GAPS2 system

traitmech:000380 · CLASS · PROPOSED

A phage defense system in which an organism possesses a GMT-encoded GAPS2 locus represented by DefenseFinder as a single-profile model, GAPS2__GAPS2, and experimentally linked to P1-vir and lambda-vir protection when expressed in E. coli.

Trait evidence (10)

DOI:10.1038/s41564-024-01840-5
We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy

Mahata et al. identify four anti-phage defense systems in Gamma-Mobile-Trio islands.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md
The GAPS2 system is composed of a single protein. It was found in Gamma-Mobile-Trio (GMT) protein containing genomic island in Vibrio, and cloned into E. coli K-12 :ref{doi=10.1101/2023.03.28.534373}. The name GAPS derives from the "GMT-encoded Anti-Phage System" acronym.

The DefenseFinder wiki describes GAPS2 as a single-protein GMT-encoded system cloned from Vibrio into E. coli K-12.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md
GAPS2 is composed of a single protein with a DNA BRCT domains :ref{doi=10.4161/cc.10.15.16312}.

The DefenseFinder wiki reports a DNA BRCT domain in the single GAPS2 protein.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md
As far as we are aware, the molecular mechanism is unknown.

The DefenseFinder wiki records the GAPS2 mechanism as unknown.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md
The GAPS2 system in *Mannheimia sp. USDA-ARS-USMARC-1261* (GCF_000521605.1, NZ_CP006942) is composed of 1 protein: GAPS2 (WP_025236539.1)

The DefenseFinder wiki illustrates a predicted single-protein GAPS2 locus in RefSeq assembly GCF_000521605.1 on NZ_CP006942.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md
Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 Origin_0[Vibrio parahaemolyticus <a href='https://ncbi.nlm.nih.gov/protein/WP_174208646.1'>WP_174208646.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> P1-vir & Lambda-vir

The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS2 source locus expressed in E. coli against P1-vir and Lambda-vir.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md
subgraph Title4[Protects against] P1-vir Lambda-vir

The DefenseFinder experimental-validation diagram lists P1-vir and Lambda-vir in the GAPS2 protects-against subgraph.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
GAPS2 | 10\.1101/2023\.03\.28\.534373 | Gamma-Mobile-Trio systems define a new class of mobile elements rich in bacterial defensive and offensive tools

The DefenseFinder article registry maps the named GAPS2 system to the Mahata et al. preprint.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
GAPS2 GAPS2 1 1 GAPS2__GAPS2

The DefenseFinder rules table models GAPS2 as a single-profile system requiring GAPS2__GAPS2.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| GAPS2__GAPS2 | GAPS2__GAPS2 | GAPS2 | Custom | 100 |

The DefenseFinder HMM inventory records GAPS2__GAPS2 under the GAPS2 system namespace.

GAPS2 loci protect against P1-vir and lambda-vir

Conservative system-level sketch linking GAPS2 locus possession to protection against P1-vir and lambda-vir.

NONMECHANISTIC · The graph captures GAPS2 as a named single-profile DefenseFinder phage-defense system while leaving natural host breadth, the molecular activity of the BRCT-domain GAPS2 component, the phage trigger, and exact GAPS2__GAPS2 profile-to-protein correspondence unresolved.

Edge evidence

GAPS2 locus contributes to P1-vir and lambda-vir protection RO:0002326
The DefenseFinder wiki links a Vibrio parahaemolyticus GAPS2 locus from Mahata et al. to protection against P1-vir and lambda-vir, and DefenseFinder models GAPS2 through the GAPS2__GAPS2 profile.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md The GAPS2 system is composed of a single protein. It was found in Gamma-Mobile-Trio (GMT) protein containing genomic island in Vibrio, and cloned into E. coli K-12 :ref{doi=10.1101/2023.03.28.534373}. The name GAPS derives from the "GMT-encoded Anti-Phage System" acronym. The DefenseFinder wiki describes GAPS2 as a single-protein GMT-encoded system cloned from Vibrio into E. coli K-12.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 Origin_0[Vibrio parahaemolyticus <a href='https://ncbi.nlm.nih.gov/protein/WP_174208646.1'>WP_174208646.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> P1-vir & Lambda-vir The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS2 source locus expressed in E. coli against P1-vir and Lambda-vir.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md subgraph Title4[Protects against] P1-vir Lambda-vir The DefenseFinder experimental-validation diagram lists P1-vir and Lambda-vir in the GAPS2 protects-against subgraph.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv GAPS2 GAPS2 1 1 GAPS2__GAPS2 The DefenseFinder rules table models GAPS2 as a single-profile system requiring GAPS2__GAPS2.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | GAPS2__GAPS2 | GAPS2__GAPS2 | GAPS2 | Custom | 100 | The DefenseFinder HMM inventory records GAPS2__GAPS2 under the GAPS2 system namespace.
P1-vir and lambda-vir protection confers GAPS2 system METPO:2007700
Protection against P1-vir and lambda-vir realizes the GAPS2 system trait.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 Origin_0[Vibrio parahaemolyticus <a href='https://ncbi.nlm.nih.gov/protein/WP_174208646.1'>WP_174208646.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> P1-vir & Lambda-vir The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS2 source locus expressed in E. coli against P1-vir and Lambda-vir.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md subgraph Title4[Protects against] P1-vir Lambda-vir The DefenseFinder experimental-validation diagram lists P1-vir and Lambda-vir in the GAPS2 protects-against subgraph.
GAPS2 system is a phage defense system rdfs:subClassOf
GAPS2 system possession is a phage-defense-system trait.
- DOI:10.1038/s41564-024-01840-5 We reveal four anti-phage defence systems encoded within GMT islands and further characterize one system, GAPS1, showing it is triggered by a phage capsid protein to induce cell dormancy Mahata et al. identify four anti-phage defense systems in Gamma-Mobile-Trio islands.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md GAPS2 | 10\.1101/2023\.03\.28\.534373 | Gamma-Mobile-Trio systems define a new class of mobile elements rich in bacterial defensive and offensive tools The DefenseFinder article registry maps the named GAPS2 system to the Mahata et al. preprint.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv GAPS2 GAPS2 1 1 GAPS2__GAPS2 The DefenseFinder rules table models GAPS2 as a single-profile system requiring GAPS2__GAPS2.

Provenance

Identifier source: TraitMech local identifier
Definition source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md

Parent traits (1)

phage defense system traitmech:000209

Synonyms (2)

GAPS2 EXACT_SYNONYM · https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md
GAPS2__GAPS2 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 (1)

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

Resolve GAPS2 natural host breadth, BRCT-domain activity, phage trigger specificity, and exact GAPS2__GAPS2 profile-to-protein correspondence before minting narrower GAPS2 mechanism traits.

KNOWLEDGE GAP OPEN gaps2-mechanism-gap · raised by codex · 2026-09-26

Attached to causal_graphs#gaps2_locus_restricts_phages

Mahata et al. support GAPS2 as a GMT-encoded anti-phage defense system that protects E. coli against P1-vir and lambda-vir when expressed from a Vibrio parahaemolyticus locus, and DefenseFinder represents GAPS2 as a single-profile system. Natural host breadth, BRCT-domain activity, the phage trigger, and exact profile-to-protein correspondence remain unresolved.

Evidence

https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md
The GAPS2 system is composed of a single protein. It was found in Gamma-Mobile-Trio (GMT) protein containing genomic island in Vibrio, and cloned into E. coli K-12 :ref{doi=10.1101/2023.03.28.534373}. The name GAPS derives from the "GMT-encoded Anti-Phage System" acronym.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md
GAPS2 is composed of a single protein with a DNA BRCT domains :ref{doi=10.4161/cc.10.15.16312}.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md
As far as we are aware, the molecular mechanism is unknown.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps2.md
Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0 Origin_0[Vibrio parahaemolyticus <a href='https://ncbi.nlm.nih.gov/protein/WP_174208646.1'>WP_174208646.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> P1-vir & Lambda-vir
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
GAPS2 GAPS2 1 1 GAPS2__GAPS2
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| GAPS2__GAPS2 | GAPS2__GAPS2 | GAPS2 | Custom | 100 |

Curation history

2026-09-26T11:26:41Z · MINTED_TRAITMECH_ID · codex
Minted GAPS2 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under phage defense system 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_v257.
2026-09-26T11:26:42Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed GAPS2 system canonical_examples and left them empty because the current sources support a Vibrio parahaemolyticus accession-level experimental validation graph, a DefenseFinder system model, and a RefSeq Mannheimia sp. example, but not a direct native microbial isolate exemplar with experimentally verified endogenous GAPS2 activity. No paid research was used.