Ukko system

traitmech:000292 · CLASS · PROPOSED

A phage defense system in which an organism possesses a Ukko locus that can protect bacteria from bacteriophage infection.

Trait evidence (11)

DOI:10.1101/2025.01.08.631966
Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun).

Mordret et al. directly name Ukko among six Streptomyces systems that increased resistance to at least one phage.
DOI:10.1101/2025.01.08.631966
The bacterial pangenome encodes an immense array of antiphage systems, yet much of their diversity remains uncharted

Mordret et al. motivate a conservative system-level record that does not assert a resolved Ukko trigger, effector output, or universal pathway.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
Ukko | 10\.1101/2025\.01\.08\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses

The DefenseFinder model registry maps the named Ukko system to the Mordret et al. antiphage-system discovery preprint.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Ukko__UkkA1 | | Ukko

The DefenseFinder HMM inventory records UkkA1 in the Ukko model namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Ukko__UkkA2 | | Ukko

The DefenseFinder HMM inventory records UkkA2 in the Ukko model namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Ukko__UkkB1 | | Ukko

The DefenseFinder HMM inventory records UkkB1 in the Ukko model namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Ukko__UkkB2 | | Ukko

The DefenseFinder HMM inventory records UkkB2 in the Ukko model namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Ukko__UkkC1 | | Ukko

The DefenseFinder HMM inventory records UkkC1 in the Ukko model namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Ukko__UkkC2 | | Ukko

The DefenseFinder HMM inventory records UkkC2 in the Ukko model namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Ukko__UkkD1 | | Ukko

The DefenseFinder HMM inventory records UkkD1 in the Ukko model namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Ukko__UkkD2 | | Ukko

The DefenseFinder HMM inventory records UkkD2 in the Ukko model namespace.

Ukko loci confer bacterial phage defense

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

NONMECHANISTIC · The graph captures Ukko as a named anti-phage system with UkkA1, UkkA2, UkkB1, UkkB2, UkkC1, UkkC2, UkkD1, and UkkD2 DefenseFinder HMM profile entries while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.

Edge evidence

Ukko locus contributes to restricted phage propagation RO:0002326
DefenseFinder maps Ukko to a protein- and genomic-language-model antiphage-system discovery preprint and catalogs UkkA1, UkkA2, UkkB1, UkkB2, UkkC1, UkkC2, UkkD1, and UkkD2 HMM profile entries in the Ukko model namespace.
- DOI:10.1101/2025.01.08.631966 Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun). Mordret et al. directly name Ukko among six Streptomyces systems that restricted at least one phage.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Ukko | 10\.1101/2025\.01\.08\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses The DefenseFinder registry maps Ukko itself to the Mordret et al. bacterial antiphage-system discovery preprint.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md Ukko__UkkA1 | | Ukko The DefenseFinder HMM inventory records UkkA1 in the Ukko model namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md Ukko__UkkA2 | | Ukko The DefenseFinder HMM inventory records UkkA2 in the Ukko model namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md Ukko__UkkB1 | | Ukko The DefenseFinder HMM inventory records UkkB1 in the Ukko model namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md Ukko__UkkB2 | | Ukko The DefenseFinder HMM inventory records UkkB2 in the Ukko model namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md Ukko__UkkC1 | | Ukko The DefenseFinder HMM inventory records UkkC1 in the Ukko model namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md Ukko__UkkC2 | | Ukko The DefenseFinder HMM inventory records UkkC2 in the Ukko model namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md Ukko__UkkD1 | | Ukko The DefenseFinder HMM inventory records UkkD1 in the Ukko model namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md Ukko__UkkD2 | | Ukko The DefenseFinder HMM inventory records UkkD2 in the Ukko model namespace.
restricted phage propagation confers Ukko system METPO:2007700
Ukko-mediated phage restriction realizes the Ukko system trait.
- DOI:10.1101/2025.01.08.631966 Among the remaining eight systems, six demonstrated increased resistance to at least one phage with more than 100 fold reduction in plaque forming units (PFU) (Figure 3a, Supplementary Figure 5). As Streptomyces are mostly soil dwelling bacteria, we named these systems after deities of the soil and earth (Ceres, Geb, Veles, Prithvi, Ukko and Oshun). Mordret et al. directly name Ukko among six systems that increased resistance to at least one phage.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Ukko | 10\.1101/2025\.01\.08\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses DefenseFinder records Ukko as a named system from the Mordret et al. antiphage discovery preprint.
Ukko system is a phage defense system rdfs:subClassOf
Ukko system possession is a phage-defense-system trait.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | Ukko | 10\.1101/2025\.01\.08\.631966 | Protein and genomic language models chart a vast landscape of antiphage defenses | DefenseFinder associates Ukko with the Mordret et al. bacterial antiphage-system discovery preprint.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1101/2025.01.08.631966

Parent traits (1)

phage defense system traitmech:000209

Synonyms (9)

Ukko EXACT_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
UkkA1 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
UkkA2 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
UkkB1 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
UkkB2 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
UkkC1 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
UkkC2 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
UkkD1 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
UkkD2 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 Ukko phage triggers and effector outputs before minting narrower Ukko mechanism children.

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

Attached to causal_graphs#ukko_locus_restricts_phage

Mordret et al. and DefenseFinder support Ukko as a named anti-phage system with UkkA1, UkkA2, UkkB1, UkkB2, UkkC1, UkkC2, UkkD1, and UkkD2 HMM profile entries, 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

2026-09-19T20:26:31Z · MINTED_TRAITMECH_ID · codex
Minted Ukko 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_v169.