_id: RO:0002326 object: reduced_bacteriophage_plaquing description: The cloned V. parahaemolyticus vp1840 integron cassette contributes to reduced bacteriophage plaquing in VSV105 plasmid-expression assays, and DefenseFinder represents the VP1840 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_RS08920\tVp1840\tY\tWP_005483293.1 \tHypothetical Protein" notes: Supplementary Table 8 lists VP_RS08920/Vp1840 as a cloned RIMD 2210633 integron cassette with protein accession WP_005483293.1. - 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-vp1840\tVSV105 carrying gene vp1840 behind the lac promoter,\ \ cloned into KpnI by In-Fusion\tThis Study" notes: Supplementary Table 12 records the VSV105-vp1840 lac-expression plasmid used to express vp1840 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: "VP1840\tBas21\t2e-09" notes: Supplementary Table 9 identifies the VP1840/Bas21 phage-plating readout as a Fold Change value of 2e-09. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx snippet: "VP1840\tLL1\t0" notes: Supplementary Table 9 identifies the VP1840/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: '>BAC60103.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]' notes: Supplementary Data 1's VP1840 worksheet labels BAC60103.1 from Vibrio parahaemolyticus RIMD 2210633 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\tAccession \nVibrio\ \ parahaemolyticus\t1\t3e-121\t100\tWP_229652597.1" notes: Supplementary Data 1's VP1840 worksheet records a full-length 100% PSI-BLAST hit from the BAC60103.1 query to the separate Vibrio parahaemolyticus homolog WP_229652597.1. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| VP1840__VP1840 | | VP1840 | Custom | 75 |' notes: The pinned DefenseFinder HMM inventory records VP1840__VP1840 as a custom VP1840 profile. - subject: reduced_bacteriophage_plaquing predicate: confers predicate_id: METPO:2007700 object: vp1840_system_trait description: VP1840-mediated bacteriophage plaquing reduction realizes the VP1840 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: "VP1840\tBas21\t2e-09" notes: Supplementary Table 9 identifies the VP1840/Bas21 phage-plating readout as a Fold Change value of 2e-09. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx snippet: "VP1840\tLL1\t0" notes: Supplementary Table 9 identifies the VP1840/LL1 phage-plating readout as a Fold Change value of 0. - subject: vp1840_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: VP1840 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: '| VP1840 | 10\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ' notes: The pinned DefenseFinder article registry maps the VP1840 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper. discussions: - discussion_id: vp1840-defensefinder-model-gap prompt: Resolve VP1840 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 VP1840 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Getz et al. support VP1840 as one of nine RIMD 2210633 integron-encoded cassettes whose cloned expression reduced phage plaquing, Supplementary Tables 8, 9, and 12 map VP1840 to VP_RS08920/Vp1840, WP_005483293.1, VSV105-vp1840, and phage-plating fold changes, and Supplementary Data 1 reports PSI-BLAST homologs. The pinned DefenseFinder HMM inventory records one VP1840 custom profile row. The pinned rules table has no VP1840 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_RS08920\tVp1840\tY\tWP_005483293.1 \tHypothetical Protein" notes: Supplementary Table 8 lists VP_RS08920/Vp1840 as a cloned RIMD 2210633 integron cassette with protein accession WP_005483293.1. - 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-vp1840\tVSV105 carrying gene vp1840 behind the lac promoter,\ \ cloned into KpnI by In-Fusion\tThis Study" notes: Supplementary Table 12 records the VSV105-vp1840 lac-expression plasmid used to express vp1840 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: "VP1840\tBas21\t2e-09" notes: Supplementary Table 9 identifies the VP1840/Bas21 phage-plating readout as a Fold Change value of 2e-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: '>BAC60103.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]' notes: Supplementary Data 1's VP1840 worksheet labels BAC60103.1 from Vibrio parahaemolyticus RIMD 2210633 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\tAccession \nVibrio\ \ parahaemolyticus\t1\t3e-121\t100\tWP_229652597.1" notes: Supplementary Data 1's VP1840 worksheet records a full-length 100% PSI-BLAST hit from the BAC60103.1 query to the separate Vibrio parahaemolyticus homolog WP_229652597.1. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| VP1840 | 10\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ' notes: The pinned DefenseFinder article registry maps the VP1840 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: '| VP1840__VP1840 | | VP1840 | Custom | 75 |' notes: The pinned DefenseFinder HMM inventory records VP1840__VP1840 as a custom VP1840 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list VP1840, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#vp1840_locus_reduces_bacteriophage_plaquing posed_by: codex posed_date: '2026-09-29' curation_history: - timestamp: '2026-09-29T02:26:23Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted VP1840 system as a DOI-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; kept the graph at cloned integron-cassette level because the molecular output and rule rows remain unresolved, and proposals/metpo_traitmech_v327 reserves the replacement placeholder. llm_assisted: true - timestamp: '2026-09-29T02:26:24Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed VP1840 system canonical_examples and left them empty because Getz et al. directly support cloned Vp1840 VSV105-plasmid assays, PSI-BLAST homologs, and a DefenseFinder VP1840 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous VP1840 activity. No paid research was used. llm_assisted: true - timestamp: '2026-09-29T02:51:42Z' curator: codex action: CLARIFIED_EVIDENCE_SNIPPETS changes: Clarified Supplementary Table 9 VP1840 phage-plating notes to name the paper's Fold Change column and expanded the Supplementary Data 1 VP1840 PSI-BLAST snippet with its column header so the WP_229652597.1 hit is self-identifying. llm_assisted: true - timestamp: '2026-09-29T03:13:39Z' curator: codex action: GROUNDED_PSIBLAST_QUERY_ACCESSION changes: Quoted the Supplementary Data 1 VP1840 worksheet query row so the BAC60103.1 PSI-BLAST query named in the WP_229652597.1 homolog-hit note is directly evidenced. llm_assisted: true - timestamp: '2026-09-29T03:27:44Z' curator: codex action: CLARIFIED_PHAGE_PLATING_SCOPE changes: Quoted the Supplementary Table 9 Fold Change header in the Bas21 and LL1 snippets and neutralized unsupported VP1840 host-clade phrasing to bacteriophage wording. llm_assisted: true - timestamp: '2026-09-29T03:45:05Z' curator: codex action: UNSTITCHED_PHAGE_PLATING_SNIPPETS changes: Removed the non-contiguous Supplementary Table 9 Fold Change header prefix from the Bas21 and LL1 snippets so each phage-plating snippet quotes only a contiguous data row. llm_assisted: true