SEFIR system

traitmech:000259 · CLASS · PROPOSED

A phage defense system in which an organism possesses a SEFIR locus represented by a bSEFIR 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 SEFIR 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 SEFIR article registry.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
SEFIR | 10\.1101/2022\.05\.11\.491447 | An expanding arsenal of immune systems that protect bacteria from phages

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

The DefenseFinder rules table models SEFIR with a bSEFIR profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
SEFIR__bSEFIR | SEFIR__bSEFIR | SEFIR

The DefenseFinder HMM inventory records bSEFIR as a SEFIR profile.

SEFIR loci confer bacterial phage defense

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

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

Edge evidence

SEFIR locus contributes to restricted phage propagation RO:0002326
DefenseFinder maps SEFIR to a bacterial anti-phage-system discovery preprint and represents SEFIR loci through the bSEFIR 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 SEFIR registry row maps to the SEFIR system.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md SEFIR | 10\.1101/2022\.05\.11\.491447 | An expanding arsenal of immune systems that protect bacteria from phages The DefenseFinder registry maps SEFIR itself to the Millman et al. bacterial antiphage-system discovery preprint.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv SEFIR SEFIR 1 1 SEFIR__bSEFIR The DefenseFinder rules table supports bSEFIR as the required SEFIR system profile.
restricted phage propagation confers SEFIR system METPO:2007700
SEFIR-mediated phage restriction realizes the SEFIR 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 SEFIR 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 SEFIR | 10\.1101/2022\.05\.11\.491447 | An expanding arsenal of immune systems that protect bacteria from phages DefenseFinder records SEFIR as a named system from the Millman et al. antiphage discovery preprint.
SEFIR system is a phage defense system rdfs:subClassOf
SEFIR 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 SEFIR 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)

SEFIR 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 SEFIR phage triggers and effector outputs before minting narrower SEFIR mechanism children.

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

Attached to causal_graphs#sefir_locus_restricts_phage

Millman et al. and DefenseFinder support SEFIR as a named anti-phage system with a bSEFIR 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

2026-09-19T01:51:02Z · MINTED_TRAITMECH_ID · codex
Minted SEFIR 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_v136.