identifier: traitmech:000294
label: Panchino gp28 system
definition: A phage defense system in which an organism possesses a Panchino gp28
  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: Panchino_gp28
  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 Panchino gp28 system in a cohort of prophage-expressed
    defenses against lytic and temperate mycobacteriophages.
- reference: DOI:10.1038/nmicrobiol.2016.251
  snippet: The Panchino restriction system (gp28) is a strong candidate for conferring
    this defense
  notes: Dedrick et al. identify Panchino gp28 as the candidate restriction system
    responsible for a heterotypic viral-defense phenotype.
- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  snippet: Panchino_gp28 | 10\.1038/nmicrobiol\.2016\.251 | Prophage-mediated defence
    against viral attack and viral counter-defence
  notes: The DefenseFinder model registry maps the named Panchino_gp28 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: Panchino_gp28__gp28                              | Panchino_gp28__gp28                              |
    Panchino_gp28
  notes: The DefenseFinder HMM inventory records gp28 in the Panchino_gp28 model namespace.
causal_graphs:
- graph_id: panchino_gp28_locus_restricts_phage
  title: Panchino gp28 loci confer bacterial phage defense
  description: 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.
  scope_status: NONMECHANISTIC
  scope_notes: 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.
  nodes:
  - node_id: panchino_gp28_locus
    label: Panchino gp28 locus
    node_type: GENETIC_ELEMENT
    description: A Panchino gp28 anti-phage defense locus cataloged in DefenseFinder
      with a gp28 HMM profile.
  - node_id: restricted_phage_propagation
    label: restricted phage propagation
    node_type: BIOLOGICAL_PROCESS
    description: Reduced propagation of bacteriophage in cells carrying the Panchino
      gp28 system.
  - node_id: panchino_gp28_system_trait
    label: Panchino gp28 system
    node_type: TRAIT
    grounding: traitmech:000294
    description: Possession of a genome-encoded Panchino gp28 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: panchino_gp28_locus
    predicate: contributes to
    predicate_id: RO:0002326
    object: restricted_phage_propagation
    description: 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.
    evidence:
    - reference: DOI:10.1038/nmicrobiol.2016.251
      snippet: The Panchino restriction system (gp28) is a strong candidate for conferring
        this defense
      notes: Dedrick et al. support Panchino gp28 as the candidate system that confers
        a Panchino defense profile.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
      snippet: Panchino_gp28__gp28                              | Panchino_gp28__gp28                              |
        Panchino_gp28
      notes: The DefenseFinder HMM inventory records gp28 in the Panchino_gp28 model
        namespace.
  - subject: restricted_phage_propagation
    predicate: confers
    predicate_id: METPO:2007700
    object: panchino_gp28_system_trait
    description: Panchino-gp28-mediated phage restriction realizes the Panchino gp28
      system trait.
    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 Panchino gp28 among Cluster N prophage systems that
        defend against phage infection.
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: Panchino_gp28 | 10\.1038/nmicrobiol\.2016\.251 | Prophage-mediated
        defence against viral attack and viral counter-defence
      notes: DefenseFinder records Panchino_gp28 as a named system from the Dedrick
        et al. prophage-defense paper.
  - subject: panchino_gp28_system_trait
    predicate: is a
    predicate_id: rdfs:subClassOf
    object: phage_defense_system
    description: Panchino gp28 system possession is a phage-defense-system trait.
    evidence:
    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
      snippet: '| Panchino_gp28 | 10\.1038/nmicrobiol\.2016\.251 | Prophage-mediated
        defence against viral attack and viral counter-defence |'
      notes: DefenseFinder associates Panchino_gp28 with the Dedrick et al. prophage-mediated
        viral-defense paper.
discussions:
- discussion_id: panchino_gp28-mechanism-gap
  prompt: Resolve the Panchino gp28 restriction target, methylation requirements,
    and homolog breadth before minting narrower Panchino gp28 mechanism children.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: 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.
  attaches_to:
  - causal_graphs#panchino_gp28_locus_restricts_phage
  posed_by: codex
  posed_date: '2026-09-19'
curation_history:
- timestamp: '2026-09-19T21:37:34Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: 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.
  llm_assisted: true
- timestamp: '2026-09-19T22:03:20Z'
  curator: codex
  action: DEMOTED_SOURCE_KEY_SYNONYM
  changes: 'Resolved PR #1085 review issue #1086 by demoting the DefenseFinder source
    key Panchino_gp28 from exact synonym to related synonym scope.'
  llm_assisted: true
- timestamp: '2026-09-19T22:07:53Z'
  curator: codex
  action: FIXED_FIXED_WIDTH_SNIPPET
  changes: 'Resolved PR #1085 review issue #1087 by removing an extra separator space
    from the two fixed-width DefenseFinder Panchino_gp28__gp28 HMM snippets.'
  llm_assisted: true
- timestamp: '2026-09-19T22:13:50Z'
  curator: codex
  action: REMOVED_AMBIGUOUS_SYNONYM
  changes: '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.'
  llm_assisted: true