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content/3.defense-systems/isg15-like.md
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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
......
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
......@@ -76,13 +90,4 @@ end
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
---
::
content/3.defense-systems/lamassu-fam.md
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## Example of genomic structure
The majority of the Lamassu-Fam systems are composed of 3 proteins: LmuA, LmuB and, an accessory LmuC proteins.
LmuA is the effector and encode for different domains depending on the subsystem.
Here is an example of a Lamassu-Fam_Cap4_nuclease found in the RefSeq database:
A total of 11 subsystems have been described for the Lamassu-Fam system.
![lamassu-fam](/lamassu-fam/Lamassu-Fam_Cap4_nuclease.svg){max-width=750px}
Here is some examples found in the RefSeq database:
Lamassu-Fam_Cap4_nuclease subsystem in the genome of *Pseudomonas sp.* (GCF_016925675.1) is composed of 3 proteins: LmuB_SMC_Hydrolase_protease (WP_205519025.1), LmuC_acc_Cap4_nuclease (WP_205478326.1)and, LmuA_effector_Cap4_nuclease_II (WP_205478325.1).
![lamassu-amidase](/lamassu-fam/Lamassu-Amidase.svg){max-width=750px}
![lamassu-fam](/lamassu-fam/Lamassu-Fam_Mrr.svg){max-width=750px}
The Lamassu-Amidase system in *Variovorax sp. PBL-H6* (GCF_901827155.1, NZ_LR594659) is composed of 2 proteins LmuA_effector_Amidase (WP_162575880.1) LmuB_SMC_Amidase (WP_162575881.1)
Lamassu-Fam_Mrr subsystem in the genome of *Escherichia coli* (GCF_011404895.1) is composed of 2 proteins: LmuA_effector_Mrr (WP_044864610.1)and, LmuB_SMC_Cap4_nuclease_II (WP_226199836.1).
![lamassu-cap4_nuclease](/lamassu-fam/Lamassu-Cap4_nuclease.svg){max-width=750px}
![lamassu-fam](/lamassu-fam/Lamassu-Fam_Hydrolase.svg){max-width=750px}
The Lamassu-Cap4_nuclease system in *Opitutus terrae* (GCF_000019965.1, NC_010571) is composed of 3 proteins LmuA_effector_Cap4_nuclease_II (WP_012377261.1) LmuC_acc_Lipase (WP_012377262.1) LmuB_SMC_Lipase (WP_012377263.1)
Lamassu-Fam_Hydrolase subsystem in the genome of *Caldisphaera lagunensis* (GCF_000317795.1) is composed of 2 proteins: LmuA_effector_Hydrolase (WP_015232255.1)and, LmuB_SMC_Hydrolase_protease (WP_015232260.1).
![lamassu-fmo](/lamassu-fam/Lamassu-FMO.svg){max-width=750px}
![lamassu-fam](/lamassu-fam/Lamassu-Fam_Lipase.svg){max-width=750px}
The Lamassu-FMO system in *Mesorhizobium sp. B2-1-8* (GCF_006442545.2, NZ_CP083952) is composed of 3 proteins LmuA_effector_FMO (WP_181178269.1) LmuC_acc_FMO (WP_140755520.1) LmuB_SMC_FMO (WP_181178271.1)
Lamassu-Fam_Lipase subsystem in the genome of *Bradyrhizobium elkanii* (GCF_012871055.1) is composed of 2 proteins: LmuA_effector_Lipase (WP_172647146.1)and, LmuB_SMC_Lipase (WP_172647148.1).
![lamassu-hydrolase_protease](/lamassu-fam/Lamassu-Hydrolase_Protease.svg){max-width=750px}
![lamassu-fam](/lamassu-fam/Lamassu-Fam_Hydrolase_protease.svg){max-width=750px}
The Lamassu-Hydrolase_Protease system in *Deefgea piscis* (GCF_013284055.1, NZ_CP054143) is composed of 4 proteins LmuA_effector_Hydrolase (WP_173533336.1) LmuA_effector_Protease (WP_173533337.1) LmuC_acc_hydrolase_protease (WP_173533338.1) LmuB_SMC_Hydrolase_protease (WP_173533339.1)
Lamassu-Fam_Hydrolase_protease subsystem in the genome of *Klebsiella pneumoniae* (GCF_022453565.1) is composed of 3 proteins: LmuB_SMC_Cap4_nuclease_II (WP_023301569.1), LmuA_effector_Protease (WP_023301563.1)and, LmuA_effector_Hydrolase (WP_023301562.1).
![lamassu-hypothetical](/lamassu-fam/Lamassu-Hypothetical.svg){max-width=750px}
![lamassu-fam](/lamassu-fam/Lamassu-Fam_Hypothetical.svg){max-width=750px}
The Lamassu-Hypothetical system in *Dehalococcoides mccartyi* (GCF_002007905.1, NZ_CP019866) is composed of 3 proteins LmuA_effector_hypothetical (WP_077975422.1) LmuC_acc_hypothetical (WP_077975423.1) LmuB_SMC_hypothetical (WP_077975424.1)
Lamassu-Fam_Hypothetical subsystem in the genome of *Streptococcus constellatus* (GCF_016127875.1) is composed of 2 proteins: LmuB_SMC_Cap4_nuclease_II (WP_198458038.1)and, LmuA_effector_hypothetical (WP_198458040.1).
![lamassu-lipase](/lamassu-fam/Lamassu-Lipase.svg){max-width=750px}
![lamassu-fam](/lamassu-fam/Lamassu-Fam_Protease.svg){max-width=750px}
The Lamassu-Lipase system in *Klebsiella michiganensis* (GCF_022869885.1, NZ_CP094999) is composed of 3 proteins LmuB_SMC_Lipase (WP_016157240.1) LmuC_acc_Lipase (WP_032931759.1) LmuA_effector_Lipase (WP_042945865.1)
Lamassu-Fam_Protease subsystem in the genome of *Azospirillum brasilense* (GCF_022023855.1) is composed of 2 proteins: LmuA_effector_Protease (WP_237905456.1)and, LmuB_SMC_Cap4_nuclease_II (WP_237905457.1).
![lamassu-mrr](/lamassu-fam/Lamassu-Mrr.svg){max-width=750px}
![lamassu-fam](/lamassu-fam/Lamassu-Fam_PDDEXK.svg){max-width=750px}
The Lamassu-Mrr system in *Agrobacterium tumefaciens* (GCF_022760295.1, NZ_CP092895) is composed of 3 proteins LmuA_effector_Mrr (WP_223215665.1) LmuC_acc_Mrr (WP_220318798.1) LmuB_SMC_Mrr (WP_220318797.1)
Lamassu-Fam_PDDEXK subsystem in the genome of *Janthinobacterium sp.* (GCF_000013625.1) is composed of 2 proteins: LmuA_effector_PDDEXK (WP_012078862.1)and, LmuB_SMC_Cap4_nuclease_II (WP_012078864.1).
![lamassu-pddexk](/lamassu-fam/Lamassu-PDDEXK.svg){max-width=750px}
![lamassu-fam](/lamassu-fam/Lamassu-Fam_Sir2.svg){max-width=750px}
The Lamassu-PDDEXK system in *Corynebacterium pseudodiphtheriticum* (GCF_023509295.1, NZ_CP091864) is composed of 3 proteins LmuC_acc_PDDEXK (WP_249620350.1) LmuB_SMC_PDDEXK (WP_249620351.1) LmuA_effector_PDDEXK (WP_249620352.1)
Lamassu-Fam_Sir2 subsystem in the genome of *Paenibacillus polymyxa* (GCF_022492955.1) is composed of 4 proteins: LmuB_SMC_Cap4_nuclease_II (WP_240753063.1), LmuB_SMC_Sir2 (WP_240753064.1), LmuC_acc_Sir2 (WP_240753066.1)and, LmuA_effector_Sir2 (WP_240753072.1).
![lamassu-protease](/lamassu-fam/Lamassu-Protease.svg){max-width=750px}
The Lamassu-Protease system in *Enterococcus hirae* (GCF_014218175.1, NZ_CP042289) is composed of 3 proteins LmuA_effector_Protease (WP_034866244.1) LmuC_acc_hydrolase_protease (WP_181916367.1) LmuB_SMC_Hydrolase_protease (WP_034866249.1)
![lamassu-fam](/lamassu-fam/Lamassu-Fam_FMO.svg){max-width=750px}
![lamassu-sir2](/lamassu-fam/Lamassu-Sir2.svg){max-width=750px}
Lamassu-Fam_FMO subsystem in the genome of *Acinetobacter johnsonii* (GCF_021496365.1) is composed of 2 proteins: LmuA_effector_FMO (WP_234965678.1)and, LmuB_SMC_FMO (WP_234965680.1).
![lamassu-fam](/lamassu-fam/Lamassu-Fam_Amidase.svg){max-width=750px}
Lamassu-Fam_Amidase subsystem in the genome of *Bradyrhizobium arachidis* (GCF_015291705.1) is composed of 2 proteins: LmuA_effector_Amidase (WP_143130692.1)and, LmuB_SMC_Amidase (WP_092217687.1).
The Lamassu-Sir2 system in *Enterococcus faecalis* (GCF_023375525.1, NZ_CP091235) is composed of 3 proteins LmuA_effector_Sir2 (WP_231436660.1) LmuC_acc_Sir2 (WP_231436659.1) LmuB_SMC_Sir2 (WP_231436658.1)
## Distribution of the system among prokaryotes
The Lamassu-Fam system is present in a total of 1189 different species.
Among the 22,803 complete genomes of RefSeq, the Lamassu-Fam is detected in 2867 genomes (12.57 %).
The system was detected in 1220 different species.
Among the 22k complete genomes of RefSeq, this system is present in 3939 genomes (17.3 %).
![lamassu-fam](/lamassu-fam/Distribution_Lamassu-Fam.svg){max-width=750px}
![lamassu-fam](/lamassu-fam/Distribution_Lamassu-Fam.svg){max-width=750}
Proportion of genome encoding the Lamassu-Fam system for the 14 phyla with more than 50 genomes in the RefSeq database.
*Proportion of genome encoding the Lamassu-Fam system for the 14 phyla with more than 50 genomes in the RefSeq database.*
## Structure
......
content/3.defense-systems/lit.md
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# Lit
## Example of genomic structure
The Lit system is composed of one protein: Lit.
The Lit is composed of 1 protein: Lit.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![lit](/lit/Lit.svg){max-width=750px}
Lit system in the genome of *Stenotrophomonas maltophilia* (GCF_012647025.1) is composed of 1 protein: Lit (WP_061201506.1).
The Lit system in *Klebsiella pneumoniae* (GCF_002180175.1, NZ_CP021686) is composed of 1 protein: Lit (WP_223861284.1)
## Distribution of the system among prokaryotes
The Lit system is present in a total of 193 different species.
Among the 22,803 complete genomes of RefSeq, the Lit is detected in 222 genomes (0.97 %).
Among the 22k complete genomes of RefSeq, this system is present in 455 genomes (2.0 %).
The system was detected in 78 different species.
![lit](/lit/Distribution_Lit.svg){max-width=750px}
*Proportion of genome encoding the Lit system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Lit system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
content/3.defense-systems/mads.md
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## To do
## Example of genomic structure
The MADS is composed of 8 proteins: mad1, mad2, mad3, mad4, mad5, mad6, mad7 and mad8.
Here is an example found in the RefSeq database:
![mads](/mads/MADS.svg){max-width=750px}
The MADS system in *Pseudomonas otitidis* (GCF_019879085.1, NZ_CP082244) is composed of 8 proteins mad1 (WP_058876992.1) mad2 (WP_208273447.1) mad3 (WP_208273444.1) mad4 (WP_208273442.1) mad5 (WP_208273440.1) mad6 (WP_208273438.1) mad7 (WP_208273430.1) mad8 (WP_233473447.1)
## Distribution of the system among prokaryotes
Among the 22,803 complete genomes of RefSeq, the MADS is detected in 72 genomes (0.32 %).
The system was detected in 63 different species.
![mads](/mads/Distribution_MADS.svg){max-width=750px}
Proportion of genome encoding the MADS system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
### MADS
......
content/3.defense-systems/mazef.md
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## To do
## Example of genomic structure
The MazEF is composed of 2 proteins: MazE and MazF.
Here is an example found in the RefSeq database:
![mazef](/mazef/MazEF.svg){max-width=750px}
The MazEF system in *Pantoea vagans* (GCF_004792415.1, NZ_CP038853) is composed of 2 proteins MazE (WP_135910538.1) MazF (WP_135908176.1)
## Distribution of the system among prokaryotes
Among the 22,803 complete genomes of RefSeq, the MazEF is detected in 4457 genomes (19.55 %).
The system was detected in 993 different species.
![mazef](/mazef/Distribution_MazEF.svg){max-width=750px}
Proportion of genome encoding the MazEF system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Experimental validation
<mermaid>
graph LR;
......
content/3.defense-systems/menshen.md
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Activator: Unknown
Effector: Unknown
PFAM: PF03235, PF05973, PF12476, PF13175, PF13304, PF13476
contributors:
- Alba Herrero del Valle
relevantAbstracts:
- doi: 10.1016/j.chom.2022.09.017
---
# Menshen
## Description
The Menshen system has been identified by Millman et al. as a three protein system NsnA, NsnB and NsnC. Menshen from *Solibacillus silvestris* StLB046 confers resistance in *E. coli* and *B. subtilis* against some phages :ref{doi=10.1016/j.chom.2022.09.017}.
## Molecular mechanism
As far as we are aware, the molecular mechanism is unknown.
## Example of genomic structure
The Menshen system is composed of 3 proteins: NsnA, NsnB and, NsnC_2623244837.
The Menshen is composed of 3 proteins: NsnA, NsnB and NsnC.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![menshen](/menshen/Menshen.svg){max-width=750px}
Menshen system in the genome of *Citrobacter freundii* (GCF_003937345.2) is composed of 3 proteins: NsnA (WP_125363058.1), NsnB (WP_197964486.1)and, NsnC_2617187710 (WP_125363056.1).
The Menshen system in *Streptomyces marincola* (GCF_020410765.1, NZ_CP084541) is composed of 3 proteins NsnA (WP_226077564.1) NsnB (WP_226077566.1) NsnC_2507451963 (WP_226077568.1)
## Distribution of the system among prokaryotes
The Menshen system is present in a total of 247 different species.
Among the 22,803 complete genomes of RefSeq, the Menshen is detected in 430 genomes (1.89 %).
Among the 22k complete genomes of RefSeq, this system is present in 446 genomes (2.0 %).
The system was detected in 263 different species.
![menshen](/menshen/Distribution_Menshen.svg){max-width=750px}
*Proportion of genome encoding the Menshen system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Menshen system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......@@ -93,13 +107,3 @@ end
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: 10.1016/j.chom.2022.09.017
---
::
content/3.defense-systems/mmb_gp29_gp30.md
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## To do
## Example of genomic structure
The MMB_gp29_gp30 is composed of 2 proteins: gp29 and gp30.
Here is an example found in the RefSeq database:
![mmb_gp29_gp30](/mmb_gp29_gp30/MMB_gp29_gp30.svg){max-width=750px}
The MMB_gp29_gp30 system in *Mycolicibacterium insubricum* (GCF_010731615.1, NZ_AP022618) is composed of 2 proteins gp29 (WP_234805905.1) gp30 (WP_083031848.1)
## Distribution of the system among prokaryotes
Among the 22,803 complete genomes of RefSeq, the MMB_gp29_gp30 is detected in 5 genomes (0.02 %).
The system was detected in 4 different species.
![mmb_gp29_gp30](/mmb_gp29_gp30/Distribution_MMB_gp29_gp30.svg){max-width=750px}
Proportion of genome encoding the MMB_gp29_gp30 system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
### MMB_gp29_gp30
......
content/3.defense-systems/mok_hok_sok.md
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# Mok_Hok_Sok
## Example of genomic structure
The Mok_Hok_Sok system is composed of 2 proteins: Mok and, Hok.
The Mok_Hok_Sok is composed of 2 proteins: Mok and Hok.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![mok_hok_sok](/mok_hok_sok/Mok_Hok_Sok.svg){max-width=750px}
Mok_Hok_Sok system in the genome of *Raoultella terrigena* (GCF_015571975.1) is composed of 2 proteins: Hok (WP_227629320.1)and, Mok (WP_227699927.1).
The Mok_Hok_Sok system in *Escherichia fergusonii* (GCF_013819565.1, NZ_CP057221) is composed of 1 protein: Hok (WP_096937776.1)
## Distribution of the system among prokaryotes
The Mok_Hok_Sok system is present in a total of 57 different species.
Among the 22,803 complete genomes of RefSeq, the Mok_Hok_Sok is detected in 1656 genomes (7.26 %).
Among the 22k complete genomes of RefSeq, this system is present in 1687 genomes (7.4 %).
The system was detected in 83 different species.
![mok_hok_sok](/mok_hok_sok/Distribution_Mok_Hok_Sok.svg){max-width=750px}
*Proportion of genome encoding the Mok_Hok_Sok system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Mok_Hok_Sok system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
content/3.defense-systems/mokosh.md
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Activator: Unknown
Effector: Unknown
PFAM: PF00069, PF07714, PF08378, PF13086, PF13087, PF13091, PF13245, PF13604
contributors:
- Marian Dominguez-Mirazo
relevantAbstract:
- doi: 10.1016/j.chom.2022.09.017
- doi: 10.1101/2022.12.12.520048
---
# Mokosh
## Description
The Mokosh system was discovered in *E. coli* by examining clusters of genes enrinched in defense islands :ref{doi=10.1016/j.chom.2022.09.017}. It contains genes with an RNA helicase domain and a predicted phospholipase D domain (PLD) nuclease domain. Mutations in the ATP-binding domain of the helicase, and in the active site of the PLD nuclease disrupt phage defense. The system is divided in two types. Mokosh type I has two genes, one gene containing the RNA helicase domain and an additional serine-threonine kinase domain (STK), and one gene containing the PLD nuclease. Type II Mokosh is formed of a single gene containing both the helicase and nuclease domains. Recent efforts have shown homology between the Mokosh system and human proteins involved in the piRNA pathway, a defense mechanism of animal germlines that prevents expression of transposable elements :ref{doi=10.1101/2022.12.12.520048}. The system gets its name from the goddess protector of women's destiny in Slavic mythology :ref{doi=10.1016/j.chom.2022.09.017}.
## Molecular mechanisms
As far as we are aware, the molecular mechanism is unknown.
## Example of genomic structure
The Mokosh system have been describe in a total of 2 subsystems.
A total of 7 subsystems have been described for the Mokosh system.
Here is some examples found in the RefSeq database:
![mokosh_typeii](/mokosh/Mokosh_TypeII.svg){max-width=750px}
The Mokosh_TypeII system in *Massilia sp. NP310* (GCF_019443485.1, NZ_CP080379) is composed of 1 protein: MkoC (WP_184237977.1)
![mokosh_type_i_a](/mokosh/Mokosh_Type_I_A.svg){max-width=750px}
The Mokosh_Type_I_A system in *Cupriavidus pauculus* (GCF_019931045.1, NZ_CP082863) is composed of 2 proteins MkoA_A (WP_170292610.1) MkoB_A (WP_150981546.1)
Here is some example found in the RefSeq database:
![mokosh_type_i_b](/mokosh/Mokosh_Type_I_B.svg){max-width=750px}
![mokosh](/mokosh/Mokosh_TypeI.svg){max-width=750px}
The Mokosh_Type_I_B system in *Collimonas pratensis* (GCF_001584185.1, NZ_CP013234) is composed of 2 proteins MkoB_B (WP_061945389.1) MkoA_B (WP_061945390.1)
Mokosh_TypeI subsystem in the genome of *Vibrio alginolyticus* (GCF_022343125.1) is composed of 2 proteins: MkoB2 (WP_238970063.1)and, MkoA2 (WP_238970065.1).
![mokosh_type_i_c](/mokosh/Mokosh_Type_I_C.svg){max-width=750px}
![mokosh](/mokosh/Mokosh_TypeII.svg){max-width=750px}
The Mokosh_Type_I_C system in *Klebsiella sp. WP7-S18-CRE-02* (GCF_014169515.1, NZ_AP022189) is composed of 2 proteins MkoB_C (WP_227674162.1) MkoA_C (WP_227674163.1)
Mokosh_TypeII subsystem in the genome of *Shigella flexneri* (GCF_022354205.1) is composed of 1 protein: MkoC (WP_000344091.1).
![mokosh_type_i_d](/mokosh/Mokosh_Type_I_D.svg){max-width=750px}
The Mokosh_Type_I_D system in *Geomonas paludis* (GCF_023221575.1, NZ_CP096574) is composed of 2 proteins MkoA_D (WP_248647094.1) MkoB_D (WP_248647095.1)
![mokosh_type_i_e](/mokosh/Mokosh_Type_I_E.svg){max-width=750px}
The Mokosh_Type_I_E system in *Planococcus faecalis* (GCF_002009235.1, NZ_CP019401) is composed of 2 proteins MkoA_E (WP_078080177.1) MkoB_E (WP_071154541.1)
## Distribution of the system among prokaryotes
The Mokosh system is present in a total of 605 different species.
Among the 22,803 complete genomes of RefSeq, the Mokosh is detected in 1607 genomes (7.05 %).
Among the 22k complete genomes of RefSeq, this system is present in 2540 genomes (11.1 %).
The system was detected in 577 different species.
![mokosh](/mokosh/Distribution_Mokosh.svg){max-width=750px}
*Proportion of genome encoding the Mokosh 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 Mokosh 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: 10.1016/j.chom.2022.09.017
---
::
content/3.defense-systems/mqsrac.md
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## Example of genomic structure
The MqsRAC system is composed of 2 proteins: mqsR and, mqsC.
The MqsRAC is composed of 2 proteins: mqsC and mqsR.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![mqsrac](/mqsrac/MqsRAC.svg){max-width=750px}
MqsRAC system in the genome of *Escherichia coli* (GCF_900636115.1) is composed of 2 proteins: mqsR (WP_024222007.1)and, mqsC (WP_021568458.1).
The MqsRAC system in *Shigella dysenteriae* (GCF_002949935.1, NZ_CP026827) is composed of 2 proteins mqsR (WP_024222007.1) mqsC (WP_157899945.1)
## Distribution of the system among prokaryotes
The MqsRAC system is present in a total of 18 different species.
Among the 22,803 complete genomes of RefSeq, the MqsRAC is detected in 26 genomes (0.11 %).
Among the 22k complete genomes of RefSeq, this system is present in 26 genomes (0.1 %).
The system was detected in 20 different species.
![mqsrac](/mqsrac/Distribution_MqsRAC.svg){max-width=750px}
*Proportion of genome encoding the MqsRAC system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the MqsRAC system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
content/3.defense-systems/nhi.md
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doi: 10.1016/j.chom.2022.03.001
abstract: |
The perpetual arms race between bacteria and their viruses (phages) has given rise to diverse immune systems, including restriction-modification and CRISPR-Cas, which sense and degrade phage-derived nucleic acids. These complex systems rely upon production and maintenance of multiple components to achieve antiphage defense. However, the prevalence and effectiveness of minimal, single-component systems that cleave DNA remain unknown. Here, we describe a unique mode of nucleic acid immunity mediated by a single enzyme with nuclease and helicase activities, herein referred to as Nhi (nuclease-helicase immunity). This enzyme provides robust protection against diverse staphylococcal phages and prevents phage DNA accumulation in cells stripped of all other known defenses. Our observations support a model in which Nhi targets and degrades phage-specific replication intermediates. Importantly, Nhi homologs are distributed in diverse bacteria and exhibit functional conservation, highlighting the versatility of such compact weapons as major players in antiphage defense.
Sensor: Unknown
Activator: Unknown
Effector: Nucleic acid degrading (?)
Sensor: Phage protein sensing
Activator: Direct binding
Effector: Nucleic acid degrading
PFAM: PF01443, PF09848, PF13604
contributors:
- Alba Herrero del Valle
relevantAbstracts:
- doi: 10.1016/j.chom.2022.03.001
- doi: 10.1016/j.chom.2022.09.017
---
# Nhi
## Description
The Nhi (nuclease-helicase immunity) system targets and degrades specific phage DNA replication intermediates :ref{doi=10.1016/j.chom.2022.03.001}. Nayeemul Bari et al. showed that Nhi from *Staphylococcus epidermidis* protects against a diverse panel of staphylococcal phages and Millman et al. showed that a protein Nhi-like (that shares the domain organization with Nhi but not the sequence) from *Bacillus cereus* protects against some Bacillus phages :ref{doi=10.1016/j.chom.2022.03.001,10.1016/j.chom.2022.09.017}.
## Molecular mechanisms
Nhi contains two domains, a nuclease and a helicase domain that are both needed for the anti-phage activity. The nuclease domain has 3′–5′ exonuclease and plasmid nicking activities while the helicase unwinds dsDNA biderctionally. Nhi specifically recognizes phage single-stranded DNA binding proteins (SSB) that cover the phage genome to target this DNA for degradation thanks to its helicase and nuclease domains :ref{doi=10.1016/j.chom.2022.03.001}.
## Example of genomic structure
The Nhi system is composed of one protein: Nhi.
The Nhi is composed of 1 protein: Nhi.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![nhi](/nhi/Nhi.svg){max-width=750px}
Nhi system in the genome of *Enterococcus avium* (GCF_003711125.1) is composed of 1 protein: Nhi (WP_148712513.1).
The Nhi system in *Staphylococcus sp. MZ9* (GCF_018622975.1, NZ_CP076029) is composed of 1 protein: Nhi (WP_045177897.1)
## Distribution of the system among prokaryotes
The Nhi system is present in a total of 56 different species.
Among the 22,803 complete genomes of RefSeq, the Nhi is detected in 199 genomes (0.87 %).
Among the 22k complete genomes of RefSeq, this system is present in 202 genomes (0.9 %).
The system was detected in 61 different species.
![nhi](/nhi/Distribution_Nhi.svg){max-width=750px}
*Proportion of genome encoding the Nhi system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Nhi 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: 10.1016/j.chom.2022.03.001
---
::
content/3.defense-systems/nixi.md
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article:
doi: 10.1101/2021.07.12.452122
doi: 10.1093/nar/gkac002
abstract: |
PLEs are phage parasites integrated into the chromosome of epidemic Vibrio cholerae. In response to infection by its viral host ICP1, PLE excises, replicates and hijacks ICP1 structural components for transduction. Through an unknown mechanism PLE prevents ICP1 from transitioning to rolling circle replication (RCR), a prerequisite for efficient packaging of the viral genome. Here, we characterize a PLE-encoded nuclease, NixI, that blocks phage development likely by nicking ICP1’s genome as it transitions to RCR. NixI-dependent cleavage sites appear in ICP1’s genome during infection of PLE(+) V. cholerae. Purified NixI demonstrates in vitro specificity for sites in ICP1’s genome and NixI activity is enhanced by a putative specificity determinant co-expressed with NixI during phage infection. Importantly, NixI is sufficient to limit ICP1 genome replication and eliminate progeny production. We identify distant NixI homologs in an expanded family of putative phage satellites in Vibrios that lack nucleotide homology to PLEs but nonetheless share genomic synteny with PLEs. More generally, our results reveal a previously unknown mechanism deployed by phage parasites to limit packaging of their viral hosts’ genome and highlight the prominent role of nuclease effectors as weapons in the arms race between antagonizing genomes.
PLEs (phage-inducible chromosomal island-like elements) are phage parasites integrated into the chromosome of epidemic Vibrio cholerae. In response to infection by its viral host ICP1, PLE excises, replicates and hijacks ICP1 structural components for transduction. Through an unknown mechanism, PLE prevents ICP1 from transitioning to rolling circle replication (RCR), a prerequisite for efficient packaging of the viral genome. Here, we characterize a PLE-encoded nuclease, NixI, that blocks phage development likely by nicking ICP1’s genome as it transitions to RCR. NixI-dependent cleavage sites appear in ICP1’s genome during infection of PLE(+) V. cholerae. Purified NixI demonstrates in vitro nuclease activity specifically for sites in ICP1’s genome and we identify a motif that is necessary for NixI-mediated cleavage. Importantly, NixI is sufficient to limit ICP1 genome replication and eliminate progeny production, representing the most inhibitory PLE-encoded mechanism revealed to date. We identify distant NixI homologs in an expanded family of putative phage parasites in vibrios that lack nucleotide homology to PLEs but nonetheless share genomic synteny with PLEs. More generally, our results reveal a previously unknown mechanism deployed by phage parasites to limit packaging of their viral hosts’ genome and highlight the prominent role of nuclease effectors as weapons in the arms race between antagonizing genomes.
Sensor: Unknown
Activator: Unknown
Effector: Nucleic acid degrading
contributors:
- Marian Dominguez Mirazo
relevantAbstracts:
- doi: 10.1093/nar/gkac002
---
# NixI
## Description
Phage-inducible chromosomal island-like elements (PLEs) are chromosomally-integrated phage parasites described in *Vibrio cholerae* :ref{doi=10.7554/eLife.53200}. PLEs excise in response to infection by phage ICP1 and halt its progeny production. PLE halts ICP1 infection by means of redirecting virion packaging and interfiring with ICP1 genome replication :ref{doi=10.1093/nar/gkz1005}. NixI is a PLE-encoded nuclease that nicks the ICP1 genome at specific sites preventing transition to the rolling circle replication (RCR) :ref{doi=10.1093/nar/gkac002}.
## Molecular mechanisms
The NixI endonuclease cleaves the ICP1 genome at the GNAANCTT motif :ref{doi=10.1093/nar/gkac002}. It creates nicks and does not cause double stranded breaks :ref{doi=10.1093/nar/gkac002}.
## Example of genomic structure
The NixI system is composed of 2 proteins: NixI and, Stix.
The NixI is composed of 2 proteins: NixI and Stix.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![nixi](/nixi/NixI.svg){max-width=750px}
NixI system in the genome of *Vibrio cholerae* (GCF_009646135.1) is composed of 2 proteins: NixI (WP_001147214.1)and, Stix (WP_000628297.1).
The NixI system in *Apilactobacillus kunkeei* (GCF_001314945.1, NZ_CP012920) is composed of 1 protein: NixI (WP_158520138.1)
## Distribution of the system among prokaryotes
The NixI system is present in a total of 8 different species.
Among the 22,803 complete genomes of RefSeq, the NixI is detected in 8 genomes (0.04 %).
Among the 22k complete genomes of RefSeq, this system is present in 19 genomes (0.1 %).
The system was detected in 5 different species.
![nixi](/nixi/Distribution_NixI.svg){max-width=750px}
*Proportion of genome encoding the NixI system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the NixI 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: 10.1101/2021.07.12.452122
---
::
content/3.defense-systems/nlr.md
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# NLR
## Example of genomic structure
The NLR system have been describe in a total of 2 subsystems.
A total of 2 subsystems have been described for the NLR system.
Here is some example found in the RefSeq database:
Here is some examples found in the RefSeq database:
![nlr](/nlr/NLR_like_bNACHT01.svg){max-width=750px}
![nlr_like_bnacht01](/nlr/NLR_like_bNACHT01.svg){max-width=750px}
NLR_like_bNACHT01 subsystem in the genome of *Pseudomonas psychrotolerans* (GCF_001913135.1) is composed of 1 protein: NLR_like_bNACHT01 (WP_074528296.1).
The NLR_like_bNACHT01 system in *Colwellia sp. Arc7-D* (GCF_003061515.1, NZ_CP028924) is composed of 1 protein: NLR_like_bNACHT01 (WP_162533747.1)
![nlr](/nlr/NLR_like_bNACHT09.svg){max-width=750px}
![nlr_like_bnacht09](/nlr/NLR_like_bNACHT09.svg){max-width=750px}
NLR_like_bNACHT09 subsystem in the genome of *Escherichia coli* (GCF_900636105.1) is composed of 1 protein: NLR_like_bNACHT09 (WP_089572057.1).
The NLR_like_bNACHT09 system in *Parabacteroides johnsonii* (GCF_020735865.1, NZ_CP085975) is composed of 1 protein: NLR_like_bNACHT09 (WP_009859882.1)
## Distribution of the system among prokaryotes
The NLR system is present in a total of 186 different species.
Among the 22,803 complete genomes of RefSeq, the NLR is detected in 453 genomes (1.99 %).
Among the 22k complete genomes of RefSeq, this system is present in 453 genomes (2.0 %).
The system was detected in 205 different species.
![nlr](/nlr/Distribution_NLR.svg){max-width=750px}
*Proportion of genome encoding the NLR 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 NLR system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
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content/3.defense-systems/old_exonuclease.md
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The Old protein of bacteriophage P2 is responsible for interference with the growth of phage lambda and for killing of recBC mutant Escherichia coli. We have purified Old fused to the maltose-binding protein to 95% purity and characterized its enzymatic properties. The Old protein fused to maltose-binding protein has exonuclease activity on double-stranded DNA as well as nuclease activity on single-stranded DNA and RNA. The direction of digestion of double-stranded DNA is from 5' to 3', and digestion initiates at either the 5'-phosphoryl or 5'-hydroxyl terminus. The nuclease is active on nicked circular DNA, degrades DNA in a processive manner, and releases 5'-phosphoryl mononucleotides.
Sensor: Unknown
Activator: Unknown
Effector: Unknown
Effector: Nucleic acid degrading
PFAM: PF13175, PF13304
contributors:
- Marian Dominguez-Mirazo
relevantAbstracts:
- doi: 10.1128/jb.177.3.497-501.1995
- doi: 10.1128/jb.177.3.497-501.1995
---
# Old_exonuclease
## Description
The OLD proteins are a family of nucleases present in bacteria, archaea, and viruses :ref{doi=10.1093/nar/gkz703}. The OLD protein found in the P2 *E.coli* prophage is the best characterized one. The protein is an exonuclease that digests dsDNA in the 5' to 3' direction :ref{doi=10.1128/jb.177.3.497-501.1995}. It also has nuclease activity against single stranded DNA and RNA :ref{doi=10.1128/jb.177.3.497-501.1995}. It's been shown to protect against phage lambda :ref{doi=10.1128/jb.177.3.497-501.1995}, and when cloned with the P2 Tin accesory gene, it was shown to protect against other *E. coli* phages :ref{doi=10.1016/j.chom.2022.02.018}. The protein also contains an ATPase domain that affects nuclease activity :ref{doi=10.1128/jb.177.3.497-501.1995}. Inhibition of the RecBCD complex activates the OLD nuclease :ref{doi=10.1016/j.mib.2023.102325}. OLD proteins are divided into two classes based on amino acid sequence conservation and gene neighborhood :ref{doi=10.1093/nar/gkz703}. The P2 associated protein belongs to class 2 :ref{doi=10.1093/nar/gkz703}.
## Molecular Mechanisms
The old_exonuclease is dsDNA exonuclease that digest in the 5' to 3' direction :ref{doi=10.1128/jb.177.3.497-501.1995}. To our knowledge, other aspects of the molecular mechanisms remain unknown.
## Example of genomic structure
The Old_exonuclease system is composed of one protein: Old_exonuclease.
The Old_exonuclease is composed of 1 protein: Old_exonuclease.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![old_exonuclease](/old_exonuclease/Old_exonuclease.svg){max-width=750px}
Old_exonuclease system in the genome of *Escherichia coli* (GCF_016904335.1) is composed of 1 protein: Old_exonuclease (WP_015979595.1).
The Old_exonuclease system in *Shewanella xiamenensis* (GCF_022453805.1, NZ_CP092630) is composed of 1 protein: Old_exonuclease (WP_240293412.1)
## Distribution of the system among prokaryotes
The Old_exonuclease system is present in a total of 53 different species.
Among the 22,803 complete genomes of RefSeq, the Old_exonuclease is detected in 102 genomes (0.45 %).
Among the 22k complete genomes of RefSeq, this system is present in 102 genomes (0.4 %).
The system was detected in 56 different species.
![old_exonuclease](/old_exonuclease/Distribution_Old_exonuclease.svg){max-width=750px}
*Proportion of genome encoding the Old_exonuclease system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Old_exonuclease system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
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## Relevant abstracts
**Rousset, F. et al. Phages and their satellites encode hotspots of antiviral systems. Cell Host & Microbe 30, 740-753.e5 (2022).**
Bacteria carry diverse genetic systems to defend against viral infection, some of which are found within prophages where they inhibit competing viruses. Phage satellites pose additional pressures on phages by hijacking key viral elements to their own benefit. Here, we show that E. coli P2-like phages and their parasitic P4-like satellites carry hotspots of genetic variation containing reservoirs of anti-phage systems. We validate the activity of diverse systems and describe PARIS, an abortive infection system triggered by a phage-encoded anti-restriction protein. Antiviral hotspots participate in inter-viral competition and shape dynamics between the bacterial host, P2-like phages, and P4-like satellites. Notably, the anti-phage activity of satellites can benefit the helper phage during competition with virulent phages, turning a parasitic relationship into a mutualistic one. Anti-phage hotspots are present across distant species and constitute a substantial source of systems that participate in the competition between mobile genetic elements.
content/3.defense-systems/olokun.md
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Sensor: Unknown
Activator: Unknown
Effector: Unknown
PFAM: PF01602, PF18742
contributors:
- Helena Shomar
- Marie Guillaume
relevantAbstracts:
- doi: 10.1016/j.chom.2022.09.017
---
# Olokun
## Description
The system Olokun is composed of 2 genes OloA (Adaptin_N domain) and OloB (nuclease domain) of unknown function.
This system was experimentally validated in _Escherichia coli_ and protects against LambdaVir and SECphi27 infection.
The system is named after a revered deity of the Yoruba religion, associated with the deep sea and depicted as an enormously powerful figure. They are believed to posses immense wealth, are associated with health, fertility and prosperity, and revered for their ability for inducing profound transformation and renewal. They are frequently depicted as a mermaid or merman, with both masculine and feminine aspects, reflecting the diversity and depth of the ocean.
## Molecular mechanisms
To our knowledde, the molecular mechanism is unknown. Please update.
## Example of genomic structure
The Olokun system is composed of 2 proteins: OloA and, OloB.
The Olokun is composed of 2 proteins: OloA and OloB.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![olokun](/olokun/Olokun.svg){max-width=750px}
Olokun system in the genome of *Vibrio cyclitrophicus* (GCF_023206035.1) is composed of 2 proteins: OloA (WP_016800143.1)and, OloB (WP_029203700.1).
The Olokun system in *Klebsiella quasipneumoniae* (GCF_015286025.1, NZ_CP063902) is composed of 2 proteins OloA (WP_227667429.1) OloB (WP_194418165.1)
## Distribution of the system among prokaryotes
The Olokun system is present in a total of 132 different species.
Among the 22,803 complete genomes of RefSeq, the Olokun is detected in 242 genomes (1.06 %).
Among the 22k complete genomes of RefSeq, this system is present in 252 genomes (1.1 %).
The system was detected in 137 different species.
![olokun](/olokun/Distribution_Olokun.svg){max-width=750px}
*Proportion of genome encoding the Olokun system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Olokun 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: 10.1016/j.chom.2022.09.017
---
::
content/3.defense-systems/pago.md
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# pAgo
## Example of genomic structure
The pAgo system is composed of one protein: pAgo_Short.
A total of 6 subsystems have been described for the pAgo system.
Here is an example found in the RefSeq database:
Here is some examples found in the RefSeq database:
![pago](/pago/pAgo.svg){max-width=750px}
![pago_longa](/pago/pAgo_LongA.svg){max-width=750px}
pAgo system in the genome of *Ensifer adhaerens* (GCF_020405145.1) is composed of 1 protein: pAgo_LongB (WP_218685258.1).
The pAgo_LongA system in *Halosimplex pelagicum* (GCF_013415905.1, NZ_CP058909) is composed of 1 protein: pAgo_LongA (WP_179918860.1)
![pago_longb](/pago/pAgo_LongB.svg){max-width=750px}
The pAgo_LongB system in *Serratia fonticola* (GCF_019252525.1, NZ_CP072742) is composed of 2 proteins pAgo_LongB (WP_218520044.1) EcAgaN (WP_235784821.1)
![pago_s1a](/pago/pAgo_S1A.svg){max-width=750px}
The pAgo_S1A system in *Parabacteroides merdae* (GCF_020735605.1, NZ_CP085927) is composed of 2 proteins pAgo_S1A (WP_227945673.1) pAgo_S1A (WP_227945674.1)
![pago_s1b](/pago/pAgo_S1B.svg){max-width=750px}
The pAgo_S1B system in *Comamonas flocculans* (GCF_007954405.1, NZ_CP042344) is composed of 2 proteins SIR2APAZ (WP_146914209.1) pAgo_S1B (WP_146913473.1)
![pago_s2b](/pago/pAgo_S2B.svg){max-width=750px}
The pAgo_S2B system in *Granulicella tundricola* (GCF_000178975.2, NC_015064) is composed of 2 proteins XAPAZ (WP_013581437.1) pAgo_S2B (WP_013581438.1)
![pago_sparta](/pago/pAgo_SPARTA.svg){max-width=750px}
The pAgo_SPARTA system in *Roseivivax sp. THAF30* (GCF_009363575.1, NZ_CP045389) is composed of 2 proteins TIRAPAZ (WP_152461295.1) pAgo_SPARTA (WP_152461296.1)
## Distribution of the system among prokaryotes
The pAgo system is present in a total of 435 different species.
Among the 22,803 complete genomes of RefSeq, the pAgo is detected in 575 genomes (2.52 %).
Among the 22k complete genomes of RefSeq, this system is present in 598 genomes (2.6 %).
The system was detected in 464 different species.
![pago](/pago/Distribution_pAgo.svg){max-width=750px}
*Proportion of genome encoding the pAgo system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the pAgo system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
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content/3.defense-systems/panchino_gp28.md
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## To do
## Example of genomic structure
The Panchino_gp28 is composed of 1 protein: gp28.
Here is an example found in the RefSeq database:
![panchino_gp28](/panchino_gp28/Panchino_gp28.svg){max-width=750px}
The Panchino_gp28 system in *Burkholderia pseudomallei* (GCF_018228585.1, NZ_CP073731) is composed of 1 protein: gp28 (WP_249212015.1)
## Distribution of the system among prokaryotes
Among the 22,803 complete genomes of RefSeq, the Panchino_gp28 is detected in 16 genomes (0.07 %).
The system was detected in 5 different species.
![panchino_gp28](/panchino_gp28/Distribution_Panchino_gp28.svg){max-width=750px}
Proportion of genome encoding the Panchino_gp28 system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
### Panchino_gp28
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content/3.defense-systems/paris.md
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## Example of genomic structure
The Paris system have been describe in a total of 4 subsystems.
A total of 2 subsystems have been described for the Rst_PARIS system.
The classical Paris is composed of two proteins AriA and AriB. The other type of Paris is the fused version with one AriAB protein.
Here is some example found in the RefSeq database:
Here is some examples found in the RefSeq database:
![paris](/paris/PARIS_I.svg){max-width=750px}
![paris_i](/paris/PARIS_I.svg){max-width=750px}
PARIS_I subsystem in the genome of *Salmonella enterica* (GCF_020715485.1) is composed of 2 proteins: AAA_15 (WP_001520831.1)and, DUF4435 (WP_010989064.1).
The PARIS_I system in *Streptomyces sampsonii* (GCF_001704195.1, NZ_CP016824) is composed of 2 proteins AriA_AAA15 (WP_079165307.1) AriB_DUF4435_I (WP_143067273.1)
![paris](/paris/PARIS_II.svg){max-width=750px}
![paris_i_merge](/paris/PARIS_I_merge.svg){max-width=750px}
PARIS_II subsystem in the genome of *Enterobacter cloacae* (GCF_023238665.1) is composed of 2 proteins: DUF4435 (WP_071830092.1)and, AAA_21 (WP_061772587.1).
![paris](/paris/PARIS_II_merge.svg){max-width=750px}
PARIS_II_merge subsystem in the genome of *Desulfovibrio desulfuricans* (GCF_017815575.1) is composed of 1 protein: AAA_21_DUF4435 (WP_209818471.1).
![paris](/paris/PARIS_I_merge.svg){max-width=750px}
PARIS_I_merge subsystem in the genome of *Sideroxydans lithotrophicus* (GCF_000025705.1) is composed of 1 protein: AAA_15_DUF4435 (WP_013030315.1).
The PARIS_I_merge system in *Rhizobium sp. SL42* (GCF_021729845.1, NZ_CP063397) is composed of 1 protein: AAA_15_DUF4435 (WP_237370054.1)
## Distribution of the system among prokaryotes
The Paris system is present in a total of 463 different species.
Among the 22,803 complete genomes of RefSeq, the Paris is detected in 1128 genomes (4.95 %).
Among the 22k complete genomes of RefSeq, this system is present in 1145 genomes (5.0 %).
The system was detected in 518 different species.
![paris](/paris/Distribution_Paris.svg){max-width=750px}
*Proportion of genome encoding the Paris 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 Paris system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
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