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content/3.defense-systems/gao_her.md
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# Gao_Her
## Example of genomic structure
The Gao_Her system have been describe in a total of 2 subsystems.
A total of 2 subsystems have been described for the Gao_Her system.
Here is some example found in the RefSeq database:
Here is some examples found in the RefSeq database:
![gao_her](/gao_her/Gao_Her_DUF.svg){max-width=750px}
![gao_her_duf](/gao_her/Gao_Her_DUF.svg){max-width=750px}
Gao_Her_DUF subsystem in the genome of *Enterobacter roggenkampii* (GCF_014524505.1) is composed of 2 proteins: DUF4297 (WP_188074283.1)and, HerA_DUF (WP_063614829.1).
The Gao_Her_DUF system in *Escherichia coli* (GCF_023657935.1, NZ_CP098183) is composed of 2 proteins DUF4297 (WP_064484828.1) HerA_DUF (WP_064484829.1)
![gao_her](/gao_her/Gao_Her_SIR.svg){max-width=750px}
![gao_her_sir](/gao_her/Gao_Her_SIR.svg){max-width=750px}
Gao_Her_SIR subsystem in the genome of *Escherichia coli* (GCF_012221565.1) is composed of 2 proteins: SIR2 (WP_167839366.1)and, HerA_SIR2 (WP_021577682.1).
The Gao_Her_SIR system in *Xanthomonas citri* (GCF_018831325.1, NZ_CP029270) is composed of 2 proteins SIR2 (WP_046831681.1) HerA_SIR2 (WP_046831680.1)
## Distribution of the system among prokaryotes
The Gao_Her system is present in a total of 127 different species.
Among the 22,803 complete genomes of RefSeq, the Gao_Her is detected in 231 genomes (1.01 %).
Among the 22k complete genomes of RefSeq, this system is present in 233 genomes (1.0 %).
The system was detected in 134 different species.
![gao_her](/gao_her/Distribution_Gao_Her.svg){max-width=750px}
*Proportion of genome encoding the Gao_Her system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.*
Proportion of genome encoding the Gao_Her system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
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content/3.defense-systems/gao_hhe.md
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Activator: Unknown
Effector: Unknown
PFAM: PF04480, PF13086, PF13087, PF13195, PF18741
contributors:
- Marian Dominguez-Mirazo
relevantAbstracts:
- doi: 10.1126/science.aba0372
---
# Gao_Hhe
## Description
The Gao_hhe system is composed by a single protein. It was predicted through a guilty by association approach independent of domain annotations and validated in a heterologous system :ref{doi=10.1093/nar/gkad317}. It contains a predicted helicase and a Vsr (very short patch repair) endonuclease domain :ref{doi=10.1093/nar/gkad317,10.1128/jvi.00599-23}.
## Molecular mechanisms
As far as we are aware, the molecular mechanism is unknown.
## Example of genomic structure
The Gao_Hhe system is composed of one protein: HheA.
The Gao_Hhe is composed of 1 protein: HheA.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![gao_hhe](/gao_hhe/Gao_Hhe.svg){max-width=750px}
Gao_Hhe system in the genome of *Klebsiella pneumoniae* (GCF_011742415.2) is composed of 1 protein: HheA (WP_021314612.1).
The Gao_Hhe system in *Thioalkalivibrio paradoxus* (GCF_000227685.2, NZ_CP007029) is composed of 1 protein: HheA (WP_006745815.1)
## Distribution of the system among prokaryotes
The Gao_Hhe system is present in a total of 49 different species.
Among the 22,803 complete genomes of RefSeq, the Gao_Hhe is detected in 276 genomes (1.21 %).
Among the 22k complete genomes of RefSeq, this system is present in 279 genomes (1.2 %).
The system was detected in 56 different species.
![gao_hhe](/gao_hhe/Distribution_Gao_Hhe.svg){max-width=750px}
*Proportion of genome encoding the Gao_Hhe system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Gao_Hhe system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
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style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
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## Relevant abstracts
::relevant-abstracts
---
items:
- doi: 10.1126/science.aba0372
---
::
content/3.defense-systems/gao_iet.md
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# Gao_Iet
## Example of genomic structure
The Gao_Iet system is composed of 2 proteins: IetS and, IetA.
The Gao_Iet is composed of 2 proteins: IetA and IetS.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![gao_iet](/gao_iet/Gao_Iet.svg){max-width=750px}
Gao_Iet system in the genome of *Escherichia coli* (GCF_014169855.1) is composed of 2 proteins: IetS (WP_001551050.1)and, IetA (WP_000385105.1).
The Gao_Iet system in *Salmonella sp. SJTUF14076* (GCF_015534835.1, NZ_CP064674) is composed of 2 proteins IetA (WP_023226994.1) IetS (WP_024148175.1)
## Distribution of the system among prokaryotes
The Gao_Iet system is present in a total of 189 different species.
Among the 22,803 complete genomes of RefSeq, the Gao_Iet is detected in 389 genomes (1.71 %).
Among the 22k complete genomes of RefSeq, this system is present in 436 genomes (1.9 %).
The system was detected in 185 different species.
![gao_iet](/gao_iet/Distribution_Gao_Iet.svg){max-width=750px}
*Proportion of genome encoding the Gao_Iet system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Gao_Iet system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
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content/3.defense-systems/gao_mza.md
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Activator: Unknown
Effector: Unknown
PFAM: PF00023, PF04542, PF04545, PF10592, PF10593, PF13589, PF13606, PF14390
contributors:
- Hugo Vaysset
relevantAbstracts:
- doi: 10.1126/science.aba0372
---
# Gao_Mza
## Description
Mza (MutL, Z1, DUF, AIPR) is a defense system composed of five proteins. Its antiphage activity was assessed by heterologous expression in *E. coli* against phages T2, T4, T5, lambda and M13 (ssDNA phage) :ref{doi=10.1126/science.aba0372}.
## Molecular mechanism
As far as we are aware, the molecular mechanism is unknown.
## Example of genomic structure
The Gao_Mza system is composed of 5 proteins: MzaB, MzaC, MzaA, MzaD and, MzaE.
The Gao_Mza is composed of 5 proteins: MzaA, MzaB, MzaC, MzaD and MzaE.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![gao_mza](/gao_mza/Gao_Mza.svg){max-width=750px}
Gao_Mza system in the genome of *Enterobacter roggenkampii* (GCF_023023065.1) is composed of 5 proteins: MzaE (WP_045418899.1), MzaD (WP_045418897.1), MzaC (WP_025912266.1), MzaB (WP_045418895.1)and, MzaA (WP_045418893.1).
The Gao_Mza system in *Massilia sp. Se16.2.3* (GCF_014171595.1, NZ_CP050451) is composed of 6 proteins MzaA (WP_182990577.1) MzaB (WP_229425381.1) MzaC (WP_182990578.1) MzaD (WP_182990579.1) MzaE (WP_182990580.1) MzaE (WP_182990581.1)
## Distribution of the system among prokaryotes
The Gao_Mza system is present in a total of 57 different species.
Among the 22,803 complete genomes of RefSeq, the Gao_Mza is detected in 68 genomes (0.3 %).
Among the 22k complete genomes of RefSeq, this system is present in 99 genomes (0.4 %).
The system was detected in 32 different species.
![gao_mza](/gao_mza/Distribution_Gao_Mza.svg){max-width=750px}
*Proportion of genome encoding the Gao_Mza system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Gao_Mza system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
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style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
## Relevant abstracts
::relevant-abstracts
---
items:
- doi: 10.1126/science.aba0372
---
::
content/3.defense-systems/gao_ppl.md
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# Gao_Ppl
## Example of genomic structure
The Gao_Ppl system is composed of one protein: PplA.
The Gao_Ppl is composed of 1 protein: PplA.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![gao_ppl](/gao_ppl/Gao_Ppl.svg){max-width=750px}
Gao_Ppl system in the genome of *Klebsiella pneumoniae* (GCF_002787755.1) is composed of 1 protein: PplA (WP_015059139.1).
The Gao_Ppl system in *Enterobacter sp. E76* (GCF_008931465.1, NZ_CP042499) is composed of 1 protein: PplA (WP_032676599.1)
## Distribution of the system among prokaryotes
The Gao_Ppl system is present in a total of 106 different species.
Among the 22,803 complete genomes of RefSeq, the Gao_Ppl is detected in 276 genomes (1.21 %).
Among the 22k complete genomes of RefSeq, this system is present in 364 genomes (1.6 %).
The system was detected in 104 different species.
![gao_ppl](/gao_ppl/Distribution_Gao_Ppl.svg){max-width=750px}
*Proportion of genome encoding the Gao_Ppl system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Gao_Ppl system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
content/3.defense-systems/gao_qat.md
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# Gao_Qat
## Example of genomic structure
The Gao_Qat system is composed of 4 proteins: QatA, QatB, QatC and, QatD.
The Gao_Qat is composed of 4 proteins: QatA, QatB, QatC and QatD.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![gao_qat](/gao_qat/Gao_Qat.svg){max-width=750px}
Gao_Qat system in the genome of *Raoultella ornithinolytica* (GCF_002214825.1) is composed of 4 proteins: QatA (WP_088883811.1), QatB (WP_127146083.1), QatC (WP_088883813.1)and, QatD (WP_088883814.1).
The Gao_Qat system in *Ralstonia wenshanensis* (GCF_021173085.1, NZ_CP076413) is composed of 4 proteins QatA (WP_232041545.1) QatB (WP_232041546.1) QatC (WP_232041547.1) QatD (WP_232043074.1)
## Distribution of the system among prokaryotes
The Gao_Qat system is present in a total of 246 different species.
Among the 22,803 complete genomes of RefSeq, the Gao_Qat is detected in 621 genomes (2.72 %).
Among the 22k complete genomes of RefSeq, this system is present in 645 genomes (2.8 %).
The system was detected in 267 different species.
![gao_qat](/gao_qat/Distribution_Gao_Qat.svg){max-width=750px}
*Proportion of genome encoding the Gao_Qat system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Gao_Qat system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
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content/3.defense-systems/gao_rl.md
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## Example of genomic structure
The Gao_RL system is composed of 4 proteins: RL_D, RL_C, RL_B and, RL_A.
The Gao_RL is composed of 4 proteins: RL_A, RL_B, RL_C and RL_D.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![gao_rl](/gao_rl/Gao_RL.svg){max-width=750px}
Gao_RL system in the genome of *Morganella morganii* (GCF_020790175.1) is composed of 4 proteins: RL_D (WP_064483389.1), RL_C (WP_064483388.1), RL_B (WP_064483387.1)and, RL_A (WP_064483386.1).
The Gao_RL system in *Methylocystis heyeri* (GCF_004802635.2, NZ_CP046053) is composed of 4 proteins RL_A (WP_136498122.1) RL_B (WP_136498123.1) RL_C (WP_154331773.1) RL_D (WP_136498124.1)
## Distribution of the system among prokaryotes
The Gao_RL system is present in a total of 77 different species.
Among the 22,803 complete genomes of RefSeq, the Gao_RL is detected in 131 genomes (0.57 %).
Among the 22k complete genomes of RefSeq, this system is present in 133 genomes (0.6 %).
The system was detected in 74 different species.
![gao_rl](/gao_rl/Distribution_Gao_RL.svg){max-width=750px}
*Proportion of genome encoding the Gao_RL system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Gao_RL system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
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content/3.defense-systems/gao_tery.md
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# Gao_TerY
## Example of genomic structure
The Gao_TerY system is composed of 3 proteins: TerYC, TerYB and, TerYA.
The Gao_TerY is composed of 3 proteins: TerYA, TerYB and TerYC.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![gao_tery](/gao_tery/Gao_TerY.svg){max-width=750px}
Gao_TerY system in the genome of *Burkholderia contaminans* (GCF_018223785.1) is composed of 3 proteins: TerYA (WP_039364687.1), TerYB (WP_039364686.1)and, TerYC (WP_039364684.1).
The Gao_TerY system in *Arachidicoccus terrestris* (GCF_020042345.1, NZ_CP083387) is composed of 3 proteins TerYA (WP_224070248.1) TerYB (WP_224070249.1) TerYC (WP_224070250.1)
## Distribution of the system among prokaryotes
The Gao_TerY system is present in a total of 69 different species.
Among the 22,803 complete genomes of RefSeq, the Gao_TerY is detected in 126 genomes (0.55 %).
Among the 22k complete genomes of RefSeq, this system is present in 126 genomes (0.6 %).
The system was detected in 74 different species.
![gao_tery](/gao_tery/Distribution_Gao_TerY.svg){max-width=750px}
*Proportion of genome encoding the Gao_TerY system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Gao_TerY system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
content/3.defense-systems/gao_tmn.md
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Sensor: Unknown
Activator: Unknown
Effector: Unknown
contributors:
- Lucas Paoli
relevantAbstracts:
- doi: 10.1126/science.aba0372
---
# Gao_Tmn
## Description
The Gao_Tmn system is named after the first author of the first paper describing it :ref{doi=10.1126/science.aba0372} and contains the description of the gene identified: a transmembrane NTPase.
## Molecular mechanisms
As far as we are aware, the molecular mechanism is unknown.
## Example of genomic structure
The Gao_Tmn system is composed of one protein: TmnA.
The Gao_Tmn is composed of 1 protein: TmnA.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![gao_tmn](/gao_tmn/Gao_Tmn.svg){max-width=750px}
Gao_Tmn system in the genome of *Salmonella enterica* (GCF_006384195.1) is composed of 1 protein: TmnA (WP_130525902.1).
The Gao_Tmn system in *Pectobacterium carotovorum* (GCF_009931215.1, NZ_CP034237) is composed of 1 protein: TmnA (WP_161509209.1)
## Distribution of the system among prokaryotes
The Gao_Tmn system is present in a total of 82 different species.
Among the 22,803 complete genomes of RefSeq, the Gao_Tmn is detected in 394 genomes (1.73 %).
Among the 22k complete genomes of RefSeq, this system is present in 414 genomes (1.8 %).
The system was detected in 84 different species.
![gao_tmn](/gao_tmn/Distribution_Gao_Tmn.svg){max-width=750px}
*Proportion of genome encoding the Gao_Tmn system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Gao_Tmn system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
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style Title4 fill:none,stroke:none,stroke-width:none
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## Relevant abstracts
::relevant-abstracts
---
items:
- doi: 10.1126/science.aba0372
---
::
content/3.defense-systems/gao_upx.md
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As far as we are aware, the molecular mechanism is unknown.
## Example of genomic structure
The Gao_Upx system is composed of one protein: UpxA.
The Gao_Upx is composed of 1 protein: UpxA.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![gao_upx](/gao_upx/Gao_Upx.svg){max-width=750px}
Gao_Upx system in the genome of *Salmonella sp.* (GCF_020268625.1) is composed of 1 protein: UpxA (WP_060647174.1).
The Gao_Upx system in *Serratia sp. JSRIV001* (GCF_019968745.1, NZ_CP074147) is composed of 1 protein: UpxA (WP_223499068.1)
## Distribution of the system among prokaryotes
The Gao_Upx system is present in a total of 31 different species.
Among the 22,803 complete genomes of RefSeq, the Gao_Upx is detected in 39 genomes (0.17 %).
Among the 22k complete genomes of RefSeq, this system is present in 39 genomes (0.2 %).
The system was detected in 33 different species.
![gao_upx](/gao_upx/Distribution_Gao_Upx.svg){max-width=750px}
*Proportion of genome encoding the Gao_Upx system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Gao_Upx system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
content/3.defense-systems/gaps1.md
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doi: 10.1101/2023.03.28.534373
abstract: |
Bacteria are found in ongoing conflicts with rivals and predators, which lead to an evolutionary arms race and the development of innate and adaptive immune systems. Although diverse bacterial immunity mechanisms have been recently identified, many remain unknown, and their dissemination within bacterial populations is poorly understood. Here, we describe a widespread genetic element, defined by the Gamma-Mobile-Trio (GMT) proteins, that serves as a mobile bacterial weapons armory. We show that GMT islands have cargo comprising various combinations of secreted antibacterial toxins, anti-phage defense systems, and secreted anti-eukaryotic toxins. This finding led us to identify four new anti-phage defense systems encoded within GMT islands and reveal their active domains and mechanisms of action. We also find the phage protein that triggers the activation of one of these systems. Thus, we can identify novel toxins and defense systems by investigating proteins of unknown function encoded within GMT islands. Our findings imply that the concept of "defense islands" may be broadened to include other types of bacterial innate immunity mechanisms, such as antibacterial and anti-eukaryotic toxins that appear to stockpile with anti-phage defense systems within GMT weapon islands.
Sensor: Phage-protein sensing
Activator: Unknown
Effector: Unknown
contributors:
- Marian Dominguez-Mirazo
relevantAbstracts:
- doi: 10.1101/2023.03.28.534373
---
# GAPS1
## To do
## Description
The GAPS1 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. GAPS1 contains a predicted nuclease domain whose mutation prevents defense activity, however DNA degradation was not detected in targeted phage :ref{doi=10.1101/2023.03.28.534373}. Mutations in the folded capsid protein (Gp10) of phage T7 result in a escape phenotype, with GAPS1 shown to be activated upon Gp10 expression, suggesting activation of the system at late stages of the infection cycle :ref{doi=10.1101/2023.03.28.534373}.
## Molecular mechanisms
The molecular mechanism remains to be fully elucidated.
## Example of genomic structure
The GAPS1 is composed of 1 protein: GAPS1.
Here is an example found in the RefSeq database:
![gaps1](/gaps1/GAPS1.svg){max-width=750px}
The GAPS1 system in *Hydrogenophaga sp. BPS33* (GCF_009859475.1, NZ_CP044549) is composed of 1 protein: GAPS1 (WP_159591124.1)
## Distribution of the system among prokaryotes
Among the 22,803 complete genomes of RefSeq, the GAPS1 is detected in 434 genomes (1.9 %).
The system was detected in 56 different species.
![gaps1](/gaps1/Distribution_GAPS1.svg){max-width=750px}
Proportion of genome encoding the GAPS1 system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
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style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
## Relevant abstract
::relevant-abstracts
---
items:
- doi: 10.1101/2023.03.28.534373
---
::
content/3.defense-systems/gaps2.md
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## To do
## Example of genomic structure
The GAPS2 is composed of 1 protein: GAPS2.
Here is an example found in the RefSeq database:
![gaps2](/gaps2/GAPS2.svg){max-width=750px}
The GAPS2 system in *Mannheimia sp. USDA-ARS-USMARC-1261* (GCF_000521605.1, NZ_CP006942) is composed of 1 protein: GAPS2 (WP_025236539.1)
## Distribution of the system among prokaryotes
Among the 22,803 complete genomes of RefSeq, the GAPS2 is detected in 725 genomes (3.18 %).
The system was detected in 208 different species.
![gaps2](/gaps2/Distribution_GAPS2.svg){max-width=750px}
Proportion of genome encoding the GAPS2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
### GAPS2
......
content/3.defense-systems/gaps4.md
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## To do
## Example of genomic structure
The GAPS4 is composed of 2 proteins: GAPS4a and GAPS4b.
Here is an example found in the RefSeq database:
![gaps4](/gaps4/GAPS4.svg){max-width=750px}
The GAPS4 system in *Hafnia alvei* (GCF_902387815.1, NZ_LR699008) is composed of 2 proteins GAPS4a (WP_111329122.1) GAPS4b (WP_111329123.1)
## Distribution of the system among prokaryotes
Among the 22,803 complete genomes of RefSeq, the GAPS4 is detected in 118 genomes (0.52 %).
The system was detected in 74 different species.
![gaps4](/gaps4/Distribution_GAPS4.svg){max-width=750px}
Proportion of genome encoding the GAPS4 system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
### GAPS4
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content/3.defense-systems/gaps6.md
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## To do
## Example of genomic structure
The GAPS6 is composed of 2 proteins: GAPS6a and GAPS6b.
Here is an example found in the RefSeq database:
![gaps6](/gaps6/GAPS6.svg){max-width=750px}
The GAPS6 system in *Escherichia coli* (GCF_013372365.1, NZ_CP054227) is composed of 2 proteins GAPS6b (WP_096985931.1) GAPS6a (WP_000346990.1)
## Distribution of the system among prokaryotes
Among the 22,803 complete genomes of RefSeq, the GAPS6 is detected in 50 genomes (0.22 %).
The system was detected in 33 different species.
![gaps6](/gaps6/Distribution_GAPS6.svg){max-width=750px}
Proportion of genome encoding the GAPS6 system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
### GAPS6
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content/3.defense-systems/gasdermin.md
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doi: 10.1126/science.abj8432
abstract: |
Gasdermin proteins form large membrane pores in human cells that release immune cytokines and induce lytic cell death. Gasdermin pore formation is triggered by caspase-mediated cleavage during inflammasome signaling and is critical for defense against pathogens and cancer. We discovered gasdermin homologs encoded in bacteria that defended against phages and executed cell death. Structures of bacterial gasdermins revealed a conserved pore-forming domain that was stabilized in the inactive state with a buried lipid modification. Bacterial gasdermins were activated by dedicated caspase-like proteases that catalyzed site-specific cleavage and the removal of an inhibitory C-terminal peptide. Release of autoinhibition induced the assembly of large and heterogeneous pores that disrupted membrane integrity. Thus, pyroptosis is an ancient form of regulated cell death shared between bacteria and animals.
Sensor: Unknown
Sensor: Phage protein
Activator: Unknown
Effector: Membrane disrupting
contributors:
- Aude Bernheim
relevantAbstracts:
- doi: 10.1126/science.abj8432
- doi: 10.1101/2023.05.28.542683
---
# GasderMIN
## Description
Gasdermin proteins were initially discovered in humans. Recently there were shown to be present in multiple bacteria, where they are almost always encoded in an operon together with a protease. The experimental validation of the antiphage activity of bacterial gasdermins was demonstrated through the heterologous experession of a 4-genes operon from Lysobacter in E. coli :ref{doi=10.1126/science.abj8432} :ref{doi=10.1101/2023.05.28.542683}.
## Molecular Mechanism
Akin to their human counterparts, bacterial gasdermins encode a C-terminal inhibotry domain. Following phage infection, proteases associated to bacterial gasdermin cleave this domain triggering oligomerization of gasdermins into large, membrane-breaching pores :ref{doi=10.1126/science.abj8432} leading to cell death:ref{doi=10.1101/2023.05.28.542683}. As such gasdermins containing systems are abortive infection systems. rIIB, a protein allowing T6 to overcome RexAB system was shown to activate gasdermin. It was further shown that CARD domain are also essential in bacterial gasdermins defense :ref{doi=10.1101/2023.05.28.542683}.
## Example of genomic structure
The GasderMIN system is composed of one protein: bGSDM.
The GasderMIN is composed of 1 protein: bGSDM.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![gasdermin](/gasdermin/GasderMIN.svg){max-width=750px}
GasderMIN system in the genome of *Rhodoplanes sp.* (GCF_001579845.1) is composed of 1 protein: bGSDM (WP_068019379.1).
The GasderMIN system in *Flavobacterium johnsoniae* (GCF_000016645.1, NC_009441) is composed of 1 protein: bGSDM (WP_012023900.1)
## Distribution of the system among prokaryotes
The GasderMIN system is present in a total of 25 different species.
Among the 22,803 complete genomes of RefSeq, the GasderMIN is detected in 27 genomes (0.12 %).
Among the 22k complete genomes of RefSeq, this system is present in 29 genomes (0.1 %).
The system was detected in 26 different species.
![gasdermin](/gasdermin/Distribution_GasderMIN.svg){max-width=750px}
*Proportion of genome encoding the GasderMIN system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the GasderMIN system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
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## Relevant abstracts
::relevant-abstracts
---
items:
- doi: 10.1126/science.abj8432
---
::
content/3.defense-systems/hachiman.md
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## Example of genomic structure
The Hachiman type I system is composed of 2 proteins: HamB and, HamA.
The Hachiman is composed of 2 proteins: HamA and HamB.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![hachiman](/hachiman/Hachiman.svg){max-width=750px}
Hachiman system in the genome of *Mesorhizobium terrae* (GCF_008727715.1) is composed of 2 proteins: HamA_1 (WP_245317480.1)and, HamB (WP_065997554.1).
The Hachiman system in *Vibrio metschnikovii* (GCF_009763925.1, NZ_CP046822) is composed of 2 proteins HamA_1 (WP_158137983.1) HamB (WP_158137986.1)
## Distribution of the system among prokaryotes
The Hachiman system is present in a total of 518 different species.
Among the 22,803 complete genomes of RefSeq, the Hachiman is detected in 1256 genomes (5.51 %).
Among the 22k complete genomes of RefSeq, this system is present in 1361 genomes (6.0 %).
The system was detected in 541 different species.
![hachiman](/hachiman/Distribution_Hachiman.svg){max-width=750px}
*Proportion of genome encoding the Hachiman system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Hachiman system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
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content/3.defense-systems/hna.md
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## To do
## Example of genomic structure
The Hna is composed of 1 protein: Hna.
Here is an example found in the RefSeq database:
![hna](/hna/Hna.svg){max-width=750px}
The Hna system in *Aggregatimonas sangjinii* (GCF_005943945.1, NZ_CP040710) is composed of 1 protein: Hna (WP_138852947.1)
## Distribution of the system among prokaryotes
Among the 22,803 complete genomes of RefSeq, the Hna is detected in 493 genomes (2.16 %).
The system was detected in 305 different species.
![hna](/hna/Distribution_Hna.svg){max-width=750px}
Proportion of genome encoding the Hna system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
### Hna
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# ISG15-like
## Example of genomic structure
The ISG15-like system is composed of 4 proteins: BilD, BilC, BilB and, BilA.
The ISG15-like is composed of 4 proteins: BilA, BilB, BilC and BilD.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![isg15-like](/isg15-like/ISG15-like.svg){max-width=750px}
ISG15-like system in the genome of *Rhizobium phaseoli* (GCF_001664285.1) is composed of 4 proteins: BilA (WP_064823699.1), BilB (WP_150124924.1), BilC (WP_150124925.1)and, BilD (WP_190304495.1).
The ISG15-like system in *Caulobacter segnis* (GCF_023935105.1, NZ_CP096040) is composed of 4 proteins BilA (WP_252632187.1) BilB (WP_252632188.1) BilC (WP_252632189.1) BilD (WP_252632190.1)
## Distribution of the system among prokaryotes
The ISG15-like system is present in a total of 28 different species.
Among the 22,803 complete genomes of RefSeq, the ISG15-like is detected in 43 genomes (0.19 %).
Among the 22k complete genomes of RefSeq, this system is present in 43 genomes (0.2 %).
The system was detected in 39 different species.
![isg15-like](/isg15-like/Distribution_ISG15-like.svg){max-width=750px}
*Proportion of genome encoding the ISG15-like system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the ISG15-like system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
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content/3.defense-systems/jukab.md
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## To do
## Example of genomic structure
The JukAB is composed of 2 proteins: JukA and JukB.
Here is an example found in the RefSeq database:
![jukab](/jukab/JukAB.svg){max-width=750px}
The JukAB system in *Kosakonia oryzae* (GCF_020544365.1, NZ_CP065358) is composed of 2 proteins JukA (WP_064562651.1) JukB (WP_064562654.1)
## Distribution of the system among prokaryotes
Among the 22,803 complete genomes of RefSeq, the JukAB is detected in 133 genomes (0.58 %).
The system was detected in 50 different species.
![jukab](/jukab/Distribution_JukAB.svg){max-width=750px}
Proportion of genome encoding the JukAB system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
### JukAB
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content/3.defense-systems/kiwa.md
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Activator: Unknown
Effector: Unknown
PFAM: PF16162
contributors:
- Lucas Paoli
relevantAbstracts:
- doi: 10.1126/science.aar4120
- doi: 10.1101/2023.02.26.530102
---
# Kiwa
## Description
The Kiwa antiviral defense system was first described in :ref{doi=10.1126/science.aar4120} and further described in :ref{doi=10.1101/2023.02.26.530102}. It is named after one of the divine guardians of the ocean in the Māori traditions. Kiwa is composed of two proteins: KwaA and KwaB.
## Molecular mechanisms
KwaA detects phage infection by detecting the inhibition of the host RNA polymerase by phages. This triggers the reponse by KwaB, which decreases phage DNA replication through a RecBCD-depdendent pathway :ref{doi=10.1101/2023.02.26.530102}.
## Example of genomic structure
The Kiwa system is composed of 2 proteins: KwaA and, KwaB.
The Kiwa is composed of 2 proteins: KwaA and KwaB.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![kiwa](/kiwa/Kiwa.svg){max-width=750px}
Kiwa system in the genome of *Aggregatibacter actinomycetemcomitans* (GCF_001690155.1) is composed of 2 proteins: KwaB (WP_005553122.1)and, KwaA (WP_005540311.1).
The Kiwa system in *Dickeya zeae* (GCF_019464635.1, NZ_CP040817) is composed of 2 proteins KwaA (WP_038908257.1) KwaB_2 (WP_192991081.1)
## Distribution of the system among prokaryotes
The Kiwa system is present in a total of 355 different species.
Among the 22,803 complete genomes of RefSeq, the Kiwa is detected in 1095 genomes (4.8 %).
Among the 22k complete genomes of RefSeq, this system is present in 1104 genomes (4.8 %).
The system was detected in 382 different species.
![kiwa](/kiwa/Distribution_Kiwa.svg){max-width=750px}
*Proportion of genome encoding the Kiwa system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Kiwa system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
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style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
## Relevant abstracts
::relevant-abstracts
---
items:
- doi: 10.1126/science.aar4120
---
::