Abi2 system

traitmech:000338 · CLASS · PROPOSED

An abortive infection system in which an organism possesses a single-component Abi-like locus represented by the DefenseFinder Abi2 model namespace and mandatory Abi2__Abi_2/PF07751 profile.

Trait evidence (9)

DOI:10.1016/j.mib.2005.06.006
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection.

Chopin et al. define the abortive-infection class of phage exclusion systems used by the DefenseFinder Abi2 registry row.
DOI:10.1128/jb.177.13.3818-3823.1995
Lactococcal phage abortive infection (AbiD1) determined by plasmid pIL105 is active on both prolate- and small-isometric-head phages

Anba et al. characterize AbiD1 as a plasmid-encoded lactococcal abortive-infection determinant active on multiple phage morphotypes.
DOI:10.1128/jb.177.13.3818-3823.1995
The Abi phenotype was found to be encoded by a single gene, designated abiD1.

Anba et al. support a single-gene AbiD1 locus used as family-level background for Abi-like abortive-infection systems.
DOI:10.1128/jb.177.13.3824-3829.1995
Phage bIL66 is unable to grow on Lactococcus lactis cells harboring the abortive infection gene abiD1.

Bidnenko et al. connect abiD1 carriage to restriction of bIL66 phage growth in Lactococcus lactis.
https://www.ebi.ac.uk/interpro/entry/pfam/PF07751/
This family, found in various bacterial species, contains sequences that are similar to the Abi group of proteins

EBI InterPro resolves PF07751 as the reviewed Pfam Abi-like protein family with short name Abi_2.
https://rest.uniprot.org/uniprotkb/Q48717.tsv?fields=accession,id,gene_names,protein_name,xref_pfam,organism_name
Q48717 Q48717_9LACT abiD1 AbiD1 PF07751; Lactococcus lactis

UniProt maps the Lactococcus lactis abiD1/AbiD1 entry to Pfam PF07751, bridging primary AbiD1 papers to the Abi_2 HMM family without making DefenseFinder Abi2 exactly equivalent to AbiD1.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
Abi2 | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme

The DefenseFinder article registry maps the named Abi2 model namespace to the Chopin et al. lactococcal abortive-infection review.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Abi2 Abi2 1 1 Abi2__Abi_2

The DefenseFinder rules table models Abi2 as a one-component system requiring the Abi2__Abi_2 profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Abi2__Abi_2 | Abi2__Abi_2 | Abi2 | PF07751.12 | 60 |

The DefenseFinder HMM inventory records Abi2__Abi_2 under the Abi2 model namespace, backed by the Pfam PF07751.12 Abi_2 profile.

Abi2 loci confer abortive-infection phage defense

Conservative system-level sketch linking possession of a DefenseFinder Abi2 locus to restricted bacteriophage propagation without asserting the unresolved phage trigger, small-RNA component, or molecular output.

NONMECHANISTIC · The graph captures Abi2 as a named DefenseFinder single-profile abortive-infection system with an Abi2__Abi_2/PF07751 HMM profile while leaving its natural locus boundaries, AbiD/F-group breadth, upstream regulatory RNA relationships, phage trigger, and direct effector activity unresolved.

Edge evidence

Abi2 locus contributes to restricted phage propagation RO:0002326
DefenseFinder represents Abi2 with the Abi2__Abi_2 Pfam profile, and Abi-like loci mediate abortive-infection phage restriction.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv Abi2 Abi2 1 1 Abi2__Abi_2 The DefenseFinder rules table models Abi2 as a one-component system requiring the Abi2__Abi_2 profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | Abi2__Abi_2 | Abi2__Abi_2 | Abi2 | PF07751.12 | 60 | The DefenseFinder HMM inventory records Abi2__Abi_2 under the Abi2 model namespace, backed by the Pfam PF07751.12 Abi_2 profile.
- DOI:10.1128/jb.177.13.3818-3823.1995 Lactococcal phage abortive infection (AbiD1) determined by plasmid pIL105 is active on both prolate- and small-isometric-head phages Anba et al. support abortive-infection antiphage activity in the Abi-like family.
restricted phage propagation confers Abi2 system METPO:2007700
Restriction of phage propagation realizes the Abi2 abortive-infection system possession trait.
- DOI:10.1128/jb.177.13.3824-3829.1995 Phage bIL66 is unable to grow on Lactococcus lactis cells harboring the abortive infection gene abiD1. Bidnenko et al. connect AbiD1-family carriage to blocked phage growth.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Abi2 | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme The DefenseFinder article registry maps the named Abi2 model namespace to the Chopin et al. lactococcal abortive-infection review.
Abi2 system is a abortive infection system rdfs:subClassOf
Abi2 system possession is an abortive-infection-system trait.
- DOI:10.1016/j.mib.2005.06.006 Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. Chopin et al. place Abi systems in the abortive-infection class of phage defense.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Abi2 | 10\.1016/j\.mib\.2005\.06\.006 | Phage abortive infection in lactococci: variations on a theme The DefenseFinder article registry maps the named Abi2 model namespace to the Chopin et al. lactococcal abortive-infection review.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1016/j.mib.2005.06.006

Parent traits (1)

abortive infection system traitmech:000214

Synonyms (3)

Abi2 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
Abi2__Abi_2 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Abi_2 RELATED_SYNONYM · https://www.ebi.ac.uk/interpro/entry/pfam/PF07751/

kg-microbe context

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

Discussions and Knowledge Gaps (1)

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

Resolve the natural Abi2 locus breadth, phage trigger, and AbiD/F-group mapping before minting narrower Abi2 mechanism children.

KNOWLEDGE GAP OPEN abi2-family-boundary-gap · raised by codex · 2026-09-21

Attached to causal_graphs#abi2_locus_restricts_phage

The DefenseFinder Abi2 model namespace requires the Abi2__Abi_2 PF07751 profile; InterPro treats PF07751 as an Abi-like family, and UniProt maps the AbiD1 protein onto the same Pfam family. This first record leaves unresolved whether DefenseFinder Abi2 exactly corresponds to AbiD1, the broader AbiD/F group, or a different subset of Abi-like loci; it therefore avoids protein-level chemistry and records only the genome-level model namespace.

Curation history

2026-09-21T14:52:53Z · MINTED_TRAITMECH_ID · codex
Minted Abi2 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_v215.