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AbiP2 system

traitmech:000343 · CLASS · PROPOSED

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.

Trait evidence (7)

AbiP2 loci confer reverse-transcriptase-associated phage defense

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.

NONMECHANISTIC · 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.

AbiP2 loci confer reverse-transcriptase-associated phage defense Interactive directed graph showing evidence-backed causal relationships for AbiP2 system.

Edge evidence

  • AbiP2 locus contributes to restricted phage propagation RO:0002326

    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.

  • restricted phage propagation confers AbiP2 system METPO:2007700

    Restriction of phage propagation realizes the AbiP2 abortive-infection system possession trait.

    • DOI:10.1128/JB.188.4.1643-1647.2006 The product of one of them exhibits reverse transcriptase activity and blocks infection of phage T5 The Odegrip et al. abstract supports a reverse-transcriptase gene in the P2-like-coliphage TO region that blocks phage T5.
  • AbiP2 system is a abortive infection system rdfs:subClassOf

    AbiP2 system possession is an abortive-infection-system trait.

    • DOI:10.1128/JB.188.4.1643-1647.2006 Identification of a Gene Encoding a Functional Reverse Transcriptase within a Highly Variable Locus in the P2-Like Coliphages Crossref metadata verifies the Odegrip et al. 2006 primary P2-like-coliphage reverse-transcriptase paper title and DOI.
    • DOI:10.1093/femsre/fuag009 UG)/Abi RT group, which also includes AbiP2 from E. coli and other predicted RTs The FEMS review explicitly places AbiP2 among UG/Abi reverse transcriptases rather than the unrelated lactococcal AbiP membrane-protein system.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1128/JB.188.4.1643-1647.2006

Parent traits (1)

Synonyms (2)

  • AbiP2 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
  • AbiP2__AbiP2 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Discussions and Knowledge Gaps (2)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

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.

KNOWLEDGE GAP OPEN abip2-ug-abi-mechanism-gap · raised by codex · 2026-09-21

Attached to causal_graphs#abip2_locus_restricts_phage_propagation

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

Resolve the DefenseFinder AbiP2 article-registry mapping before using List_system_article.md as positive system literature evidence.

CURATION TODO OPEN abip2-defensefinder-article-registry-gap · raised by codex · 2026-09-21

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

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

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    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.

  2. · ADDRESS_PR_REVIEW · codex

    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.