identifier: traitmech:000278 label: Dpd system definition: A phage defense system in which an organism possesses a Dpd genomic island whose dpdA-K genes install 7-deazaguanine derivatives into DNA and are modeled by DefenseFinder as a multi-profile Dpd system. definition_source: DOI:10.1073/pnas.1518570113 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Dpd synonym_type: EXACT_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: dpdA-K synonym_type: RELATED_SYNONYM source: DOI:10.1073/pnas.1518570113 evidence: - reference: DOI:10.1073/pnas.1518570113 snippet: 2'-deoxy-preQ0 and 2'-deoxy-7-amido-7-deazaguanosine in enzymatic hydrolysates of DNA extracted from the pathogenic, Gram-negative bacteria Salmonella enterica serovar Montevideo notes: Thiaville et al. experimentally detected 7-deazaguanine-derived DNA modifications in a bacterium carrying the Dpd island. - reference: DOI:10.1073/pnas.1518570113 snippet: rename the genes of the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA notes: Thiaville et al. name the S. Montevideo 7-deazapurine DNA-modification cluster as dpdA-K. - reference: DOI:10.1073/pnas.1518570113 snippet: the modifications were detected in DNA from other organisms containing these clusters, including Kineococcus radiotolerans, Comamonas testosteroni, and Sphingopyxis alaskensis notes: Thiaville et al. support treating Dpd as a recurrent bacterial system rather than a one-off S. Montevideo sequence feature. - reference: DOI:10.1073/pnas.1518570113 snippet: strongly suggests a restriction-modification role for the cluster in Enterobacteriaceae notes: Thiaville et al. connect the Dpd cluster to a likely restriction-modification role based on transformation efficiencies of modified and unmodified plasmids. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Dpd | 10\.1073/pnas\.1518570113 | Novel genomic island modifies DNA with 7-deazaguanine derivatives notes: The DefenseFinder article registry maps the named Dpd system to the Thiaville et al. DNA-modification paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Dpd\tDpd\t4\t4\tDpd__DpdA, Dpd__DpdB, Dpd__DpdC, Dpd__DpdD, Dpd__DpdE,\ \ Dpd__DpdF, Dpd__DpdG, Dpd__DpdH, Dpd__DpdI, Dpd__DpdJ, Dpd__DpdK" notes: The DefenseFinder rules table models Dpd as a multi-profile defense system requiring a subset of DpdA-K profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Dpd__DpdA | Dpd__DpdA | Dpd notes: The DefenseFinder HMM inventory records DpdA in the Dpd model namespace. causal_graphs: - graph_id: dpd_dna_modification_defense title: Dpd islands install 7-deazaguanine DNA modifications description: Conservative system-level sketch linking a Dpd genomic island to 7-deazaguanine DNA modification, a likely restriction-modification output, and the Dpd system trait. scope_status: NONMECHANISTIC scope_notes: The graph captures Dpd as a DNA-modification system with a DefenseFinder model while leaving its exact restriction target, modified motif, phage substrate range, DpdA-K component functions, and optional FolE/QueC/QueD/QueE profile requirements unresolved. nodes: - node_id: dpd_genomic_island label: Dpd genomic island node_type: GENETIC_ELEMENT description: A dpdA-K 7-deazapurine DNA-modification locus represented by a multi-profile DefenseFinder Dpd model. - node_id: deazaguanine_dna_modification label: 7-deazaguanine DNA modification node_type: BIOLOGICAL_PROCESS description: Installation of 7-deazaguanine-derived deoxynucleosides in bacterial DNA. - node_id: restriction_modification_behavior label: restriction-modification behavior node_type: BIOLOGICAL_PROCESS description: Self/non-self discrimination associated with a bacterial DNA-modification island. - node_id: dpd_system_trait label: Dpd system node_type: TRAIT grounding: traitmech:000278 description: Possession of a genome-encoded Dpd 7-deazaguanine DNA-modification 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: dpd_genomic_island predicate: contributes to predicate_id: RO:0002326 object: deazaguanine_dna_modification description: The Dpd cluster installs 7-deazaguanine derivatives in DNA. evidence: - reference: DOI:10.1073/pnas.1518570113 snippet: rename the genes of the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA notes: Thiaville et al. name the genes of the 7-deazapurine DNA-modification cluster as dpdA-K. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Dpd__DpdA | Dpd__DpdA | Dpd notes: DefenseFinder includes DpdA in the custom Dpd model profile inventory. - subject: deazaguanine_dna_modification predicate: contributes to predicate_id: RO:0002326 object: restriction_modification_behavior description: Modified Dpd DNA is associated with restriction-modification behavior in Enterobacteriaceae. evidence: - reference: DOI:10.1073/pnas.1518570113 snippet: strongly suggests a restriction-modification role for the cluster in Enterobacteriaceae notes: Thiaville et al. connect Dpd modification to a likely restriction-modification role without resolving the exact restriction component or substrate. - subject: restriction_modification_behavior predicate: confers predicate_id: METPO:2007700 object: dpd_system_trait description: DefenseFinder models Dpd as a multi-profile defense system rooted in DpdA-K DNA modification. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Dpd\tDpd\t4\t4\tDpd__DpdA, Dpd__DpdB, Dpd__DpdC, Dpd__DpdD, Dpd__DpdE,\ \ Dpd__DpdF, Dpd__DpdG, Dpd__DpdH, Dpd__DpdI, Dpd__DpdJ, Dpd__DpdK" notes: The DefenseFinder rules table supports Dpd as a named defense-system model with DpdA-K profiles. - subject: dpd_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Dpd system possession is a phage-defense-system trait. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Dpd | 10\.1073/pnas\.1518570113 | Novel genomic island modifies DNA with 7-deazaguanine derivatives notes: DefenseFinder associates Dpd with the Thiaville et al. DNA-modification paper. discussions: - discussion_id: dpd-restriction-mechanism-gap prompt: Resolve Dpd restriction targets, phage specificity, and DpdA-K component functions before minting narrower Dpd mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Thiaville et al. support dpdA-K-dependent installation of 7-deazaguanine derivatives into DNA and a likely restriction-modification role, and DefenseFinder supports Dpd as a named multi-profile defense model. This first record does not yet resolve the universal restriction target, modified motif, antiphage substrate breadth, or the necessity of each profiled component across natural Dpd loci. attaches_to: - causal_graphs#dpd_dna_modification_defense posed_by: codex posed_date: '2026-09-19' curation_history: - timestamp: '2026-09-19T18:31:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Dpd 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_v155. llm_assisted: true