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content/3.defense-systems/pd-lambda-1.md
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......@@ -10,28 +10,43 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF10544, PF13250, PF13455
contributors:
- Alba Herrero del Valle
relevantAbstracts:
- doi: 10.1038/s41564-022-01219-4
---
# PD-Lambda-1
## Description
The PD-Lambda-1 system is composed of one protein, PD-Lambda-1, and confers resistance to LambdaVir :ref{doi=10.1038/s41564-022-01219-4}.
## Molecular mechanism
As far as we are aware, the molecular mechanism is unknown.
## Example of genomic structure
The PD-Lambda-1 system is composed of one protein: PD-Lambda-1.
The PD-Lambda-1 is composed of 1 protein: PD-Lambda-1.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![pd-lambda-1](/pd-lambda-1/PD-Lambda-1.svg){max-width=750px}
PD-Lambda-1 system in the genome of *Olleya sp.* (GCF_002831645.1) is composed of 1 protein: PD-Lambda-1 (WP_101017806.1).
The PD-Lambda-1 system in *Gemmata massiliana* (GCF_901538265.1, NZ_LR593886) is composed of 1 protein: PD-Lambda-1 (WP_197909633.1)
## Distribution of the system among prokaryotes
The PD-Lambda-1 system is present in a total of 445 different species.
Among the 22,803 complete genomes of RefSeq, the PD-Lambda-1 is detected in 1301 genomes (5.71 %).
Among the 22k complete genomes of RefSeq, this system is present in 1323 genomes (5.8 %).
The system was detected in 483 different species.
![pd-lambda-1](/pd-lambda-1/Distribution_PD-Lambda-1.svg){max-width=750px}
*Proportion of genome encoding the PD-Lambda-1 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the PD-Lambda-1 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: 10.1038/s41564-022-01219-4
---
::
content/3.defense-systems/pd-lambda-2.md
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# PD-Lambda-2
## Example of genomic structure
The PD-Lambda-2 system is composed of 3 proteins: PD-Lambda-2_C, PD-Lambda-2_B and, PD-Lambda-2_A.
The PD-Lambda-2 is composed of 3 proteins: PD-Lambda-2_A, PD-Lambda-2_B and PD-Lambda-2_C.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![pd-lambda-2](/pd-lambda-2/PD-Lambda-2.svg){max-width=750px}
PD-Lambda-2 system in the genome of *Pseudomonas aeruginosa* (GCF_013341295.1) is composed of 3 proteins: PD-Lambda-2_C (WP_023115149.1), PD-Lambda-2_B (WP_014833925.1)and, PD-Lambda-2_A (WP_003116393.1).
The PD-Lambda-2 system in *Vibrio parahaemolyticus* (GCF_013393845.1, NZ_CP040100) is composed of 3 proteins PD-Lambda-2_C (WP_116869984.1) PD-Lambda-2_B (WP_029809306.1) PD-Lambda-2_A (WP_029809305.1)
## Distribution of the system among prokaryotes
The PD-Lambda-2 system is present in a total of 52 different species.
Among the 22,803 complete genomes of RefSeq, the PD-Lambda-2 is detected in 122 genomes (0.54 %).
Among the 22k complete genomes of RefSeq, this system is present in 122 genomes (0.5 %).
The system was detected in 59 different species.
![pd-lambda-2](/pd-lambda-2/Distribution_PD-Lambda-2.svg){max-width=750px}
*Proportion of genome encoding the PD-Lambda-2 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the PD-Lambda-2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
content/3.defense-systems/pd-lambda-3.md
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Activator: Unknown
Effector: Unknown
PFAM: PF09509
contributors:
- Héloïse Georjon
relevantAbstracts:
- doi: 10.1038/s41564-022-01219-4
---
# PD-Lambda-3
## Description
PD-Lambda-3 systems were discovered to be anti-phage systems during an experimental screen performed on *E.coli* :ref{doi=10.1038/s41564-022-01219-4}
## Molecular mechanisms
As far as we are aware, the molecular mechanism is unknown.
## Example of genomic structure
The PD-Lambda-3 system is composed of 2 proteins: PD-Lambda-3_B and, PD-Lambda-3_A.
The PD-Lambda-3 is composed of 2 proteins: PD-Lambda-3_A and PD-Lambda-3_B.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![pd-lambda-3](/pd-lambda-3/PD-Lambda-3.svg){max-width=750px}
PD-Lambda-3 system in the genome of *Serratia rubidaea* (GCF_900478395.1) is composed of 2 proteins: PD-Lambda-3_A (WP_227673955.1)and, PD-Lambda-3_B (WP_047063039.1).
The PD-Lambda-3 system in *Enterobacter sp. CRENT-193* (GCF_002787395.1, NZ_CP024812) is composed of 2 proteins PD-Lambda-3_A (WP_001542736.1) PD-Lambda-3_B (WP_039268887.1)
## Distribution of the system among prokaryotes
The PD-Lambda-3 system is present in a total of 24 different species.
Among the 22,803 complete genomes of RefSeq, the PD-Lambda-3 is detected in 72 genomes (0.32 %).
Among the 22k complete genomes of RefSeq, this system is present in 74 genomes (0.3 %).
The system was detected in 28 different species.
![pd-lambda-3](/pd-lambda-3/Distribution_PD-Lambda-3.svg){max-width=750px}
*Proportion of genome encoding the PD-Lambda-3 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the PD-Lambda-3 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: 10.1038/s41564-022-01219-4
---
::
content/3.defense-systems/pd-lambda-4.md
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# PD-Lambda-4
## Example of genomic structure
The PD-Lambda-4 system is composed of 2 proteins: PD-Lambda-4_A and, PD-Lambda-4_B.
The PD-Lambda-4 is composed of 2 proteins: PD-Lambda-4_A and PD-Lambda-4_B.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![pd-lambda-4](/pd-lambda-4/PD-Lambda-4.svg){max-width=750px}
PD-Lambda-4 system in the genome of *Enterobacter asburiae* (GCF_023023265.1) is composed of 2 proteins: PD-Lambda-4_A (WP_246916891.1)and, PD-Lambda-4_B (WP_241182936.1).
The PD-Lambda-4 system in *Serratia sp. LS-1* (GCF_003719595.1, NZ_CP033504) is composed of 2 proteins PD-Lambda-4_B (WP_123061920.1) PD-Lambda-4_A (WP_123061921.1)
## Distribution of the system among prokaryotes
The PD-Lambda-4 system is present in a total of 13 different species.
Among the 22,803 complete genomes of RefSeq, the PD-Lambda-4 is detected in 69 genomes (0.3 %).
Among the 22k complete genomes of RefSeq, this system is present in 75 genomes (0.3 %).
The system was detected in 14 different species.
![pd-lambda-4](/pd-lambda-4/Distribution_PD-Lambda-4.svg){max-width=750px}
*Proportion of genome encoding the PD-Lambda-4 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the PD-Lambda-4 system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
content/3.defense-systems/pd-lambda-5.md
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Activator: Unknown
Effector: Unknown
PFAM: PF02086
contributors:
- Nathalie Bechon
relevantAbstracts:
- doi: 10.1038/s41564-022-01219-4
---
# PD-Lambda-5
##Description
PD-lambda-5 is a two-gene system identified in a P2-like prophage. It encodes a protein with a nuclease and a HEPN domain, and a predicted methyltransferase. It confers broad anti-phage defense and does not seem to mediate abortive infection.
##Molecular mechanism
PD-lambda-5 molecular mechanism has not been described to date. It confers protection against a broad range of phages, and does not seem to be an abortive infection system.
## Example of genomic structure
The PD-Lambda-5 system is composed of 2 proteins: PD-Lambda-5_A and, PD-Lambda-5_B.
The PD-Lambda-5 is composed of 2 proteins: PD-Lambda-5_A and PD-Lambda-5_B.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![pd-lambda-5](/pd-lambda-5/PD-Lambda-5.svg){max-width=750px}
PD-Lambda-5 system in the genome of *Chromobacterium rhizoryzae* (GCF_020544465.1) is composed of 2 proteins: PD-Lambda-5_B (WP_227108065.1)and, PD-Lambda-5_A (WP_227108067.1).
The PD-Lambda-5 system in *Plantactinospora sp. BB1* (GCF_003030385.1, NZ_CP028159) is composed of 2 proteins PD-Lambda-5_A (WP_159104731.1) PD-Lambda-5_B (WP_199853739.1)
## Distribution of the system among prokaryotes
The PD-Lambda-5 system is present in a total of 210 different species.
Among the 22,803 complete genomes of RefSeq, the PD-Lambda-5 is detected in 286 genomes (1.25 %).
Among the 22k complete genomes of RefSeq, this system is present in 361 genomes (1.6 %).
The system was detected in 186 different species.
![pd-lambda-5](/pd-lambda-5/Distribution_PD-Lambda-5.svg){max-width=750px}
*Proportion of genome encoding the PD-Lambda-5 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the PD-Lambda-5 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: 10.1038/s41564-022-01219-4
---
::
content/3.defense-systems/pd-lambda-6.md
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# PD-Lambda-6
## Example of genomic structure
The PD-Lambda-6 system is composed of one protein: PD-Lambda-6.
The PD-Lambda-6 is composed of 1 protein: PD-Lambda-6.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![pd-lambda-6](/pd-lambda-6/PD-Lambda-6.svg){max-width=750px}
PD-Lambda-6 system in the genome of *Escherichia albertii* (GCF_003864095.1) is composed of 1 protein: PD-Lambda-6 (WP_125059614.1).
The PD-Lambda-6 system in *Enterobacter asburiae* (GCF_013782005.1, NZ_CP056126) is composed of 1 protein: PD-Lambda-6 (WP_181599444.1)
## Distribution of the system among prokaryotes
The PD-Lambda-6 system is present in a total of 12 different species.
Among the 22,803 complete genomes of RefSeq, the PD-Lambda-6 is detected in 20 genomes (0.09 %).
Among the 22k complete genomes of RefSeq, this system is present in 21 genomes (0.1 %).
The system was detected in 11 different species.
![pd-lambda-6](/pd-lambda-6/Distribution_PD-Lambda-6.svg){max-width=750px}
*Proportion of genome encoding the PD-Lambda-6 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the PD-Lambda-6 system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
content/3.defense-systems/pd-t4-1.md
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# PD-T4-1
## Example of genomic structure
The PD-T4-1 system is composed of one protein: PD-T4-1.
The PD-T4-1 is composed of 1 protein: PD-T4-1.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![pd-t4-1](/pd-t4-1/PD-T4-1.svg){max-width=750px}
PD-T4-1 system in the genome of *Bradyrhizobium diazoefficiens* (GCF_016616885.1) is composed of 1 protein: PD-T4-1 (WP_200471933.1).
The PD-T4-1 system in *Macrococcus armenti* (GCF_020097055.1, NZ_CP083595) is composed of 1 protein: PD-T4-1 (WP_224185715.1)
## Distribution of the system among prokaryotes
The PD-T4-1 system is present in a total of 38 different species.
Among the 22,803 complete genomes of RefSeq, the PD-T4-1 is detected in 209 genomes (0.92 %).
Among the 22k complete genomes of RefSeq, this system is present in 209 genomes (0.9 %).
The system was detected in 38 different species.
![pd-t4-1](/pd-t4-1/Distribution_PD-T4-1.svg){max-width=750px}
*Proportion of genome encoding the PD-T4-1 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the PD-T4-1 system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
content/3.defense-systems/pd-t4-10.md
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Sensor: Unknown
Activator: Unknown
Effector: Unknown
PFAM: Unknown
contributors:
- Alba Herrero del Valle
relevantAbstracts:
- doi: 10.1038/s41564-022-01219-4
---
# PD-T4-10
## Description
The PD-T4-10 system is composed of 2 proteins: PD-T4-10_B and, PD-T4-10_A. This ORFs are overlapping and PD-T4-10_B is toxic while PD-T4-10_A neutralizes its toxicity, hinting to a toxin-antitoxin (TA) mechanism. It confers resitance to T2, T4, T6 and SECphi27 through an Abi defense mechanism :ref{doi=10.1038/s41564-022-01219-4}.
## Molecular mechanism
As far as we are aware, the molecular mechanism is unknown.
## Example of genomic structure
The PD-T4-10 system is composed of 2 proteins: PD-T4-10_B and, PD-T4-10_A.
The PD-T4-10 is composed of 2 proteins: PD-T4-10_A and PD-T4-10_B.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![pd-t4-10](/pd-t4-10/PD-T4-10.svg){max-width=750px}
PD-T4-10 system in the genome of *Salmonella enterica* (GCF_022559465.1) is composed of 2 proteins: PD-T4-10_A (WP_109288182.1)and, PD-T4-10_B (WP_001585426.1).
The PD-T4-10 system in *Escherichia fergusonii* (GCF_019047545.1, NZ_CP077242) is composed of 2 proteins PD-T4-10_A (WP_032236482.1) PD-T4-10_B (WP_032236481.1)
## Distribution of the system among prokaryotes
The PD-T4-10 system is present in a total of 40 different species.
Among the 22,803 complete genomes of RefSeq, the PD-T4-10 is detected in 33 genomes (0.14 %).
Among the 22k complete genomes of RefSeq, this system is present in 68 genomes (0.3 %).
The system was detected in 23 different species.
![pd-t4-10](/pd-t4-10/Distribution_PD-T4-10.svg){max-width=750px}
*Proportion of genome encoding the PD-T4-10 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the PD-T4-10 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: 10.1371/journal.pgen.1010065
---
::
content/3.defense-systems/pd-t4-2.md
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# PD-T4-2
## Example of genomic structure
The PD-T4-2 system is composed of 2 proteins: PD-T4-2_B and, PD-T4-2_A.
The PD-T4-2 is composed of 2 proteins: PD-T4-2_A and PD-T4-2_B.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![pd-t4-2](/pd-t4-2/PD-T4-2.svg){max-width=750px}
PD-T4-2 system in the genome of *Microcystis viridis* (GCF_003945305.1) is composed of 2 proteins: PD-T4-2_B (WP_164517006.1)and, PD-T4-2_A (WP_125731928.1).
The PD-T4-2 system in *Jeotgalibaca sp. PTS2502* (GCF_001975685.1, NZ_CP019433) is composed of 2 proteins PD-T4-2_A (WP_083686895.1) PD-T4-2_B (WP_076765701.1)
## Distribution of the system among prokaryotes
The PD-T4-2 system is present in a total of 28 different species.
Among the 22,803 complete genomes of RefSeq, the PD-T4-2 is detected in 33 genomes (0.14 %).
Among the 22k complete genomes of RefSeq, this system is present in 33 genomes (0.1 %).
The system was detected in 28 different species.
![pd-t4-2](/pd-t4-2/Distribution_PD-T4-2.svg){max-width=750px}
*Proportion of genome encoding the PD-T4-2 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the PD-T4-2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
content/3.defense-systems/pd-t4-3.md
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Sensor: Unknown
Activator: Unknown
Effector: Unknown
contributors:
- Ernest Mordret
relevant abstracts:
- doi: 10.1038/s41564-022-01219-4
---
# PD-T4-3
## Description
PD-T4-3 is a single gene system isolated during an experimental screen of fosmids derived from 71 strains of diverse E.coli, and cloned back in a derivative of K12. Fragments containing the PD-T4-3 gene were shown to provide resistance to phage T4. The protein is characterized by a GIY-YIG nuclease domain, and mutations inactivating this domain abolished the resistance phenotype. It was originally found on a µ-like prophage
## Molecular mechanism
the molecular mechanism of this system is unknown
## Example of genomic structure
The PD-T4-3 system is composed of one protein: PD-T4-3.
The PD-T4-3 is composed of 1 protein: PD-T4-3.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![pd-t4-3](/pd-t4-3/PD-T4-3.svg){max-width=750px}
PD-T4-3 system in the genome of *Salmonella enterica* (GCF_009664795.1) is composed of 1 protein: PD-T4-3 (WP_000353908.1).
The PD-T4-3 system in *Morganella morganii* (GCF_018802485.1, NZ_CP064826) is composed of 1 protein: PD-T4-3 (WP_214179544.1)
## Distribution of the system among prokaryotes
The PD-T4-3 system is present in a total of 139 different species.
Among the 22,803 complete genomes of RefSeq, the PD-T4-3 is detected in 1314 genomes (5.76 %).
Among the 22k complete genomes of RefSeq, this system is present in 1313 genomes (5.8 %).
The system was detected in 172 different species.
![pd-t4-3](/pd-t4-3/Distribution_PD-T4-3.svg){max-width=750px}
*Proportion of genome encoding the PD-T4-3 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the PD-T4-3 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: 10.1038/s41564-022-01219-4
---
::
content/3.defense-systems/pd-t4-4.md
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Activator: Unknown
Effector: Unknown
PFAM: PF13175, PF13304
contributors:
- Nathalie Bechon
relevantAbstracts:
- doi: 10.1038/s41564-022-01219-4
---
# PD-T4-4
## Description
PD-T4-4 is a defense system composed of two proteins, a P-loop NTPase and a nuclease, that is most likely protecting the bacterial population through abortive infection. It was identified from an ICE in an *E. coli* genome.
## Molecular mechanisms
PD-T4-4 molecular mechanism is currently unknown, although it is most likely an abortive infection system.
## Example of genomic structure
The PD-T4-4 system is composed of 2 proteins: PD-T4-4_A and, PD-T4-4_B.
The PD-T4-4 is composed of 2 proteins: PD-T4-4_A and PD-T4-4_B.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![pd-t4-4](/pd-t4-4/PD-T4-4.svg){max-width=750px}
PD-T4-4 system in the genome of *Escherichia coli* (GCF_013376895.1) is composed of 2 proteins: PD-T4-4_B (WP_176670803.1)and, PD-T4-4_A (WP_027920142.1).
The PD-T4-4 system in *Thiothrix subterranea* (GCF_016772315.1, NZ_CP053482) is composed of 2 proteins PD-T4-4_A (WP_202716711.1) PD-T4-4_B (WP_202716712.1)
## Distribution of the system among prokaryotes
The PD-T4-4 system is present in a total of 40 different species.
Among the 22,803 complete genomes of RefSeq, the PD-T4-4 is detected in 50 genomes (0.22 %).
Among the 22k complete genomes of RefSeq, this system is present in 53 genomes (0.2 %).
The system was detected in 37 different species.
![pd-t4-4](/pd-t4-4/Distribution_PD-T4-4.svg){max-width=750px}
*Proportion of genome encoding the PD-T4-4 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the PD-T4-4 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: 10.1038/s41564-022-01219-4
---
::
content/3.defense-systems/pd-t4-5.md
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# PD-T4-5
## Example of genomic structure
The PD-T4-5 system is composed of one protein: PD-T4-5.
The PD-T4-5 is composed of 1 protein: PD-T4-5.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![pd-t4-5](/pd-t4-5/PD-T4-5.svg){max-width=750px}
PD-T4-5 system in the genome of *Achromobacter sp.* (GCF_020541125.1) is composed of 1 protein: PD-T4-5 (WP_180098530.1).
The PD-T4-5 system in *Grimontia hollisae* (GCF_009665295.1, NZ_CP035690) is composed of 1 protein: PD-T4-5 (WP_154124046.1)
## Distribution of the system among prokaryotes
The PD-T4-5 system is present in a total of 113 different species.
Among the 22,803 complete genomes of RefSeq, the PD-T4-5 is detected in 587 genomes (2.57 %).
Among the 22k complete genomes of RefSeq, this system is present in 587 genomes (2.6 %).
The system was detected in 128 different species.
![pd-t4-5](/pd-t4-5/Distribution_PD-T4-5.svg){max-width=750px}
*Proportion of genome encoding the PD-T4-5 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the PD-T4-5 system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
content/3.defense-systems/pd-t4-6.md
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article:
doi: 10.1038/s41564-022-01219-4
abstract: |
The ancient, ongoing coevolutionary battle between bacteria and their viruses, bacteriophages, has given rise to sophisticated immune systems including restriction-modification and CRISPR-Cas. Many additional anti-phage systems have been identified using computational approaches based on genomic co-location within defence islands, but these screens may not be exhaustive. Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands. Additionally, our work indicates that intact prophages and mobile genetic elements are primary reservoirs and distributors of defence systems in E. coli, with defence systems typically carried in specific locations or hotspots. These hotspots encode dozens of additional uncharacterized defence system candidates. Our findings reveal an extended landscape of antiviral immunity in E. coli and provide an approach for mapping defence systems in other species.
The ancient, ongoing coevolutionary battle between bacteria and their viruses, bacteriophages, has given rise to sophisticated immune systems including restriction-modification and CRISPR-Cas. Many additional anti-phage systems have been identified using computational approaches based on genomic co-location within defence islands, but these screens may not be exhaustive. Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse *E. coli* strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands. Additionally, our work indicates that intact prophages and mobile genetic elements are primary reservoirs and distributors of defence systems in *E. coli*, with defence systems typically carried in specific locations or hotspots. These hotspots encode dozens of additional uncharacterized defence system candidates. Our findings reveal an extended landscape of antiviral immunity in *E. coli* and provide an approach for mapping defence systems in other species.
Sensor: Unknown
Activator: Unknown
Effector: Unknown
PFAM: PF00069, PF03793, PF07714
contributors:
- Marian Dominguez-Mirazo
relevantAbstracts:
- doi: 10.1038/s41564-022-01219-4
---
# PD-T4-6
## Description
The PD-T4-6 system is composed of a single protein. It was discovered via a selection screening of 71 *E. coli* strains challenged with diverse phage. The name stands from Phage Defense (PD) and the phage with which the strain was challenge (T4) :ref{doi=10.1038/s41564-022-01219-4}. The system has been identified as an Abortive Infection (Abi) system :ref{doi=10.1038/s41564-022-01219-4,10.1016/j.mib.2023.102312}. The protein was found within a P2-like prophage and contains a predicted Der/Thr kinase domain. Site-specific mutation in the domain reduces phage protection :ref{doi=10.1038/s41564-022-01219-4}.
## Molecular mechanisms
As far as we are aware, the molecular mechanism is unknown.
## Example of genomic structure
The PD-T4-6 system is composed of one protein: PD-T4-6.
The PD-T4-6 is composed of 1 protein: PD-T4-6.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![pd-t4-6](/pd-t4-6/PD-T4-6.svg){max-width=750px}
PD-T4-6 system in the genome of *Pseudomonas aeruginosa* (GCF_016584725.1) is composed of 1 protein: PD-T4-6 (WP_023875836.1).
The PD-T4-6 system in *Streptococcus ruminantium* (GCF_021654555.1, NZ_AP025333) is composed of 1 protein: PD-T4-6 (WP_024532776.1)
## Distribution of the system among prokaryotes
The PD-T4-6 system is present in a total of 18 different species.
Among the 22,803 complete genomes of RefSeq, the PD-T4-6 is detected in 88 genomes (0.39 %).
Among the 22k complete genomes of RefSeq, this system is present in 88 genomes (0.4 %).
The system was detected in 18 different species.
![pd-t4-6](/pd-t4-6/Distribution_PD-T4-6.svg){max-width=750px}
*Proportion of genome encoding the PD-T4-6 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the PD-T4-6 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: 10.1038/s41564-022-01219-4
---
::
content/3.defense-systems/pd-t4-7.md
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Sensor: Unknown
Activator: Unknown
Effector: Unknown
contributors:
- Ernest Mordret
relevantAbstracts:
- doi: 10.1038/s41564-022-01219-4
---
# PD-T4-7
## Description
PD-T4-7 is a single gene system. Its protein contains a RelE domain and a phage Sheath.
protect against T2,T4,T6
## Molecular mechanism
Vassalo et al. :ref{doi=10.1038/s41564-022-01219-4} state that PD-T4-7 functions through an abortive infection mechanism
## Example of genomic structure
The PD-T4-7 system is composed of one protein: PD-T4-7.
The PD-T4-7 is composed of 1 protein: PD-T4-7.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![pd-t4-7](/pd-t4-7/PD-T4-7.svg){max-width=750px}
PD-T4-7 system in the genome of *Providencia alcalifaciens* (GCF_915401745.1) is composed of 1 protein: PD-T4-7 (WP_036975088.1).
The PD-T4-7 system in *Thalassospira sp. B30-1* (GCF_015767575.1, NZ_CP065232) is composed of 1 protein: PD-T4-7 (WP_139190007.1)
## Distribution of the system among prokaryotes
The PD-T4-7 system is present in a total of 97 different species.
Among the 22,803 complete genomes of RefSeq, the PD-T4-7 is detected in 155 genomes (0.68 %).
Among the 22k complete genomes of RefSeq, this system is present in 156 genomes (0.7 %).
The system was detected in 100 different species.
![pd-t4-7](/pd-t4-7/Distribution_PD-T4-7.svg){max-width=750px}
*Proportion of genome encoding the PD-T4-7 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the PD-T4-7 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: 10.1038/s41564-022-01219-4
---
::
content/3.defense-systems/pd-t4-8.md
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Activator: Unknown
Effector: Unknown
PFAM: PF14082
contributors:
- Alba Herrero del Valle
relevantAbstracts:
- doi: 10.1371/journal.pgen.1010065
---
# PD-T4-8
## Description
PD-T4-8 is composed of a single protein that contains a DUF4263 domain found in the [Shedu](/defense-systems/shedu) defence system :ref{doi=10.1038/s41564-022-01219-4}. PD-T4-8 from *Escherichia coli* RCP52534.1 confers resistance against T2, T4, T6, SECphi18 and SECphi27.
## Molecular mechanisms
As far as we are aware, the molecular mechanism is unknown.
## Example of genomic structure
The PD-T4-8 system is composed of one protein: PD-T4-8.
The PD-T4-8 is composed of 1 protein: PD-T4-8.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![pd-t4-8](/pd-t4-8/PD-T4-8.svg){max-width=750px}
PD-T4-8 system in the genome of *Pectobacterium brasiliense* (GCF_001932635.1) is composed of 1 protein: PD-T4-8 (WP_075277998.1).
The PD-T4-8 system in *Algoriphagus sp. Y33* (GCF_014838715.1, NZ_CP061947) is composed of 1 protein: PD-T4-8 (WP_144603961.1)
## Distribution of the system among prokaryotes
The PD-T4-8 system is present in a total of 48 different species.
Among the 22,803 complete genomes of RefSeq, the PD-T4-8 is detected in 89 genomes (0.39 %).
Among the 22k complete genomes of RefSeq, this system is present in 91 genomes (0.4 %).
The system was detected in 50 different species.
![pd-t4-8](/pd-t4-8/Distribution_PD-T4-8.svg){max-width=750px}
*Proportion of genome encoding the PD-T4-8 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the PD-T4-8 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: 10.1038/s41564-022-01219-4
---
::
content/3.defense-systems/pd-t4-9.md
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# PD-T4-9
## Example of genomic structure
The PD-T4-9 system is composed of 3 proteins: PD-T4-9_C, PD-T4-9_B and, PD-T4-9_A.
The PD-T4-9 is composed of 3 proteins: PD-T4-9_A, PD-T4-9_B and PD-T4-9_C.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![pd-t4-9](/pd-t4-9/PD-T4-9.svg){max-width=750px}
PD-T4-9 system in the genome of *Escherichia coli* (GCF_018223665.1) is composed of 3 proteins: PD-T4-9_A (WP_061089969.1), PD-T4-9_B (WP_061089970.1)and, PD-T4-9_C (WP_061089971.1).
The PD-T4-9 system in *Vibrio parahaemolyticus* (GCF_001700835.1, NZ_CP010883) is composed of 3 proteins PD-T4-9_C (WP_065870458.1) PD-T4-9_B (WP_141106056.1) PD-T4-9_A (WP_065870460.1)
## Distribution of the system among prokaryotes
The PD-T4-9 system is present in a total of 93 different species.
Among the 22,803 complete genomes of RefSeq, the PD-T4-9 is detected in 141 genomes (0.62 %).
Among the 22k complete genomes of RefSeq, this system is present in 148 genomes (0.6 %).
The system was detected in 88 different species.
![pd-t4-9](/pd-t4-9/Distribution_PD-T4-9.svg){max-width=750px}
*Proportion of genome encoding the PD-T4-9 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the PD-T4-9 system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
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content/3.defense-systems/pd-t7-1.md
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# PD-T7-1
## Example of genomic structure
The PD-T7-1 system is composed of one protein: PD-T7-1.
The PD-T7-1 is composed of 1 protein: PD-T7-1.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![pd-t7-1](/pd-t7-1/PD-T7-1.svg){max-width=750px}
PD-T7-1 system in the genome of *Escherichia coli* (GCF_007833255.1) is composed of 1 protein: PD-T7-1 (WP_000008839.1).
The PD-T7-1 system in *Klebsiella sp. P1927* (GCF_018204675.1, NZ_CP073377) is composed of 1 protein: PD-T7-1 (WP_004150873.1)
## Distribution of the system among prokaryotes
The PD-T7-1 system is present in a total of 136 different species.
Among the 22,803 complete genomes of RefSeq, the PD-T7-1 is detected in 748 genomes (3.28 %).
Among the 22k complete genomes of RefSeq, this system is present in 755 genomes (3.3 %).
The system was detected in 146 different species.
![pd-t7-1](/pd-t7-1/Distribution_PD-T7-1.svg){max-width=750px}
*Proportion of genome encoding the PD-T7-1 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the PD-T7-1 system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
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content/3.defense-systems/pd-t7-2.md
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# PD-T7-2
## Example of genomic structure
The PD-T7-2 system is composed of 2 proteins: PD-T7-2_A and, PD-T7-2_B.
The PD-T7-2 is composed of 2 proteins: PD-T7-2_A and PD-T7-2_B.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![pd-t7-2](/pd-t7-2/PD-T7-2.svg){max-width=750px}
PD-T7-2 system in the genome of *Sphingobium amiense* (GCF_003967075.1) is composed of 2 proteins: PD-T7-2_B (WP_066704003.1)and, PD-T7-2_A (WP_066704000.1).
The PD-T7-2 system in *Lederbergia lenta* (GCF_900478165.1, NZ_LS483476) is composed of 2 proteins PD-T7-2_A (WP_066145327.1) PD-T7-2_B (WP_066145329.1)
## Distribution of the system among prokaryotes
The PD-T7-2 system is present in a total of 606 different species.
Among the 22,803 complete genomes of RefSeq, the PD-T7-2 is detected in 1483 genomes (6.5 %).
Among the 22k complete genomes of RefSeq, this system is present in 1535 genomes (6.7 %).
The system was detected in 667 different species.
![pd-t7-2](/pd-t7-2/Distribution_PD-T7-2.svg){max-width=750px}
*Proportion of genome encoding the PD-T7-2 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the PD-T7-2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
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content/3.defense-systems/pd-t7-3.md
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Sensor: Unknown
Activator: Unknown
Effector: Unknown
contributors:
- Héloïse Georjon
relevantAbstracts:
- doi: 10.1038/s41564-022-01219-4
---
# PD-T7-3
## Description
PD-T7-3 systems were discovered to be anti-phage systems during an experimental screen performed on *E. coli* strains :ref{doi=10.1038/s41564-022-01219-4}
## Molecular mechanisms
As far as we are aware, the molecular mechanism of PD-T7-3 is unknown.
## Example of genomic structure
The PD-T7-3 system is composed of one protein: PD-T7-3.
The PD-T7-3 is composed of 1 protein: PD-T7-3.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![pd-t7-3](/pd-t7-3/PD-T7-3.svg){max-width=750px}
PD-T7-3 system in the genome of *Alistipes sp.* (GCF_009557455.1) is composed of 1 protein: PD-T7-3 (WP_153498146.1).
The PD-T7-3 system in *Paraglaciecola psychrophila* (GCF_000347635.1, NC_020514) is composed of 1 protein: PD-T7-3 (WP_007636449.1)
## Distribution of the system among prokaryotes
The PD-T7-3 system is present in a total of 127 different species.
Among the 22,803 complete genomes of RefSeq, the PD-T7-3 is detected in 209 genomes (0.92 %).
Among the 22k complete genomes of RefSeq, this system is present in 215 genomes (0.9 %).
The system was detected in 130 different species.
![pd-t7-3](/pd-t7-3/Distribution_PD-T7-3.svg){max-width=750px}
*Proportion of genome encoding the PD-T7-3 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the PD-T7-3 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: 10.1038/s41564-022-01219-4
---
::
content/3.defense-systems/pd-t7-4.md
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# PD-T7-4
## Example of genomic structure
The PD-T7-4 system is composed of one protein: PD-T7-4.
The PD-T7-4 is composed of 1 protein: PD-T7-4.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![pd-t7-4](/pd-t7-4/PD-T7-4.svg){max-width=750px}
PD-T7-4 system in the genome of *Parashewanella tropica* (GCF_004358445.1) is composed of 1 protein: PD-T7-4 (WP_133406898.1).
The PD-T7-4 system in *Salinibacterium hongtaonis* (GCF_003065485.1, NZ_CP026951) is composed of 1 protein: PD-T7-4 (WP_108515598.1)
## Distribution of the system among prokaryotes
The PD-T7-4 system is present in a total of 204 different species.
Among the 22,803 complete genomes of RefSeq, the PD-T7-4 is detected in 492 genomes (2.16 %).
Among the 22k complete genomes of RefSeq, this system is present in 501 genomes (2.2 %).
The system was detected in 218 different species.
![pd-t7-4](/pd-t7-4/Distribution_PD-T7-4.svg){max-width=750px}
*Proportion of genome encoding the PD-T7-4 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the PD-T7-4 system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
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