GAPS6 system

traitmech:000381 · CLASS · PROPOSED

A phage defense system in which an organism possesses a GMT-encoded GAPS6 locus represented by DefenseFinder as a two-profile model, GAPS6__GAPS6a and GAPS6__GAPS6b, and experimentally linked to T7, T4, 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/gaps6.md
GAPS6 is composed of two proteins, [GAPS6a](https://www.ncbi.nlm.nih.gov/protein/WP_248387294.1/) and [GAPS6b](https://www.ncbi.nlm.nih.gov/protein/WP_248387295.1/). These two proteins are encoded together in diverse Gram-negative bacteria.

The DefenseFinder wiki describes GAPS6 as a two-protein system with GAPS6a and GAPS6b encoded together.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md
GAPS6b is essential for the defense phenotype, however it is not known whether GAPS6b could be sufficient.

The DefenseFinder wiki reports that GAPS6b is essential for GAPS6 defense but leaves GAPS6b sufficiency unresolved.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md
GAPS6b is composed of TPR repeats at the N-terminus, possibly allowing ligand binding and a predicted RNAse domain (PINc, PF08745.14) at the C-terminus. PINc domains have been implicated as toxins in bacterial toxin-antitoxin modules :ref{doi=10.1093/protein/gzq081}. The PINc domain is required for the anti-phage defense activity of GAPS6.

The DefenseFinder wiki reports that GAPS6b carries TPR repeats and a PINc domain required for GAPS6 anti-phage activity.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md
The GAPS6 system in *Escherichia coli* (GCF_013372365.1, NZ_CP054227) is composed of 2 proteins GAPS6b (WP_096985931.1) GAPS6a (WP_000346990.1)

The DefenseFinder wiki illustrates a predicted two-protein GAPS6 locus in RefSeq assembly GCF_013372365.1 on NZ_CP054227.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.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_248387294.1'>WP_248387294.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_248387295.1'>WP_248387295.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir

The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS6 source locus expressed in E. coli against T7, T4, P1-vir, and Lambda-vir.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
GAPS6 | 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 GAPS6 system to the Mahata et al. preprint.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
GAPS6 GAPS6 2 2 GAPS6__GAPS6a, GAPS6__GAPS6b

The DefenseFinder rules table models GAPS6 as a two-profile system requiring GAPS6__GAPS6a and GAPS6__GAPS6b.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| GAPS6__GAPS6a | GAPS6__GAPS6a | GAPS6 | Custom | 20 |

The DefenseFinder HMM inventory records GAPS6__GAPS6a under the GAPS6 system namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| GAPS6__GAPS6b | GAPS6__GAPS6b | GAPS6 | Custom | 20 |

The DefenseFinder HMM inventory records GAPS6__GAPS6b under the GAPS6 system namespace.

GAPS6 loci protect against T7, T4, P1-vir, and lambda-vir

Conservative system-level sketch linking GAPS6 locus possession to protection against T7, T4, P1-vir, and lambda-vir.

NONMECHANISTIC · The graph captures GAPS6 as a named two-profile DefenseFinder phage-defense system while leaving natural host breadth, the activity of GAPS6a, GAPS6b sufficiency and trigger specificity, and exact GAPS6a/GAPS6b profile-to-protein correspondence unresolved.

Edge evidence

GAPS6 locus contributes to T7, T4, P1-vir, and lambda-vir protection RO:0002326
The DefenseFinder wiki links a Vibrio parahaemolyticus GAPS6 locus from Mahata et al. to protection against T7, T4, P1-vir, and lambda-vir, and DefenseFinder models GAPS6 through two mandatory profiles.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md GAPS6 is composed of two proteins, [GAPS6a](https://www.ncbi.nlm.nih.gov/protein/WP_248387294.1/) and [GAPS6b](https://www.ncbi.nlm.nih.gov/protein/WP_248387295.1/). These two proteins are encoded together in diverse Gram-negative bacteria. The DefenseFinder wiki describes GAPS6 as a two-protein system with GAPS6a and GAPS6b encoded together.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.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_248387294.1'>WP_248387294.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_248387295.1'>WP_248387295.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS6 source locus expressed in E. coli against T7, T4, P1-vir, and Lambda-vir.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv GAPS6 GAPS6 2 2 GAPS6__GAPS6a, GAPS6__GAPS6b The DefenseFinder rules table models GAPS6 as a two-profile system requiring GAPS6__GAPS6a and GAPS6__GAPS6b.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | GAPS6__GAPS6a | GAPS6__GAPS6a | GAPS6 | Custom | 20 | The DefenseFinder HMM inventory records GAPS6__GAPS6a under the GAPS6 system namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | GAPS6__GAPS6b | GAPS6__GAPS6b | GAPS6 | Custom | 20 | The DefenseFinder HMM inventory records GAPS6__GAPS6b under the GAPS6 system namespace.
T7, T4, P1-vir, and lambda-vir protection confers GAPS6 system METPO:2007700
Protection against T7, T4, P1-vir, and lambda-vir realizes the GAPS6 system trait.
- https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.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_248387294.1'>WP_248387294.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_248387295.1'>WP_248387295.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir The DefenseFinder experimental-validation diagram links Mahata et al. to a Vibrio parahaemolyticus GAPS6 source locus expressed in E. coli against T7, T4, P1-vir, and Lambda-vir.
GAPS6 system is a phage defense system rdfs:subClassOf
GAPS6 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 GAPS6 | 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 GAPS6 system to the Mahata et al. preprint.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv GAPS6 GAPS6 2 2 GAPS6__GAPS6a, GAPS6__GAPS6b The DefenseFinder rules table models GAPS6 as a two-profile system requiring GAPS6__GAPS6a and GAPS6__GAPS6b.

Provenance

Identifier source: TraitMech local identifier
Definition source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md

Parent traits (1)

phage defense system traitmech:000209

Synonyms (3)

GAPS6 EXACT_SYNONYM · https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md
GAPS6__GAPS6a RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
GAPS6__GAPS6b 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 GAPS6 natural host breadth, GAPS6a activity, GAPS6b sufficiency and trigger specificity, and exact GAPS6a/GAPS6b profile-to-protein correspondence before minting narrower GAPS6 mechanism traits.

KNOWLEDGE GAP OPEN gaps6-mechanism-gap · raised by codex · 2026-09-26

Attached to causal_graphs#gaps6_locus_restricts_phages

Mahata et al. support GAPS6 as a GMT-encoded anti-phage defense system that protects E. coli against T7, T4, P1-vir, and lambda-vir when expressed from a Vibrio parahaemolyticus locus, and DefenseFinder represents GAPS6 as a two-profile system. Natural host breadth, GAPS6a activity, GAPS6b sufficiency, 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/gaps6.md
GAPS6 is composed of two proteins, [GAPS6a](https://www.ncbi.nlm.nih.gov/protein/WP_248387294.1/) and [GAPS6b](https://www.ncbi.nlm.nih.gov/protein/WP_248387295.1/). These two proteins are encoded together in diverse Gram-negative bacteria.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md
GAPS6b is essential for the defense phenotype, however it is not known whether GAPS6b could be sufficient.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.md
GAPS6b is composed of TPR repeats at the N-terminus, possibly allowing ligand binding and a predicted RNAse domain (PINc, PF08745.14) at the C-terminus. PINc domains have been implicated as toxins in bacterial toxin-antitoxin modules :ref{doi=10.1093/protein/gzq081}. The PINc domain is required for the anti-phage defense activity of GAPS6.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/gaps6.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_248387294.1'>WP_248387294.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_248387295.1'>WP_248387295.1</a>] --> Expressed_0[Escherichia coli] Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
GAPS6 GAPS6 2 2 GAPS6__GAPS6a, GAPS6__GAPS6b
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| GAPS6__GAPS6a | GAPS6__GAPS6a | GAPS6 | Custom | 20 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| GAPS6__GAPS6b | GAPS6__GAPS6b | GAPS6 | Custom | 20 |

Curation history

2026-09-26T11:58:13Z · MINTED_TRAITMECH_ID · codex
Minted GAPS6 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_v258.
2026-09-26T11:58:14Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed GAPS6 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 Escherichia coli example, but not a direct native microbial isolate exemplar with experimentally verified endogenous GAPS6 activity. No paid research was used.