identifier: traitmech:000485 label: VP1823 system definition: A phage defense system in which an organism possesses a VP1823-family locus represented by the DefenseFinder VP1823__VP1823 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1823 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: VP1823 synonym_type: EXACT_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: VP1823__VP1823 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_RS08795\tVP1823\tY\tWP_079749463.1 \tHypothetical Protein" notes: Supplementary Table 8 lists VP_RS08795/VP1823 as a cloned RIMD 2210633 integron cassette with protein accession WP_079749463.1. - 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-vp1823\tVSV105 carrying gene vp1823 behind the lac promoter, cloned\ \ into KpnI by In-Fusion\tThis Study" notes: Supplementary Table 12 records the VSV105-vp1823 lac-expression plasmid used to express vp1823 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: "VP1823\tBas30\t0.0003" notes: Supplementary Table 9 identifies the VP1823/Bas30 phage-plating readout as a Fold Change value of 0.0003. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx snippet: "VP1823\tT4\t1e-05" notes: Supplementary Table 9 identifies the VP1823/T4 phage-plating readout as a Fold Change value of 1e-05. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx snippet: '>BAC60086.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]' notes: Supplementary Data 1's VP1823 worksheet labels BAC60086.1 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\t2e-166\t100\tWP_237666972.1" notes: Supplementary Data 1's VP1823 worksheet records a full-length 100% PSI-BLAST hit from the BAC60086.1 query to the separate Vibrio parahaemolyticus homolog WP_237666972.1. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| VP1823 | 10\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ' notes: The pinned DefenseFinder article registry maps the VP1823 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: '| VP1823__VP1823 | | VP1823 | Custom | 200 |' notes: The pinned DefenseFinder HMM inventory records VP1823__VP1823 as a custom VP1823 profile. causal_graphs: - graph_id: vp1823_locus_reduces_bacteriophage_plaquing title: VP1823 loci reduce bacteriophage plaquing description: Conservative system-level sketch linking VP1823-family locus possession to reduced bacteriophage plaquing without resolving VP1823 component function or molecular output. scope_status: NONMECHANISTIC scope_notes: The graph captures VP1823 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: vp1823_locus label: VP1823 locus node_type: GENETIC_ELEMENT description: A VP1823-like integron cassette locus represented in the pinned DefenseFinder HMM inventory by the VP1823__VP1823 custom profile. - node_id: reduced_bacteriophage_plaquing label: reduced bacteriophage plaquing node_type: BIOLOGICAL_PROCESS description: Reduced plaquing of bacteriophages in cells expressing cloned vp1823. - node_id: vp1823_system_trait label: VP1823 system node_type: TRAIT grounding: traitmech:000485 description: Possession of a genome-encoded VP1823 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: vp1823_locus predicate: contributes to predicate_id: RO:0002326 object: reduced_bacteriophage_plaquing description: The cloned V. parahaemolyticus vp1823 integron cassette contributes to reduced bacteriophage plaquing in VSV105 plasmid-expression assays, and DefenseFinder represents the VP1823 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_RS08795\tVP1823\tY\tWP_079749463.1 \tHypothetical Protein" notes: Supplementary Table 8 lists VP_RS08795/VP1823 as a cloned RIMD 2210633 integron cassette with protein accession WP_079749463.1. - 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-vp1823\tVSV105 carrying gene vp1823 behind the lac promoter,\ \ cloned into KpnI by In-Fusion\tThis Study" notes: Supplementary Table 12 records the VSV105-vp1823 lac-expression plasmid used to express vp1823 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: "VP1823\tBas30\t0.0003" notes: Supplementary Table 9 identifies the VP1823/Bas30 phage-plating readout as a Fold Change value of 0.0003. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx snippet: "VP1823\tT4\t1e-05" notes: Supplementary Table 9 identifies the VP1823/T4 phage-plating readout as a Fold Change value of 1e-05. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx snippet: '>BAC60086.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]' notes: Supplementary Data 1's VP1823 worksheet labels BAC60086.1 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\t2e-166\t100\tWP_237666972.1" notes: Supplementary Data 1's VP1823 worksheet records a full-length 100% PSI-BLAST hit from the BAC60086.1 query to the separate Vibrio parahaemolyticus homolog WP_237666972.1. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| VP1823__VP1823 | | VP1823 | Custom | 200 |' notes: The pinned DefenseFinder HMM inventory records VP1823__VP1823 as a custom VP1823 profile. - subject: reduced_bacteriophage_plaquing predicate: confers predicate_id: METPO:2007700 object: vp1823_system_trait description: VP1823-mediated bacteriophage plaquing reduction realizes the VP1823 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: "VP1823\tBas30\t0.0003" notes: Supplementary Table 9 identifies the VP1823/Bas30 phage-plating readout as a Fold Change value of 0.0003. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx snippet: "VP1823\tT4\t1e-05" notes: Supplementary Table 9 identifies the VP1823/T4 phage-plating readout as a Fold Change value of 1e-05. - subject: vp1823_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: VP1823 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: '| VP1823 | 10\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ' notes: The pinned DefenseFinder article registry maps the VP1823 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper. discussions: - discussion_id: vp1823-defensefinder-model-gap prompt: Resolve VP1823 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 VP1823 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Getz et al. support VP1823 as one of nine RIMD 2210633 integron-encoded cassettes whose cloned expression reduced phage plaquing, Supplementary Tables 8, 9, and 12 map VP1823 to VP_RS08795/VP1823, WP_079749463.1, VSV105-vp1823, and phage-plating fold changes, and Supplementary Data 1 reports PSI-BLAST homologs. The pinned DefenseFinder HMM inventory records one VP1823 custom profile row. The pinned rules table has no VP1823 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_RS08795\tVP1823\tY\tWP_079749463.1 \tHypothetical Protein" notes: Supplementary Table 8 lists VP_RS08795/VP1823 as a cloned RIMD 2210633 integron cassette with protein accession WP_079749463.1. - 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-vp1823\tVSV105 carrying gene vp1823 behind the lac promoter,\ \ cloned into KpnI by In-Fusion\tThis Study" notes: Supplementary Table 12 records the VSV105-vp1823 lac-expression plasmid used to express vp1823 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: "VP1823\tBas30\t0.0003" notes: Supplementary Table 9 identifies the VP1823/Bas30 phage-plating readout as a Fold Change value of 0.0003. - reference: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx snippet: '>BAC60086.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]' notes: Supplementary Data 1's VP1823 worksheet labels BAC60086.1 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\t2e-166\t100\tWP_237666972.1" notes: Supplementary Data 1's VP1823 worksheet records a full-length 100% PSI-BLAST hit from the BAC60086.1 query to the separate Vibrio parahaemolyticus homolog WP_237666972.1. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| VP1823 | 10\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | ' notes: The pinned DefenseFinder article registry maps the VP1823 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: '| VP1823__VP1823 | | VP1823 | Custom | 200 |' notes: The pinned DefenseFinder HMM inventory records VP1823__VP1823 as a custom VP1823 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: The pinned DefenseFinder rules table does not list VP1823, leaving rule-level detection criteria unresolved. attaches_to: - causal_graphs#vp1823_locus_reduces_bacteriophage_plaquing posed_by: codex posed_date: '2026-09-30' curation_history: - timestamp: '2026-09-30T06:58:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted VP1823 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_v362 reserves the replacement placeholder. llm_assisted: true - timestamp: '2026-09-30T06:58:01Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed VP1823 system canonical_examples and left them empty because Getz et al. directly support cloned VP1823 VSV105-plasmid assays, PSI-BLAST homologs, and a DefenseFinder VP1823 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous VP1823 activity. No paid research was used. llm_assisted: true