identifier: traitmech:000296 label: Phrann gp29-gp30 system definition: A phage defense system in which an organism possesses a Phrann gp29-gp30 locus that can protect bacteria from bacteriophage infection. definition_source: DOI:10.1038/nmicrobiol.2016.251 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Phrann_gp29_gp30 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md evidence: - reference: DOI:10.1038/nmicrobiol.2016.251 snippet: at least five distinct prophage-expressed viral defense systems that interfere with infection notes: Dedrick et al. place the Cluster N Phrann gp29-gp30 system in a cohort of prophage-expressed defenses against lytic and temperate mycobacteriophages. - reference: DOI:10.1038/nmicrobiol.2016.251 snippet: 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 notes: Dedrick et al. localize part of the Phrann prophage-mediated heterotypic defense phenotype to genes 29 and 30. - reference: DOI:10.1038/nmicrobiol.2016.251 snippet: expressing Phrann genes 29 and 30 reproduce the Phrann defense against Tweety and Gaia notes: Dedrick et al. show that recombinant Phrann genes 29 and 30 are sufficient to reproduce Phrann defense against Tweety and Gaia. - reference: DOI:10.1038/nmicrobiol.2016.251 snippet: Phrann prophage-mediated defense is strictly heterotypic, and Phrann gp29/gp30 does not defend against Phrann or other Cluster N phages notes: Dedrick et al. delimit the Phrann gp29-gp30 defense profile as heterotypic rather than Cluster N superinfection exclusion. - reference: DOI:10.1038/nmicrobiol.2016.251 snippet: Prophage-mediated defense by (p)ppGpp synthetases is a new and intriguing system for defense against viral attack notes: Dedrick et al. interpret Phrann gp29 as a putative (p)ppGpp synthetase in a prophage-mediated viral-defense system. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Phrann_gp29_gp30 | 10\.1038/nmicrobiol\.2016\.251 | Prophage-mediated defence against viral attack and viral counter-defence notes: The DefenseFinder model registry maps the named Phrann_gp29_gp30 system to the Dedrick et al. prophage-mediated viral-defense paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Phrann_gp29_gp30__gp29 | Phrann_gp29_gp30__gp29 | Phrann_gp29_gp30 notes: The DefenseFinder HMM inventory records a Phrann gp29-gp30 profile for Phrann_gp29_gp30__gp29 in the Phrann_gp29_gp30 model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Phrann_gp29_gp30__gp30 | Phrann_gp29_gp30__gp30 | Phrann_gp29_gp30 notes: The DefenseFinder HMM inventory records a Phrann gp29-gp30 profile for Phrann_gp29_gp30__gp30 in the Phrann_gp29_gp30 model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Phrann_gp29_gp30\tPhrann_gp29_gp30\t2\t2\tPhrann_gp29_gp30__gp29, Phrann_gp29_gp30__gp30" notes: The DefenseFinder rules table models Phrann_gp29_gp30 as a two-component system requiring gp29 and gp30 profiles. causal_graphs: - graph_id: phrann_gp29_gp30_locus_restricts_phage title: Phrann gp29-gp30 loci confer heterotypic phage defense description: 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. scope_status: NONMECHANISTIC scope_notes: 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. nodes: - node_id: phrann_gp29_gp30_locus label: Phrann gp29-gp30 locus node_type: GENETIC_ELEMENT description: A Phrann gp29-gp30 anti-phage defense locus cataloged in DefenseFinder with gp29 and gp30 HMM profiles. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced propagation of bacteriophage in cells carrying the Phrann gp29-gp30 system. - node_id: phrann_gp29_gp30_system_trait label: Phrann gp29-gp30 system node_type: TRAIT grounding: traitmech:000296 description: Possession of a genome-encoded Phrann gp29-gp30 phage-defense system. - node_id: phage_defense_system label: phage defense system node_type: TRAIT grounding: traitmech:000209 description: Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection. edges: - subject: phrann_gp29_gp30_locus predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: 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. evidence: - reference: DOI:10.1038/nmicrobiol.2016.251 snippet: 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 notes: Dedrick et al. connect Phrann genes 29 and 30 to Phrann defense against Tweety and Gaia. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Phrann_gp29_gp30__gp29 | Phrann_gp29_gp30__gp29 | Phrann_gp29_gp30 notes: The DefenseFinder HMM inventory records a Phrann gp29-gp30 profile for Phrann_gp29_gp30__gp29 in the Phrann_gp29_gp30 model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Phrann_gp29_gp30__gp30 | Phrann_gp29_gp30__gp30 | Phrann_gp29_gp30 notes: The DefenseFinder HMM inventory records a Phrann gp29-gp30 profile for Phrann_gp29_gp30__gp30 in the Phrann_gp29_gp30 model namespace. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Phrann_gp29_gp30\tPhrann_gp29_gp30\t2\t2\tPhrann_gp29_gp30__gp29,\ \ Phrann_gp29_gp30__gp30" notes: The DefenseFinder rules table models Phrann_gp29_gp30 as a two-component system requiring gp29 and gp30 profiles. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: phrann_gp29_gp30_system_trait description: Phrann-gp29-gp30-mediated defense against Tweety and Gaia realizes the Phrann gp29-gp30 system trait. evidence: - reference: DOI:10.1038/nmicrobiol.2016.251 snippet: expressing Phrann genes 29 and 30 reproduce the Phrann defense against Tweety and Gaia notes: Dedrick et al. show that genes 29 and 30 are sufficient to reproduce Phrann defense against Tweety and Gaia. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Phrann_gp29_gp30 | 10\.1038/nmicrobiol\.2016\.251 | Prophage-mediated defence against viral attack and viral counter-defence notes: DefenseFinder records Phrann_gp29_gp30 as a named system from the Dedrick et al. prophage-defense paper. - subject: phrann_gp29_gp30_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Phrann gp29-gp30 system possession is a phage-defense-system trait. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| Phrann_gp29_gp30 | 10\.1038/nmicrobiol\.2016\.251 | Prophage-mediated defence against viral attack and viral counter-defence |' notes: DefenseFinder associates Phrann_gp29_gp30 with the Dedrick et al. prophage-mediated viral-defense paper. discussions: - discussion_id: phrann_gp29_gp30-mechanism-gap prompt: 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. kind: KNOWLEDGE_GAP status: OPEN rationale: 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. attaches_to: - causal_graphs#phrann_gp29_gp30_locus_restricts_phage posed_by: codex posed_date: '2026-09-19' curation_history: - timestamp: '2026-09-19T23:37:58Z' curator: codex action: MINTED_TRAITMECH_ID changes: 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. llm_assisted: true - timestamp: '2026-09-19T23:47:14Z' curator: codex action: CURATION_REVIEW_REVISION changes: '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.' llm_assisted: true - timestamp: '2026-09-19T23:56:21Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: '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.' llm_assisted: true