identifier: traitmech:000343 label: AbiP2 system definition: An abortive infection system in which an organism possesses a single-component AbiP2-family reverse-transcriptase-like locus represented by DefenseFinder as a mandatory AbiP2__AbiP2 profile. definition_source: DOI:10.1128/JB.188.4.1643-1647.2006 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000214 synonyms: - synonym_text: AbiP2 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv - synonym_text: AbiP2__AbiP2 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md evidence: - reference: DOI:10.1128/JB.188.4.1643-1647.2006 snippet: Identification of a Gene Encoding a Functional Reverse Transcriptase within a Highly Variable Locus in the P2-Like Coliphages notes: Crossref metadata verifies the Odegrip et al. 2006 primary P2-like-coliphage reverse-transcriptase paper title and DOI. - reference: DOI:10.1128/JB.188.4.1643-1647.2006 snippet: The product of one of them exhibits reverse transcriptase activity and blocks infection of phage T5 notes: The Odegrip et al. abstract supports a reverse-transcriptase gene in the P2-like-coliphage TO region that blocks phage T5. - reference: DOI:10.1093/nar/gkac467 snippet: 'UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions' notes: Mestre et al. describe the broad UG/Abi reverse-transcriptase family that the FEMS review places AbiP2 within. - reference: DOI:10.1093/femsre/fuag009 snippet: UG)/Abi RT group, which also includes AbiP2 from E. coli and other predicted RTs notes: The FEMS review explicitly places AbiP2 among UG/Abi reverse transcriptases rather than the unrelated lactococcal AbiP membrane-protein system. - reference: DOI:10.1093/nar/gkac772 snippet: 'two Abi polymerases: AbiK and Abi-P2' notes: Figiel et al. structurally characterize Abi-P2 as a template-independent Abi polymerase but do not resolve the in vivo phage trigger or infected-cell output. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiP2\tAbiP2\t1\t1\tAbiP2__AbiP2\t\t\t" notes: The DefenseFinder rules table models AbiP2 as a one-component system requiring the AbiP2__AbiP2 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiP2__AbiP2 | AbiP2__AbiP2 | AbiP2 | Custom | 400 |' notes: The DefenseFinder HMM inventory records AbiP2__AbiP2 under the AbiP2 model namespace. causal_graphs: - graph_id: abip2_locus_restricts_phage_propagation title: AbiP2 loci confer reverse-transcriptase-associated phage defense description: Conservative system-level sketch linking possession of a DefenseFinder AbiP2 locus to restricted bacteriophage propagation without asserting the unresolved phage trigger, protein-primed polymerase product, or host-arrest route. scope_status: NONMECHANISTIC scope_notes: The graph captures AbiP2 as a named single-profile reverse-transcriptase-like abortive-infection system with the DefenseFinder AbiP2__AbiP2 HMM while leaving its direct phage trigger, in vivo Abi-P2 polymerase product, UG/Abi family boundary, prophage host range, and cell-arrest or death route unresolved. nodes: - node_id: abip2_locus label: AbiP2 locus node_type: GENETIC_ELEMENT description: An AbiP2-family abortive-infection locus represented by the DefenseFinder AbiP2__AbiP2 profile. - node_id: restricted_phage_propagation label: restricted phage propagation node_type: BIOLOGICAL_PROCESS description: Reduced bacteriophage propagation in cells carrying an AbiP2-family abortive-infection system. - node_id: abip2_system_trait label: AbiP2 system node_type: TRAIT grounding: traitmech:000343 description: Possession of a genome-encoded AbiP2 abortive-infection phage-defense system. - node_id: abortive_infection_system_trait label: abortive infection system node_type: TRAIT grounding: traitmech:000214 description: Possession of a genome-encoded abortive-infection phage-defense system. edges: - subject: abip2_locus predicate: contributes to predicate_id: RO:0002326 object: restricted_phage_propagation description: The DefenseFinder AbiP2 namespace is modeled as a one-profile AbiP2__AbiP2 system, matching the one-gene reverse-transcriptase-associated P2-like coliphage defense architecture. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiP2\tAbiP2\t1\t1\tAbiP2__AbiP2\t\t\t" notes: The DefenseFinder rules table models AbiP2 as a one-component system requiring the AbiP2__AbiP2 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiP2__AbiP2 | AbiP2__AbiP2 | AbiP2 | Custom | 400 |' notes: The DefenseFinder HMM inventory records AbiP2__AbiP2 under the AbiP2 model namespace. - reference: DOI:10.1128/JB.188.4.1643-1647.2006 snippet: The product of one of them exhibits reverse transcriptase activity and blocks infection of phage T5 notes: The Odegrip et al. abstract supports a reverse-transcriptase gene in the P2-like-coliphage TO region that blocks phage T5. - subject: restricted_phage_propagation predicate: confers predicate_id: METPO:2007700 object: abip2_system_trait description: Restriction of phage propagation realizes the AbiP2 abortive-infection system possession trait. evidence: - reference: DOI:10.1128/JB.188.4.1643-1647.2006 snippet: The product of one of them exhibits reverse transcriptase activity and blocks infection of phage T5 notes: The Odegrip et al. abstract supports a reverse-transcriptase gene in the P2-like-coliphage TO region that blocks phage T5. - subject: abip2_system_trait predicate: is a predicate_id: rdfs:subClassOf object: abortive_infection_system_trait description: AbiP2 system possession is an abortive-infection-system trait. evidence: - reference: DOI:10.1128/JB.188.4.1643-1647.2006 snippet: Identification of a Gene Encoding a Functional Reverse Transcriptase within a Highly Variable Locus in the P2-Like Coliphages notes: Crossref metadata verifies the Odegrip et al. 2006 primary P2-like-coliphage reverse-transcriptase paper title and DOI. - reference: DOI:10.1093/femsre/fuag009 snippet: UG)/Abi RT group, which also includes AbiP2 from E. coli and other predicted RTs notes: The FEMS review explicitly places AbiP2 among UG/Abi reverse transcriptases rather than the unrelated lactococcal AbiP membrane-protein system. discussions: - discussion_id: abip2-ug-abi-mechanism-gap prompt: Resolve the AbiP2 natural locus breadth, phage trigger, protein-primed polymerase output, and growth-arrest or cell-death route before minting narrower AbiP2 mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Odegrip et al. support a P2-like-coliphage reverse transcriptase gene that blocks phage T5 infection, Mestre et al. describe the UG/Abi reverse-transcriptase family, the FEMS review places AbiP2 in that family rather than the unrelated lactococcal AbiP family, Figiel et al. structurally characterize Abi-P2 as a template-independent Abi polymerase, and DefenseFinder represents AbiP2 with a mandatory AbiP2__AbiP2 profile. This first system-level record therefore leaves the direct phage trigger, in vivo DNA product, exact relationship to broader UG/Abi systems, prophage host breadth, and growth-arrest or cell-death route unresolved. evidence: - reference: DOI:10.1128/JB.188.4.1643-1647.2006 snippet: The product of one of them exhibits reverse transcriptase activity and blocks infection of phage T5 notes: The Odegrip et al. abstract supports a reverse-transcriptase gene in the P2-like-coliphage TO region that blocks phage T5. - reference: DOI:10.1093/nar/gkac467 snippet: 'UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions' notes: Mestre et al. describe the broad UG/Abi reverse-transcriptase family that the FEMS review places AbiP2 within. - reference: DOI:10.1093/femsre/fuag009 snippet: UG)/Abi RT group, which also includes AbiP2 from E. coli and other predicted RTs notes: The FEMS review explicitly places AbiP2 among UG/Abi reverse transcriptases rather than the unrelated lactococcal AbiP membrane-protein system. - reference: DOI:10.1093/nar/gkac772 snippet: 'two Abi polymerases: AbiK and Abi-P2' notes: Figiel et al. structurally characterize Abi-P2 as a template-independent Abi polymerase but do not resolve the in vivo phage trigger or infected-cell output. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "AbiP2\tAbiP2\t1\t1\tAbiP2__AbiP2\t\t\t" notes: The DefenseFinder rules table models AbiP2 as a one-component system requiring the AbiP2__AbiP2 profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| AbiP2__AbiP2 | AbiP2__AbiP2 | AbiP2 | Custom | 400 |' notes: The DefenseFinder HMM inventory records AbiP2__AbiP2 under the AbiP2 model namespace. attaches_to: - causal_graphs#abip2_locus_restricts_phage_propagation posed_by: codex posed_date: '2026-09-21' - discussion_id: abip2-defensefinder-article-registry-gap prompt: Resolve the DefenseFinder AbiP2 article-registry mapping before using List_system_article.md as positive system literature evidence. kind: CURATION_TODO status: OPEN rationale: The pinned DefenseFinder HMM inventory and rules table support AbiP2 as a one-profile model namespace, but its article registry row maps AbiP2 to a 2005 lactococcal abortive-infection review that predates Odegrip et al. 2006. This record therefore leaves the registry-to-primary link unresolved and relies on Odegrip et al., Mestre et al., the FEMS review, Figiel et al., and pinned DefenseFinder HMM/rule rows for AbiP2 identity and system coverage. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| AbiP2 | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme |' notes: The pinned DefenseFinder article registry maps AbiP2 to a 2005 lactococcal Abi review; that row is tracked as unresolved model-to-publication triage rather than positive AbiP2 primary literature evidence. posed_by: codex posed_date: '2026-09-21' curation_history: - timestamp: '2026-09-21T19:10:26Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted AbiP2 system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v220. llm_assisted: true - timestamp: '2026-09-21T19:50:08Z' curator: codex action: ADDRESS_PR_REVIEW changes: 'Addressed review issues #1215 and #1216 by renaming the NONMECHANISTIC AbiP2 graph id to omit T5 specificity and by documenting the unresolved DefenseFinder article-registry row that maps AbiP2 to a 2005 lactococcal review.' llm_assisted: true