Panchino gp28 system

traitmech:000294 · CLASS · PROPOSED

A phage defense system in which an organism possesses a Panchino gp28 locus that can protect bacteria from bacteriophage infection.

Trait evidence (4)

DOI:10.1038/nmicrobiol.2016.251
at least five distinct prophage-expressed viral defense systems that interfere with infection

Dedrick et al. place the Cluster N Panchino gp28 system in a cohort of prophage-expressed defenses against lytic and temperate mycobacteriophages.
DOI:10.1038/nmicrobiol.2016.251
The Panchino restriction system (gp28) is a strong candidate for conferring this defense

Dedrick et al. identify Panchino gp28 as the candidate restriction system responsible for a heterotypic viral-defense phenotype.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
Panchino_gp28 | 10\.1038/nmicrobiol\.2016\.251 | Prophage-mediated defence against viral attack and viral counter-defence

The DefenseFinder model registry maps the named Panchino_gp28 system to the Dedrick et al. prophage-mediated viral-defense paper.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Panchino_gp28__gp28 | Panchino_gp28__gp28 | Panchino_gp28

The DefenseFinder HMM inventory records gp28 in the Panchino_gp28 model namespace.

Panchino gp28 loci confer bacterial phage defense

Conservative system-level sketch linking possession of a Panchino gp28 locus to restricted bacteriophage propagation without asserting the unresolved restriction target, methylation context, or target-phage breadth.

NONMECHANISTIC · The graph captures Panchino gp28 as a named anti-phage system with a DefenseFinder gp28 profile while leaving its restriction target, methylation requirements, and target-phage breadth unresolved.

Edge evidence

Panchino gp28 locus contributes to restricted phage propagation RO:0002326
Dedrick et al. identify Panchino gp28 as a prophage-expressed viral-defense candidate, and DefenseFinder catalogs a gp28 profile in the Panchino_gp28 model namespace.
- DOI:10.1038/nmicrobiol.2016.251 The Panchino restriction system (gp28) is a strong candidate for conferring this defense Dedrick et al. support Panchino gp28 as the candidate system that confers a Panchino defense profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md Panchino_gp28__gp28 | Panchino_gp28__gp28 | Panchino_gp28 The DefenseFinder HMM inventory records gp28 in the Panchino_gp28 model namespace.
restricted phage propagation confers Panchino gp28 system METPO:2007700
Panchino-gp28-mediated phage restriction realizes the Panchino gp28 system trait.
- DOI:10.1038/nmicrobiol.2016.251 at least five distinct prophage-expressed viral defense systems that interfere with infection Dedrick et al. place Panchino gp28 among Cluster N prophage systems that defend against phage infection.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Panchino_gp28 | 10\.1038/nmicrobiol\.2016\.251 | Prophage-mediated defence against viral attack and viral counter-defence DefenseFinder records Panchino_gp28 as a named system from the Dedrick et al. prophage-defense paper.
Panchino gp28 system is a phage defense system rdfs:subClassOf
Panchino gp28 system possession is a phage-defense-system trait.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | Panchino_gp28 | 10\.1038/nmicrobiol\.2016\.251 | Prophage-mediated defence against viral attack and viral counter-defence | DefenseFinder associates Panchino_gp28 with the Dedrick et al. prophage-mediated viral-defense paper.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1038/nmicrobiol.2016.251

Parent traits (1)

phage defense system traitmech:000209

Synonyms (1)

Panchino_gp28 RELATED_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 the Panchino gp28 restriction target, methylation requirements, and homolog breadth before minting narrower Panchino gp28 mechanism children.

KNOWLEDGE GAP OPEN panchino_gp28-mechanism-gap · raised by codex · 2026-09-19

Attached to causal_graphs#panchino_gp28_locus_restricts_phage

Dedrick et al. and DefenseFinder support Panchino gp28 as a named anti-phage system with a gp28 profile, but the restriction target, methylation context, and full target-phage breadth are not resolved enough here to assert a narrower mechanistic child trait.

Curation history

2026-09-19T21:37:34Z · MINTED_TRAITMECH_ID · codex
Minted Panchino gp28 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_v171.
2026-09-19T22:03:20Z · DEMOTED_SOURCE_KEY_SYNONYM · codex
Resolved PR #1085 review issue #1086 by demoting the DefenseFinder source key Panchino_gp28 from exact synonym to related synonym scope.
2026-09-19T22:07:53Z · FIXED_FIXED_WIDTH_SNIPPET · codex
Resolved PR #1085 review issue #1087 by removing an extra separator space from the two fixed-width DefenseFinder Panchino_gp28__gp28 HMM snippets.
2026-09-19T22:13:50Z · REMOVED_AMBIGUOUS_SYNONYM · codex
Resolved PR #1085 review issue #1088 by dropping the ambiguous bare gp28 related synonym while retaining the pinned Panchino_gp28__gp28 HMM profile as evidence.