SoFIC system

traitmech:000260 · CLASS · PROPOSED

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

Trait evidence (5)

DOI:10.1016/j.chom.2022.09.017
discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments

Millman et al. report the computational and experimental cohort that DefenseFinder cites for SoFIC as a bacterial anti-phage system.
DOI:10.1101/2022.05.11.491447
discovery of 21 new defense systems that protect bacteria from phages, based on computational genomic analyses and phage infection experiments

The bioRxiv version of Millman et al. independently carries the 21-system discovery claim linked from DefenseFinder's SoFIC article registry.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
SoFIC | 10\.1101/2022\.05\.11\.491447 | An expanding arsenal of immune systems that protect bacteria from phages

The DefenseFinder model registry maps the named SoFIC system to the Millman et al. antiphage-system discovery preprint.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
SoFIC SoFic 1 1 SoFic__SoFic

The DefenseFinder rules table models SoFIC with a SoFic profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
SoFic__SoFic | SoFic__SoFic | SoFic

The DefenseFinder HMM inventory records SoFic in the SoFic model namespace for the SoFIC system.

SoFIC loci confer bacterial phage defense

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

NONMECHANISTIC · The graph captures SoFIC as a named anti-phage system with the required DefenseFinder SoFic profile while leaving its phage trigger, molecular substrate, antiviral effector output, and subtype breadth unresolved.

Edge evidence

SoFIC locus contributes to restricted phage propagation RO:0002326
DefenseFinder maps SoFIC to a bacterial anti-phage-system discovery preprint and represents SoFIC loci through the SoFic component profile.
- DOI:10.1016/j.chom.2022.09.017 discovery of 21 defense systems that protect bacteria from phages Millman et al. describe the anti-phage discovery cohort that the DefenseFinder SoFIC registry row maps to the SoFIC system.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md SoFIC | 10\.1101/2022\.05\.11\.491447 | An expanding arsenal of immune systems that protect bacteria from phages The DefenseFinder registry maps SoFIC itself to the Millman et al. bacterial antiphage-system discovery preprint.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv SoFIC SoFic 1 1 SoFic__SoFic The DefenseFinder rules table supports SoFic as the required SoFIC system profile.
restricted phage propagation confers SoFIC system METPO:2007700
SoFIC-mediated phage restriction realizes the SoFIC system trait.
- DOI:10.1016/j.chom.2022.09.017 discovery of 21 defense systems that protect bacteria from phages Millman et al. place the SoFIC discovery cohort in the set of bacterial systems that protect against phages.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md SoFIC | 10\.1101/2022\.05\.11\.491447 | An expanding arsenal of immune systems that protect bacteria from phages DefenseFinder records SoFIC as a named system from the Millman et al. antiphage discovery preprint.
SoFIC system is a phage defense system rdfs:subClassOf
SoFIC system possession is a phage-defense-system trait.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md An expanding arsenal of immune systems that protect bacteria from phages DefenseFinder associates SoFIC with the Millman et al. bacterial antiphage-system discovery paper.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1016/j.chom.2022.09.017

Parent traits (1)

phage defense system traitmech:000209

Synonyms (1)

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

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

Attached to causal_graphs#sofic_locus_restricts_phage

Millman et al. and DefenseFinder support SoFIC as a named anti-phage system with a SoFic 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

2026-09-19T02:18:00Z · MINTED_TRAITMECH_ID · codex
Minted SoFIC 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_v137.