Ogmios system

traitmech:000286 · CLASS · PROPOSED

A phage defense system in which an organism possesses an Ogmios locus represented by a VCA0308 profile that can protect bacteria from bacteriophage infection.

Trait evidence (4)

DOI:10.1126/science.ads0768
nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions

Darracq et al. support treating the newly discovered Vibrio cholerae SCI antiphage cassettes as bacterial anti-phage systems.
DOI:10.1126/science.ads0768
Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest

Darracq et al. support a conservative system record that does not assert a resolved Ogmios trigger, effector output, or universal pathway.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
Ogmios | 10\.1126/science\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems

The DefenseFinder model registry maps the named Ogmios system to the Darracq et al. SCI antiphage-system paper.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Ogmios__VCA0308 | | Ogmios

The DefenseFinder HMM inventory records VCA0308 in the Ogmios model namespace.

Ogmios loci confer bacterial phage defense

Conservative system-level sketch linking possession of an Ogmios locus to restricted bacteriophage propagation without asserting the unresolved phage trigger or molecular output.

NONMECHANISTIC · The graph captures Ogmios as a named SCI-derived anti-phage system with a VCA0308 DefenseFinder profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.

Edge evidence

Ogmios locus contributes to restricted phage propagation RO:0002326
DefenseFinder maps Ogmios to an SCI anti-phage-system discovery paper and represents Ogmios loci through the VCA0308 component profile.
- DOI:10.1126/science.ads0768 nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel antiphage functions Darracq et al. describe the newly discovered antiphage-system cohort that the DefenseFinder Ogmios registry row maps to the Ogmios system.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md Ogmios__VCA0308 | | Ogmios The DefenseFinder HMM inventory supports VCA0308 as the Ogmios component profile.
restricted phage propagation confers Ogmios system METPO:2007700
Ogmios-mediated phage restriction realizes the Ogmios system trait.
- DOI:10.1126/science.ads0768 Most of these novel systems have little or no similarity to previously known ones, with several providing defense through cell lysis or growth arrest Darracq et al. place the Ogmios discovery cohort in a set of novel bacterial systems that protect against phages.
Ogmios system is a phage defense system rdfs:subClassOf
Ogmios system possession is a phage-defense-system trait.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Ogmios | 10\.1126/science\.ads0768 | Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems DefenseFinder associates Ogmios with the Darracq et al. bacterial antiphage-system paper.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1126/science.ads0768

Parent traits (1)

phage defense system traitmech:000209

Synonyms (2)

Ogmios EXACT_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
VCA0308 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 Ogmios phage triggers and effector outputs before minting narrower Ogmios mechanism children.

KNOWLEDGE GAP OPEN ogmios-mechanism-gap · raised by codex · 2026-09-19

Attached to causal_graphs#ogmios_locus_restricts_phage

Darracq et al. and DefenseFinder support Ogmios as a named anti-phage system with a VCA0308 profile, but the trigger, molecular substrate, antiviral effector output, and subtype-specific mechanism are not resolved enough here to assert a narrower mechanistic child trait.

Curation history

2026-09-19T16:33:14Z · MINTED_TRAITMECH_ID · codex
Minted Ogmios system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v163.