VP1840 system

traitmech:000450 · CLASS · PROPOSED

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.

Trait evidence (9)

DOI:10.1038/s41564-025-01927-7
Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.

Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems.
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx
VP_RS08920 Vp1840 Y WP_005483293.1 Hypothetical Protein

Supplementary Table 8 lists VP_RS08920/Vp1840 as a cloned RIMD 2210633 integron cassette with protein accession WP_005483293.1.
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx
VSV105-vp1840 VSV105 carrying gene vp1840 behind the lac promoter, cloned into KpnI by In-Fusion This Study

Supplementary Table 12 records the VSV105-vp1840 lac-expression plasmid used to express vp1840 behind the lac promoter.
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx
VP1840 Bas21 2e-09

Supplementary Table 9 identifies the VP1840/Bas21 phage-plating readout as a Fold Change value of 2e-09.
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx
VP1840 LL1 0

Supplementary Table 9 identifies the VP1840/LL1 phage-plating readout as a Fold Change value of 0.
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx
>BAC60103.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]

Supplementary Data 1's VP1840 worksheet labels BAC60103.1 from Vibrio parahaemolyticus RIMD 2210633 as the PSI-BLAST query protein.
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx
Scientific Name Query Cover E value Per. ident Accession Vibrio parahaemolyticus 1 3e-121 100 WP_229652597.1

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.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| VP1840 | 10\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus |

The pinned DefenseFinder article registry maps the VP1840 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| VP1840__VP1840 | | VP1840 | Custom | 75 |

The pinned DefenseFinder HMM inventory records VP1840__VP1840 as a custom VP1840 profile.

VP1840 loci reduce bacteriophage plaquing

Conservative system-level sketch linking VP1840-family locus possession to reduced bacteriophage plaquing without resolving VP1840 component function or molecular output.

NONMECHANISTIC · 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.

Edge evidence

VP1840 locus contributes to reduced bacteriophage plaquing RO:0002326
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.
- https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx VP_RS08920 Vp1840 Y WP_005483293.1 Hypothetical Protein Supplementary Table 8 lists VP_RS08920/Vp1840 as a cloned RIMD 2210633 integron cassette with protein accession WP_005483293.1.
- https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx VSV105-vp1840 VSV105 carrying gene vp1840 behind the lac promoter, cloned into KpnI by In-Fusion This Study Supplementary Table 12 records the VSV105-vp1840 lac-expression plasmid used to express vp1840 behind the lac promoter.
- https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx VP1840 Bas21 2e-09 Supplementary Table 9 identifies the VP1840/Bas21 phage-plating readout as a Fold Change value of 2e-09.
- https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx VP1840 LL1 0 Supplementary Table 9 identifies the VP1840/LL1 phage-plating readout as a Fold Change value of 0.
- https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx >BAC60103.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633] Supplementary Data 1's VP1840 worksheet labels BAC60103.1 from Vibrio parahaemolyticus RIMD 2210633 as the PSI-BLAST query protein.
- https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx Scientific Name Query Cover E value Per. ident Accession Vibrio parahaemolyticus 1 3e-121 100 WP_229652597.1 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.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | VP1840__VP1840 | | VP1840 | Custom | 75 | The pinned DefenseFinder HMM inventory records VP1840__VP1840 as a custom VP1840 profile.
reduced bacteriophage plaquing confers VP1840 system METPO:2007700
VP1840-mediated bacteriophage plaquing reduction realizes the VP1840 system trait.
- https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx VP1840 Bas21 2e-09 Supplementary Table 9 identifies the VP1840/Bas21 phage-plating readout as a Fold Change value of 2e-09.
- https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx VP1840 LL1 0 Supplementary Table 9 identifies the VP1840/LL1 phage-plating readout as a Fold Change value of 0.
VP1840 system is a phage defense system rdfs:subClassOf
VP1840 system possession is a phage-defense-system trait.
- DOI:10.1038/s41564-025-01927-7 Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence. Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | VP1840 | 10\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | The pinned DefenseFinder article registry maps the VP1840 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1038/s41564-025-01927-7

Parent traits (1)

phage defense system traitmech:000209

Synonyms (3)

VP1840 EXACT_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
Vp1840 RELATED_SYNONYM · https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx
VP1840__VP1840 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Discussions and Knowledge Gaps (1)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

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.

KNOWLEDGE GAP OPEN vp1840-defensefinder-model-gap · raised by codex · 2026-09-29

Attached to causal_graphs#vp1840_locus_reduces_bacteriophage_plaquing

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

DOI:10.1038/s41564-025-01927-7
Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx
VP_RS08920 Vp1840 Y WP_005483293.1 Hypothetical Protein
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx
VSV105-vp1840 VSV105 carrying gene vp1840 behind the lac promoter, cloned into KpnI by In-Fusion This Study
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx
VP1840 Bas21 2e-09
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx
>BAC60103.1 hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx
Scientific Name Query Cover E value Per. ident Accession Vibrio parahaemolyticus 1 3e-121 100 WP_229652597.1
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| VP1840 | 10\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| VP1840__VP1840 | | VP1840 | Custom | 75 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-29T02:26:23Z · MINTED_TRAITMECH_ID · codex
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.
2026-09-29T02:26:24Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
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.
2026-09-29T02:51:42Z · CLARIFIED_EVIDENCE_SNIPPETS · codex
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.
2026-09-29T03:13:39Z · GROUNDED_PSIBLAST_QUERY_ACCESSION · codex
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.
2026-09-29T03:27:44Z · CLARIFIED_PHAGE_PLATING_SCOPE · codex
Quoted the Supplementary Table 9 Fold Change header in the Bas21 and LL1 snippets and neutralized unsupported VP1840 host-clade phrasing to bacteriophage wording.
2026-09-29T03:45:05Z · UNSTITCHED_PHAGE_PLATING_SNIPPETS · codex
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.