Phrann gp29-gp30 system

traitmech:000296 · CLASS · PROPOSED

A phage defense system in which an organism possesses a Phrann gp29-gp30 locus that can protect bacteria from bacteriophage infection.

Trait evidence (9)

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 Phrann gp29-gp30 system in a cohort of prophage-expressed defenses against lytic and temperate mycobacteriophages.
DOI:10.1038/nmicrobiol.2016.251
Phrann genes 29 and/or 30 are involved in defense against Tweety and Gaia, as a mutant lysogen lacking Phrann 29 loses defense against these phages

Dedrick et al. localize part of the Phrann prophage-mediated heterotypic defense phenotype to genes 29 and 30.
DOI:10.1038/nmicrobiol.2016.251
expressing Phrann genes 29 and 30 reproduce the Phrann defense against Tweety and Gaia

Dedrick et al. show that recombinant Phrann genes 29 and 30 are sufficient to reproduce Phrann defense against Tweety and Gaia.
DOI:10.1038/nmicrobiol.2016.251
Phrann prophage-mediated defense is strictly heterotypic, and Phrann gp29/gp30 does not defend against Phrann or other Cluster N phages

Dedrick et al. delimit the Phrann gp29-gp30 defense profile as heterotypic rather than Cluster N superinfection exclusion.
DOI:10.1038/nmicrobiol.2016.251
Prophage-mediated defense by (p)ppGpp synthetases is a new and intriguing system for defense against viral attack

Dedrick et al. interpret Phrann gp29 as a putative (p)ppGpp synthetase in a prophage-mediated viral-defense system.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
Phrann_gp29_gp30 | 10\.1038/nmicrobiol\.2016\.251 | Prophage-mediated defence against viral attack and viral counter-defence

The DefenseFinder model registry maps the named Phrann_gp29_gp30 system to the Dedrick et al. prophage-mediated viral-defense paper.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Phrann_gp29_gp30__gp29 | Phrann_gp29_gp30__gp29 | Phrann_gp29_gp30

The DefenseFinder HMM inventory records a Phrann gp29-gp30 profile for Phrann_gp29_gp30__gp29 in the Phrann_gp29_gp30 model namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Phrann_gp29_gp30__gp30 | Phrann_gp29_gp30__gp30 | Phrann_gp29_gp30

The DefenseFinder HMM inventory records a Phrann gp29-gp30 profile for Phrann_gp29_gp30__gp30 in the Phrann_gp29_gp30 model namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Phrann_gp29_gp30 Phrann_gp29_gp30 2 2 Phrann_gp29_gp30__gp29, Phrann_gp29_gp30__gp30

The DefenseFinder rules table models Phrann_gp29_gp30 as a two-component system requiring gp29 and gp30 profiles.

Phrann gp29-gp30 loci confer heterotypic phage defense

Conservative system-level sketch linking possession of a Phrann gp29-gp30 locus to restricted bacteriophage propagation without asserting the unresolved lytic trigger, gp29-gp30 interaction, or downstream arrest mechanism.

NONMECHANISTIC · The graph captures Phrann gp29-gp30 as a named anti-phage system with DefenseFinder gp29 and gp30 profiles while leaving the direct lytic trigger, Phrann gp30 regulatory role, and exact (p)ppGpp-linked arrest mechanism unresolved.

Edge evidence

Phrann gp29-gp30 locus contributes to restricted phage propagation RO:0002326
Dedrick et al. support Phrann genes 29 and 30 in heterotypic phage defense, and DefenseFinder catalogs gp29 and gp30 profiles in the Phrann_gp29_gp30 model namespace.
- DOI:10.1038/nmicrobiol.2016.251 Phrann genes 29 and/or 30 are involved in defense against Tweety and Gaia, as a mutant lysogen lacking Phrann 29 loses defense against these phages Dedrick et al. connect Phrann genes 29 and 30 to Phrann defense against Tweety and Gaia.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md Phrann_gp29_gp30__gp29 | Phrann_gp29_gp30__gp29 | Phrann_gp29_gp30 The DefenseFinder HMM inventory records a Phrann gp29-gp30 profile for Phrann_gp29_gp30__gp29 in the Phrann_gp29_gp30 model namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md Phrann_gp29_gp30__gp30 | Phrann_gp29_gp30__gp30 | Phrann_gp29_gp30 The DefenseFinder HMM inventory records a Phrann gp29-gp30 profile for Phrann_gp29_gp30__gp30 in the Phrann_gp29_gp30 model namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv Phrann_gp29_gp30 Phrann_gp29_gp30 2 2 Phrann_gp29_gp30__gp29, Phrann_gp29_gp30__gp30 The DefenseFinder rules table models Phrann_gp29_gp30 as a two-component system requiring gp29 and gp30 profiles.
restricted phage propagation confers Phrann gp29-gp30 system METPO:2007700
Phrann-gp29-gp30-mediated defense against Tweety and Gaia realizes the Phrann gp29-gp30 system trait.
- DOI:10.1038/nmicrobiol.2016.251 expressing Phrann genes 29 and 30 reproduce the Phrann defense against Tweety and Gaia Dedrick et al. show that genes 29 and 30 are sufficient to reproduce Phrann defense against Tweety and Gaia.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Phrann_gp29_gp30 | 10\.1038/nmicrobiol\.2016\.251 | Prophage-mediated defence against viral attack and viral counter-defence DefenseFinder records Phrann_gp29_gp30 as a named system from the Dedrick et al. prophage-defense paper.
Phrann gp29-gp30 system is a phage defense system rdfs:subClassOf
Phrann gp29-gp30 system possession is a phage-defense-system trait.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | Phrann_gp29_gp30 | 10\.1038/nmicrobiol\.2016\.251 | Prophage-mediated defence against viral attack and viral counter-defence | DefenseFinder associates Phrann_gp29_gp30 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)

Phrann_gp29_gp30 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 Phrann gp29-gp30 contribution to TM4 defense, Phrann gp30 regulator role, lytic trigger, (p)ppGpp synthetase activity, and remaining target-phage breadth before minting narrower Phrann gp29-gp30 mechanism children.

KNOWLEDGE GAP OPEN phrann_gp29_gp30-mechanism-gap · raised by codex · 2026-09-19

Attached to causal_graphs#phrann_gp29_gp30_locus_restricts_phage

Dedrick et al. and DefenseFinder support Phrann gp29-gp30 as a named anti-phage system with gp29 and gp30 profiles, but the Phrann gp30 regulatory role, lytic-phage trigger, direct (p)ppGpp activation mechanism, relative contribution to TM4 defense, and remaining target breadth are not resolved enough here to assert a narrower mechanistic child trait.

Curation history

2026-09-19T23:37:58Z · MINTED_TRAITMECH_ID · codex
Minted Phrann gp29-gp30 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_v173.
2026-09-19T23:47:14Z · CURATION_REVIEW_REVISION · codex
Resolved PR #1092 review issues #1093 and #1094 by replacing a restriction-implying Phrann gp29-gp30 edge description with generic defense wording and narrowing the breadth knowledge gap to the unresolved TM4 contribution and remaining target-phage breadth.
2026-09-19T23:56:21Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed the PR #1092 canonical_examples gap and left canonical_examples empty: the current Phrann gp29-gp30 evidence supports a named phage-defense system and DefenseFinder profiles, but the curated record does not yet cite a source-backed bacterial taxon with a directly observed Phrann gp29-gp30 locus. No paid research was used.