diff --git a/content/2.defense-systems/abi2.md b/content/2.defense-systems/abi2.md
index 7403ca3a6f6e1fde45a7f6a23d4fb2e14e44da27..6f8549ec2378baf5dd358518c8fe643e1b09cf1e 100644
--- a/content/2.defense-systems/abi2.md
+++ b/content/2.defense-systems/abi2.md
@@ -5,9 +5,12 @@ tableColumns:
doi: 10.1016/j.mib.2005.06.006
abstract: |
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
+ Sensor: ''
+ Activator: ''
+ Effector: ''
+ PFAM: PF07751
---
-# Abi2
# Abi2
The Abi2 system is composed of one protein: Abi_2.
@@ -29,3 +32,4 @@ Among the 22k complete genomes of RefSeq, this system is present in 1210 genomes
## Relevant abstracts
+
diff --git a/content/2.defense-systems/abia.md b/content/2.defense-systems/abia.md
index 9061dfd6d46e667b9b165803d9f04eb913bed0b0..dfc59ca9e0a56774c04b0d861df26f408a994ff5 100644
--- a/content/2.defense-systems/abia.md
+++ b/content/2.defense-systems/abia.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00078, PF18160, PF18732
---
-# AbiA
# AbiA
The AbiA system have been describe in a total of 2 subsystems.
@@ -51,3 +51,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abib.md b/content/2.defense-systems/abib.md
index 62da9295d03f1aa158574ed57792e008971a261c..1951d72efc0a0b40b11bb23a8c58971447be652a 100644
--- a/content/2.defense-systems/abib.md
+++ b/content/2.defense-systems/abib.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiB
# AbiB
The AbiB system is composed of one protein: AbiB.
diff --git a/content/2.defense-systems/abic.md b/content/2.defense-systems/abic.md
index efd2c8e3947da2ab82048370998c1cdf5830667d..aa9f9f3989d296e8510b974ef64da50ccc397831 100644
--- a/content/2.defense-systems/abic.md
+++ b/content/2.defense-systems/abic.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF16872
---
-# AbiC
# AbiC
The AbiC system is composed of one protein: AbiC.
@@ -52,3 +52,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abid.md b/content/2.defense-systems/abid.md
index 26d443aa4c31a72358114ac5a4baebd26d60f9bb..41f5e4b64c25a1c057f2d36ef4aa23ed1b803695 100644
--- a/content/2.defense-systems/abid.md
+++ b/content/2.defense-systems/abid.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF07751
---
-# AbiD
# AbiD
The AbiD system is composed of one protein: AbiD.
@@ -46,3 +46,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abie.md b/content/2.defense-systems/abie.md
index aa61f1dd6e96d275a0f4113494d8cff854be5924..b6b5fac03abfb8be32c796de20db579a012d9ea3 100644
--- a/content/2.defense-systems/abie.md
+++ b/content/2.defense-systems/abie.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF08843, PF09407, PF09952, PF11459, PF13338, PF17194
---
-# AbiE
# AbiE
AbiE is a family of an anti-phage defense systems. They act through a Toxin-Antitoxin mechanism, and are comprised of a pair of genes, with one gene being toxic while the other confers immunity to this toxicity.Â
@@ -59,3 +59,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abig.md b/content/2.defense-systems/abig.md
index 8593fa97e5961328cadb67b5b381a7ced63f7f09..56d3ffb4370530c962717394ada45d7238f4ccc8 100644
--- a/content/2.defense-systems/abig.md
+++ b/content/2.defense-systems/abig.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF10899, PF16873
---
-# AbiG
# AbiG
The AbiG system is composed of 2 proteins: AbiGi and, AbiGii.
@@ -46,3 +46,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abih.md b/content/2.defense-systems/abih.md
index 5fdab8fa0c8a883a94ec0bef354f4cafe86b3ad1..c03615dfae2e97a8500c5ebf87bef623d337968d 100644
--- a/content/2.defense-systems/abih.md
+++ b/content/2.defense-systems/abih.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF14253
---
-# AbiH
# AbiH
## Example of genomic structure
@@ -49,3 +49,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abii.md b/content/2.defense-systems/abii.md
index c30ab04cf8918b5b36878b66f303fe6c95e37fcd..92b213f971c0feb2ef1c2c7dcb981056176ff1ef 100644
--- a/content/2.defense-systems/abii.md
+++ b/content/2.defense-systems/abii.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiI
# AbiI
## Example of genomic structure
diff --git a/content/2.defense-systems/abij.md b/content/2.defense-systems/abij.md
index 56e1d908a5d54d8f75f6f45a7e2da463375b5b17..b2e9663d83e5debd9233fe7cf08fefac56011434 100644
--- a/content/2.defense-systems/abij.md
+++ b/content/2.defense-systems/abij.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF14355
---
-# AbiJ
# AbiJ
## Example of genomic structure
@@ -48,3 +48,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abik.md b/content/2.defense-systems/abik.md
index 3f5c36c34e8ab5c07f5b6a4413b7c29f075a640f..e8646b5d79a21964895df036d223599d6601b128 100644
--- a/content/2.defense-systems/abik.md
+++ b/content/2.defense-systems/abik.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00078
---
-# AbiK
# AbiK
## Example of genomic structure
@@ -49,3 +49,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abil.md b/content/2.defense-systems/abil.md
index 1841dd43f82d445436e5a69b125a5c4eb5fcbd64..dedac3928dbd4e72daa1ba2e78b2a00c22323946 100644
--- a/content/2.defense-systems/abil.md
+++ b/content/2.defense-systems/abil.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF13175, PF13304, PF13707
---
-# AbiL
# AbiL
## Example of genomic structure
@@ -48,3 +48,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abin.md b/content/2.defense-systems/abin.md
index cc2692a59916c3a06df4ae3723e638346a5a1e7d..466e2528e2532a76cd5309384012892150294908 100644
--- a/content/2.defense-systems/abin.md
+++ b/content/2.defense-systems/abin.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiN
# AbiN
## Example of genomic structure
diff --git a/content/2.defense-systems/abio.md b/content/2.defense-systems/abio.md
index ab5f15f6844e38a13769ba4cc9d85b802e6ed17f..c445c3c4e485909ae142bd4200e8f22ec231d7ae 100644
--- a/content/2.defense-systems/abio.md
+++ b/content/2.defense-systems/abio.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF01443, PF09848
---
-# AbiO
# AbiO
## Example of genomic structure
@@ -48,3 +48,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abip2.md b/content/2.defense-systems/abip2.md
index f9ea0dddbbd972f161349cbf8025b675322ec17f..d3882bf2ae5f0aca68a944add1795e46233a2440 100644
--- a/content/2.defense-systems/abip2.md
+++ b/content/2.defense-systems/abip2.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00078
---
-# AbiP2
# AbiP2
## Example of genomic structure
@@ -51,3 +51,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abiq.md b/content/2.defense-systems/abiq.md
index 0b4e4c7965af44309e77b9fcb9c0c31ab62be160..c1a359849799420dbff796ce8ee5c457bbfa0b70 100644
--- a/content/2.defense-systems/abiq.md
+++ b/content/2.defense-systems/abiq.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF13958
---
-# AbiQ
# AbiQ
## Example of genomic structure
@@ -49,3 +49,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abir.md b/content/2.defense-systems/abir.md
index 7004d5a1d13dbb03ca4627dff54e8483a3a7b01a..f61928982035e5504a08f08fb5bb2532a5e19826 100644
--- a/content/2.defense-systems/abir.md
+++ b/content/2.defense-systems/abir.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00176, PF00271, PF04545, PF04851, PF13091
---
-# AbiR
# AbiR
## Example of genomic structure
@@ -48,3 +48,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abit.md b/content/2.defense-systems/abit.md
index 5d32c87784e766b69ef045d3b2987cef394f5d74..745ffd703703817924ec544c16af1eeb086b20eb 100644
--- a/content/2.defense-systems/abit.md
+++ b/content/2.defense-systems/abit.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF18864
---
-# AbiT
# AbiT
## Example of genomic structure
@@ -48,3 +48,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abiu.md b/content/2.defense-systems/abiu.md
index c1b8e9b3bd37ecd398f106665fc3f26da93efca7..aab3cac16d94b81e7cca26db96e83940d463a1f9 100644
--- a/content/2.defense-systems/abiu.md
+++ b/content/2.defense-systems/abiu.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF10592
---
-# AbiU
# AbiU
## Example of genomic structure
@@ -48,3 +48,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abiv.md b/content/2.defense-systems/abiv.md
index 4b369c634933c7d619c3c6f78726b4e82f26a47b..9264f4ba1520f766ebccde291c3fc529bf9a9ee8 100644
--- a/content/2.defense-systems/abiv.md
+++ b/content/2.defense-systems/abiv.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF18728
---
-# AbiV
# AbiV
## Example of genomic structure
@@ -48,3 +48,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abiz.md b/content/2.defense-systems/abiz.md
index 267a963e41654fdf34af62beed6b33742dcf24d3..b58ed7f172d5bfea10c12f482e526bf05e1317ad 100644
--- a/content/2.defense-systems/abiz.md
+++ b/content/2.defense-systems/abiz.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Membrane disrupting
---
-# AbiZ
# AbiZ
## Example of genomic structure
diff --git a/content/2.defense-systems/aditi.md b/content/2.defense-systems/aditi.md
index b3c286380e1226c462a9c22de9292542731dfa29..7cf403946c1550dd53e5c9b0edc09e0f0aa37259 100644
--- a/content/2.defense-systems/aditi.md
+++ b/content/2.defense-systems/aditi.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF18928
---
-# Aditi
# Aditi
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/avast.md b/content/2.defense-systems/avs.md
similarity index 71%
rename from content/2.defense-systems/avast.md
rename to content/2.defense-systems/avs.md
index 558e0f782db2910b61917f7ee11d0d1b7d1129ee..a154ec61a6717209793a035c25a43d5c5360a6a9 100644
--- a/content/2.defense-systems/avast.md
+++ b/content/2.defense-systems/avs.md
@@ -1,5 +1,5 @@
---
-title: AVAST
+title: Avs
tableColumns:
article:
doi: 10.1126/science.aba0372
@@ -9,52 +9,53 @@ tableColumns:
Activator: Direct binding
Effector: Diverse effectors (Nucleic acid degrading, putative Nucleotide modifying, putative Membrane disrupting)
+ PFAM: PF00753, PF13289, PF13365
---
-# AVAST
-# AVAST
+# Avs
+
## Description
-AVAST (antiviral ATPases/NTPases of the STAND superfamily) is a group of anti-phage defense systems, active against some dsDNA phages.Â
+Avs (antiviral ATPases/NTPases of the STAND superfamily) is a group of anti-phage defense systems, active against some dsDNA phages.Â
-AVAST systems are composed of NTPases of the STAND (signal transduction ATPases with numerous associated domains) superfamily (1). Â STAND-NTPases typically contain a C-terminal helical sensor domain that activates the N-terminal effector domain upon target recognition (1).
+Avs systems are composed of NTPases of the STAND (signal transduction ATPases with numerous associated domains) superfamily (1). Â STAND-NTPases typically contain a C-terminal helical sensor domain that activates the N-terminal effector domain upon target recognition (1).
-In eukaryotes, STAND-NTPases are associated with programmed cell death, therefore Gao and colleagues hypothesized that AVAST might function through an Abortive infection mechanism.
+In eukaryotes, STAND-NTPases are associated with programmed cell death, therefore Gao and colleagues hypothesized that Avs might function through an Abortive infection mechanism.
## Example of genomic structure
-The AVAST system have been describe in a total of 5 subsystems.
+The Avs system have been describe in a total of 5 subsystems.
Here is some example found in the RefSeq database:
-{max-width=750px}
+{max-width=750px}
-AVAST_I subsystem in the genome of *Vibrio sp.* (GCF_905175355.1) is composed of 3 proteins: Avs1A (WP_208445041.1), Avs1B (WP_208445042.1)and, Avs1C (WP_108173272.1).
+Avs_I subsystem in the genome of *Vibrio sp.* (GCF_905175355.1) is composed of 3 proteins: Avs1A (WP_208445041.1), Avs1B (WP_208445042.1)and, Avs1C (WP_108173272.1).
-{max-width=750px}
+{max-width=750px}
-AVAST_II subsystem in the genome of *Escherichia coli* (GCF_018884505.1) is composed of 1 protein: Avs2A (WP_032199984.1).
+Avs_II subsystem in the genome of *Escherichia coli* (GCF_018884505.1) is composed of 1 protein: Avs2A (WP_032199984.1).
-{max-width=750px}
+{max-width=750px}
-AVAST_III subsystem in the genome of *Enterobacter cancerogenus* (GCF_002850575.1) is composed of 2 proteins: Avs3B (WP_199559884.1)and, Avs3A (WP_101737373.1).
+Avs_III subsystem in the genome of *Enterobacter cancerogenus* (GCF_002850575.1) is composed of 2 proteins: Avs3B (WP_199559884.1)and, Avs3A (WP_101737373.1).
-{max-width=750px}
+{max-width=750px}
-AVAST_IV subsystem in the genome of *Escherichia coli* (GCF_016903595.1) is composed of 1 protein: Avs4A (WP_000240574.1).
+Avs_IV subsystem in the genome of *Escherichia coli* (GCF_016903595.1) is composed of 1 protein: Avs4A (WP_000240574.1).
-{max-width=750px}
+{max-width=750px}
-AVAST_V subsystem in the genome of *Leclercia adecarboxylata* (GCF_006171285.1) is composed of 1 protein: Avs5A (WP_139565349.1).
+Avs_V subsystem in the genome of *Leclercia adecarboxylata* (GCF_006171285.1) is composed of 1 protein: Avs5A (WP_139565349.1).
## Distribution of the system among prokaryotes
-The AVAST system is present in a total of 363 different species.
+The Avs system is present in a total of 363 different species.
Among the 22k complete genomes of RefSeq, this system is present in 1046 genomes (4.6 %).
-{max-width=750px}
+{max-width=750px}
-*Proportion of genome encoding the AVAST 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 Avs 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.*
## Structure
@@ -77,7 +78,7 @@ dataUrl: /avast/AVAST_I,AVAST_I__Avs1B,0,V-plddts_80.96481.pdb
## Experimental validation
-AVAST systems were experimentally validated using:
+Avs systems were experimentally validated using:
Subsystem SIR2-STAND with a system from *Escherichia fergusonii's PICI (EfCIRHB19-C05)* in *Escherichia coli* has an anti-phage effect against T4, Lambda, HK97, HK544, HK578, T7 (Fillol-Salom et al., 2022)
@@ -127,3 +128,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/azaca.md b/content/2.defense-systems/azaca.md
index 3b38e0a9f544bb9a5ea9c94f1533d42e04e74899..68d725948eafebb2029bdbe35b29d563e520cb04 100644
--- a/content/2.defense-systems/azaca.md
+++ b/content/2.defense-systems/azaca.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00271
---
-# Azaca
# Azaca
## Example of genomic structure
@@ -49,3 +49,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/borvo.md b/content/2.defense-systems/borvo.md
index c17923bc7677fc9c26e56ea9e01d15a5218065ee..204dda167d23077dc76df2b5f6fc35aab126b8c2 100644
--- a/content/2.defense-systems/borvo.md
+++ b/content/2.defense-systems/borvo.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF12770
---
-# Borvo
# Borvo
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/brex.md b/content/2.defense-systems/brex.md
index 71046b353e7f306340d48dffa0dd8fc500a26d51..00a9a263d5c0c4b6af90c80cee3777d3a28f0356 100644
--- a/content/2.defense-systems/brex.md
+++ b/content/2.defense-systems/brex.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00069, PF00176, PF00270, PF00271, PF01507, PF01555, PF02384, PF04851, PF07669, PF07714, PF08378, PF08665, PF08747, PF08849, PF10923, PF13337, PF16565
---
-# BREX
# BREX
## Description
@@ -87,3 +87,4 @@ items:
**2. Nunes-Alves C. Bacterial physiology: putting the 'BREX' on phage replication. Nat Rev Microbiol. 2015 Mar;13(3):129. doi: 10.1038/nrmicro3437. Epub 2015 Feb 2. PMID: 25639679.**
**3. Sumby P, Smith MC. Phase variation in the phage growth limitation system of Streptomyces coelicolor A3(2). J Bacteriol. 2003;185(15):4558-4563. doi:10.1128/JB.185.15.4558-4563.2003**
+
diff --git a/content/2.defense-systems/bsta.md b/content/2.defense-systems/bsta.md
index 1fa1c169541fd04caab491006034012834fe0a35..3b06e7f678675390648c33eee58022f074783c08 100644
--- a/content/2.defense-systems/bsta.md
+++ b/content/2.defense-systems/bsta.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# BstA
# BstA
## Description
diff --git a/content/2.defense-systems/bunzi.md b/content/2.defense-systems/bunzi.md
index e747f3f44e2c35be9d9311a68ad346f21798dee2..8b1612a2339da71206d410ab416f7ff14d5639cb 100644
--- a/content/2.defense-systems/bunzi.md
+++ b/content/2.defense-systems/bunzi.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Bunzi
# Bunzi
## Example of genomic structure
diff --git a/content/2.defense-systems/butters_gp30_gp31.md b/content/2.defense-systems/butters_gp30_gp31.md
new file mode 100644
index 0000000000000000000000000000000000000000..6f03ec356a475f5d3fefdcc9be8a029562e06729
--- /dev/null
+++ b/content/2.defense-systems/butters_gp30_gp31.md
@@ -0,0 +1,21 @@
+---
+title: Butters_gp30_gp31
+tableColumns:
+ article:
+ doi: 10.1128/mSystems.00534-20
+ abstract: |
+ Many sequenced bacterial genomes, including those of pathogenic bacteria, contain prophages. Some prophages encode defense systems that protect their bacterial host against heterotypic viral attack. Understanding the mechanisms undergirding these defense systems is crucial to appreciate the scope of bacterial immunity against viral infections and will be critical for better implementation of phage therapy that would require evasion of these defenses. Furthermore, such knowledge of prophage-encoded defense mechanisms may be useful for developing novel genetic tools for engineering phage-resistant bacteria of industrial importance., A diverse set of prophage-mediated mechanisms protecting bacterial hosts from infection has been recently uncovered within cluster N mycobacteriophages isolated on the host, Mycobacterium smegmatis mc2155. In that context, we unveil a novel defense mechanism in cluster N prophage Butters. By using bioinformatics analyses, phage plating efficiency experiments, microscopy, and immunoprecipitation assays, we show that Butters genes located in the central region of the genome play a key role in the defense against heterotypic viral attack. Our study suggests that a two-component system, articulated by interactions between protein products of genes 30 and 31, confers defense against heterotypic phage infection by PurpleHaze (cluster A/subcluster A3) or Alma (cluster A/subcluster A9) but is insufficient to confer defense against attack by the heterotypic phage Island3 (cluster I/subcluster I1). Therefore, based on heterotypic phage plating efficiencies on the Butters lysogen, additional prophage genes required for defense are implicated and further show specificity of prophage-encoded defense systems., IMPORTANCE Many sequenced bacterial genomes, including those of pathogenic bacteria, contain prophages. Some prophages encode defense systems that protect their bacterial host against heterotypic viral attack. Understanding the mechanisms undergirding these defense systems is crucial to appreciate the scope of bacterial immunity against viral infections and will be critical for better implementation of phage therapy that would require evasion of these defenses. Furthermore, such knowledge of prophage-encoded defense mechanisms may be useful for developing novel genetic tools for engineering phage-resistant bacteria of industrial importance.
+---
+
+# Butters_gp30_gp31
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1128/mSystems.00534-20
+
+---
+::
diff --git a/content/2.defense-systems/butters_gp57r.md b/content/2.defense-systems/butters_gp57r.md
new file mode 100644
index 0000000000000000000000000000000000000000..520d08dd6ba5461d8674e8a32e7b1cddad0dbafb
--- /dev/null
+++ b/content/2.defense-systems/butters_gp57r.md
@@ -0,0 +1,21 @@
+---
+title: Butters_gp57r
+tableColumns:
+ article:
+ doi: 10.1101/2023.01.03.522681
+ abstract: |
+ During lysogeny temperate phages establish a truce with the bacterial host. In this state, the phage genome (prophage) is maintained within the host environment. Consequently, many prophages have evolved systems to protect the host from heterotypic viral attack. This phenomenon of prophages mediating defense of their host against competitor phages is widespread among temperate mycobacteriophages. We previously showed that the Mycobacterium phage Butters prophage encodes a two-component system (gp30/31) that inhibits infection from a subset of mycobacteriophages that include PurpleHaze, but not Island3. Here we show that Butters gp57r is both necessary and sufficient to inhibit infection by Island3 and other phages. Gp57r acts post-DNA injection and its antagonism results in the impairment of Island3 DNA amplification. Gp57r inhibition of Island3 is absolute with no defense escape mutants. However, mutations mapping to minor tail proteins allow PurpleHaze to overcome gp57r defense. Gp57r has a HEPN domain which is present in many proteins involved in inter-genomic conflicts, suggesting that gp57r may inhibit heterotypic phage infections via its HEPN domain. We also show that Butters gp57r has orthologues in clinical isolates of Mycobacterium abscessus sp. including the phage therapy candidate strain GD91 which was found to be resistant to the panel of phages tested. It is conceivable that this GD91 orthologue of gp57r may mediate resistance to the subset of phages tested. Challenges of this nature underscore the importance of elucidating mechanisms of antiphage systems and mutations that allow for escape from inhibition. IMPORTANCE The evolutionary arms race between phages and their bacteria host is ancient. During lysogeny, temperate phages establish a ceasefire with the host where they do not kill the host but derive shelter from it. Within the phenomenon of prophage-mediated defense, some temperate phages contribute genes that make their host more fit and resistant to infections by other phages. This arrangement has significance for both phage and bacterial evolutionary dynamics. Further, the prevalence of such antiphage systems poses a challenge to phage therapy. Thus, studies aimed at elucidating antiphage systems will further our understanding of phage-bacteria evolution as well as help with efforts to engineer therapeutic phages that circumvent antiphage systems.
+---
+
+# Butters_gp57r
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.01.03.522681
+
+---
+::
diff --git a/content/2.defense-systems/caprel.md b/content/2.defense-systems/caprel.md
index ee88be4fac12e211b0dec51d1976a1274d727c80..0af2ca37b32220765b3a5da7b0427e21a055523b 100644
--- a/content/2.defense-systems/caprel.md
+++ b/content/2.defense-systems/caprel.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Sensing of phage protein
Activator: Direct
Effector: Nucleic acid degrading (pyrophosphorylates tRNAs)
+ PFAM: PF04607
---
-# CapRel
# CapRel
## Description
@@ -67,3 +67,4 @@ items:
## References
Zhang T, Tamman H, Coppieters 't Wallant K, Kurata T, LeRoux M, Srikant S, Brodiazhenko T, Cepauskas A, Talavera A, Martens C, Atkinson GC, Hauryliuk V, Garcia-Pino A, Laub MT. Direct activation of a bacterial innate immune system by a viral capsid protein. Nature. 2022 Dec;612(7938):132-140. doi: 10.1038/s41586-022-05444-z. Epub 2022 Nov 16. PMID: 36385533.
+
diff --git a/content/2.defense-systems/card_nlr.md b/content/2.defense-systems/card_nlr.md
new file mode 100644
index 0000000000000000000000000000000000000000..10d7c9591a06cd3b7be26f48907ae14b62bb9807
--- /dev/null
+++ b/content/2.defense-systems/card_nlr.md
@@ -0,0 +1,23 @@
+---
+title: CARD_NLR
+tableColumns:
+ article:
+ doi: 10.1101/2023.05.28.542683
+ abstract: |
+ Caspase recruitment domains (CARDs) and pyrin domains are important facilitators of inflammasome activity and pyroptosis. Upon pathogen recognition by NLR proteins, CARDs recruit and activate caspases, which, in turn, activate gasdermin pore forming proteins to and induce pyroptotic cell death. Here we show that CARD-like domains are present in defense systems that protect bacteria against phage. The bacterial CARD is essential for protease-mediated activation of certain bacterial gasdermins, which promote cell death once phage infection is recognized. We further show that multiple anti-phage defense systems utilize CARD-like domains to activate a variety of cell death effectors. We find that these systems are triggered by a conserved immune evasion protein that phages use to overcome the bacterial defense system RexAB, demonstrating that phage proteins inhibiting one defense system can activate another. We also detect a phage protein with a predicted CARD-like structure that can inhibit the CARD-containing bacterial gasdermin system. Our results suggest that CARD domains represent an ancient component of innate immune systems conserved from bacteria to humans, and that CARD-dependent activation of gasdermins is conserved in organisms across the tree of life.
+ PFAM: PF00082, PF00089, PF00614, PF01223, PF13091, PF13191, PF13365
+---
+
+# CARD_NLR
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.05.28.542683
+
+---
+::
+
diff --git a/content/2.defense-systems/cbass.md b/content/2.defense-systems/cbass.md
index 12d4998c34b4e159fa1979e362985886160706f6..0283bb78b55a2a9d92166e95d60f7965b0961696 100644
--- a/content/2.defense-systems/cbass.md
+++ b/content/2.defense-systems/cbass.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Signaling molecules
Effector: Divers (Nucleic acid degrading, Nucleotide modifying, Membrane disrupting)
+ PFAM: PF00004, PF00027, PF00899, PF01048, PF01734, PF06508, PF10137, PF14461, PF14464, PF18134, PF18138, PF18144, PF18145, PF18153, PF18159, PF18167, PF18173, PF18178, PF18179, PF18186, PF18303, PF18967
---
-# CBASS
# CBASS
## Example of genomic structure
@@ -69,3 +69,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/charlie_gp32.md b/content/2.defense-systems/charlie_gp32.md
new file mode 100644
index 0000000000000000000000000000000000000000..39c1703a5407cddf35c48368bf0ce73e2110b2a5
--- /dev/null
+++ b/content/2.defense-systems/charlie_gp32.md
@@ -0,0 +1,21 @@
+---
+title: Charlie_gp32
+tableColumns:
+ article:
+ doi: 10.1038/nmicrobiol.2016.251
+ abstract: |
+ Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.
+---
+
+# Charlie_gp32
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1038/nmicrobiol.2016.251
+
+---
+::
diff --git a/content/2.defense-systems/dartg.md b/content/2.defense-systems/dartg.md
index ce8d8989c31016297127dae7b409c4c53cdfcc06..433601261823f0fc8af508c5fdfd0f987a7f2b5e 100644
--- a/content/2.defense-systems/dartg.md
+++ b/content/2.defense-systems/dartg.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Nucleic acid degrading (ADP-ribosylation)
+ PFAM: PF01661, PF14487
---
-# DarTG
# DarTG
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/dazbog.md b/content/2.defense-systems/dazbog.md
index 349869bc031c8e68aaa135e9780f7d5d9b88ed9c..8bd4c17ffa9b1a2d19e21dd194b1c5e4d56b07c1 100644
--- a/content/2.defense-systems/dazbog.md
+++ b/content/2.defense-systems/dazbog.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Dazbog
# Dazbog
## Example of genomic structure
diff --git a/content/2.defense-systems/dctpdeaminase.md b/content/2.defense-systems/dctpdeaminase.md
index f4747904f0cccbd61ff53960abd93676bb37f3b4..76e0ef11d34b4047f45f4f1adb9b37d46382140c 100644
--- a/content/2.defense-systems/dctpdeaminase.md
+++ b/content/2.defense-systems/dctpdeaminase.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Monitoring of the host cell machinery integrity
Activator: Direct
Effector: Nucleotide modifying
+ PFAM: PF00383, PF14437
---
-# dCTPdeaminase
# dCTPdeaminase
## Description
dCTPdeaminase is a family of systems. dCTPdeaminase from Escherichia coli has been shown to provide resistance against various lytic phages when express heterologously in another Escherichia coli.
@@ -64,3 +64,4 @@ items:
- doi: 10.1038/s41564-022-01162-4
---
::
+
diff --git a/content/2.defense-systems/detocs.md b/content/2.defense-systems/detocs.md
new file mode 100644
index 0000000000000000000000000000000000000000..f85fdc513baee5ca8cc41674e05c65fcd083868e
--- /dev/null
+++ b/content/2.defense-systems/detocs.md
@@ -0,0 +1,23 @@
+---
+title: Detocs
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2023.07.020
+ abstract: |
+ During viral infection, cells can deploy immune strategies that deprive viruses of molecules essential for their replication. Here, we report a family of immune effectors in bacteria that, upon phage infection, degrade cellular adenosine triphosphate (ATP) and deoxyadenosine triphosphate (dATP) by cleaving the N-glycosidic bond between the adenine and sugar moieties. These ATP nucleosidase effectors are widely distributed within multiple bacterial defense systems, including cyclic oligonucleotide-based antiviral signaling systems (CBASS), prokaryotic argonautes, and nucleotide-binding leucine-rich repeat (NLR)-like proteins, and we show that ATP and dATP degradation during infection halts phage propagation. By analyzing homologs of the immune ATP nucleosidase domain, we discover and characterize Detocs, a family of bacterial defense systems with a two-component phosphotransfer-signaling architecture. The immune ATP nucleosidase domain is also encoded within diverse eukaryotic proteins with immune-like architectures, and we show biochemically that eukaryotic homologs preserve the ATP nucleosidase activity. Our findings suggest that ATP and dATP degradation is a cell-autonomous innate immune strategy conserved across the tree of life.
+ PFAM: PF01048, PF18742
+---
+
+# Detocs
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2023.07.020
+
+---
+::
+
diff --git a/content/2.defense-systems/dgtpase.md b/content/2.defense-systems/dgtpase.md
index 9c2c4b66c59d0d8df45b8c6bfaed44dde6179e69..0002507cef49ae0063b9029b8dc1582bf6e69bc2 100644
--- a/content/2.defense-systems/dgtpase.md
+++ b/content/2.defense-systems/dgtpase.md
@@ -8,11 +8,9 @@ tableColumns:
Sensor: Monitoring of the host cell machinery integrity
Activator: Direc
Effector: Nucleotide modifying
+ PFAM: PF01966, PF13286
---
-# dGTPase
-# dGTPase
-# dGTPase
# dGTPase
## Example of genomic structure
@@ -55,3 +53,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/disarm.md b/content/2.defense-systems/disarm.md
index 6f04047978a519d8e13e60f4e68cf6fa63bd6e13..fd21a80e4a8460e3736ba9f6395ddbda683939c2 100644
--- a/content/2.defense-systems/disarm.md
+++ b/content/2.defense-systems/disarm.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00145, PF00176, PF00271, PF04851, PF09369, PF13091
---
-# DISARM
# DISARM
## Description
@@ -72,3 +72,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/dmdde.md b/content/2.defense-systems/dmdde.md
index b77c8a641232d59a637704e040ebf4af8ea90f0c..1aa12aa14d24f65d1851f88af2ba19dcaa0aef08 100644
--- a/content/2.defense-systems/dmdde.md
+++ b/content/2.defense-systems/dmdde.md
@@ -4,10 +4,9 @@ tableColumns:
article:
doi: 10.1038/s41586-022-04546-y
abstract: |
- Horizontal gene transfer can trigger rapid shifts in bacterial evolution. Driven by a variety of mobile genetic elements—in particular bacteriophages and plasmids—the ability to share genes within and across species underpins the exceptional adaptability of bacteria. Nevertheless, invasive mobile genetic elements can also present grave risks to the host; bacteria have therefore evolved a vast array of defences against these elements1. Here we identify two plasmid defence systems conserved in the Vibrio cholerae El Tor strains responsible for the ongoing seventh cholera pandemic2–4. These systems, termed DdmABC and DdmDE, are encoded on two major pathogenicity islands that are a hallmark of current pandemic strains. We show that the modules cooperate to rapidly eliminate small multicopy plasmids by degradation. Moreover, the DdmABC system is widespread and can defend against bacteriophage infection by triggering cell suicide (abortive infection, or Abi). Notably, we go on to show that, through an Abi-like mechanism, DdmABC increases the burden of large low-copy-number conjugative plasmids, including a broad-host IncC multidrug resistance plasmid, which creates a fitness disadvantage that counterselects against plasmid-carrying cells. Our results answer the long-standing question of why plasmids, although abundant in environmental strains, are rare in pandemic strains; have implications for understanding the dissemination of antibiotic resistance plasmids; and provide insights into how the interplay between two defence systems has shaped the evolution of the most successful lineage of pandemic V. cholerae.
+ Horizontal gene transfer can trigger rapid shifts in bacterial evolution. Driven by a variety of mobile genetic elements—in particular bacteriophages and plasmids—the ability to share genes within and across species underpins the exceptional adaptability of bacteria. Nevertheless, invasive mobile genetic elements can also present grave risks to the host; bacteria have therefore evolved a vast array of defences against these elements1. Here we identify two plasmid defence systems conserved in the Vibrio cholerae El Tor strains responsible for the ongoing seventh cholera pandemic2-4. These systems, termed DdmABC and DdmDE, are encoded on two major pathogenicity islands that are a hallmark of current pandemic strains. We show that the modules cooperate to rapidly eliminate small multicopy plasmids by degradation. Moreover, the DdmABC system is widespread and can defend against bacteriophage infection by triggering cell suicide (abortive infection, or Abi). Notably, we go on to show that, through an Abi-like mechanism, DdmABC increases the burden of large low-copy-number conjugative plasmids, including a broad-host IncC multidrug resistance plasmid, which creates a fitness disadvantage that counterselects against plasmid-carrying cells. Our results answer the long-standing question of why plasmids, although abundant in environmental strains, are rare in pandemic strains; have implications for understanding the dissemination of antibiotic resistance plasmids; and provide insights into how the interplay between two defence systems has shaped the evolution of the most successful lineage of pandemic V. cholerae.
---
-# DmdDE
# DmdDE
## Example of genomic structure
diff --git a/content/2.defense-systems/dnd.md b/content/2.defense-systems/dnd.md
index 1c5201d9f5383b45e8e1871eb47f6a4f27ef21d8..bb5b8f4071b74a37b625748135ba725bfa91e6b5 100644
--- a/content/2.defense-systems/dnd.md
+++ b/content/2.defense-systems/dnd.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Detecting invading nucleic acid
Activator: Unknown
Effector: Nucleic acid degrading
+ PFAM: PF00266, PF01507, PF01935, PF08870, PF13476, PF14072
---
-# Dnd
# Dnd
## Example of genomic structure
@@ -52,3 +52,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/dodola.md b/content/2.defense-systems/dodola.md
index 8e4cddbba34e716bc8ddae0abef4e96662eaa9c5..546c3eb7b153996ba268f80440c9ae4b1365dae6 100644
--- a/content/2.defense-systems/dodola.md
+++ b/content/2.defense-systems/dodola.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00004, PF07724, PF07728
---
-# Dodola
# Dodola
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/dpd.md b/content/2.defense-systems/dpd.md
index 76d7220211ffc678b38f119aed70b495b2be70c9..eb479e92349b842da5e8a76006fe53e10d1e1638 100644
--- a/content/2.defense-systems/dpd.md
+++ b/content/2.defense-systems/dpd.md
@@ -4,10 +4,10 @@ tableColumns:
article:
doi: 10.1073/pnas.1518570113
abstract: |
- The discovery of ?20-kb gene clusters containing a family of paralogs of tRNA guanosine transglycosylase genes, called tgtA5, alongside 7-cyano-7-deazaguanine (preQ0) synthesis and DNA metabolism genes, led to the hypothesis that 7-deazaguanine derivatives are inserted in DNA. This was established by detecting 2’-deoxy-preQ0 and 2’-deoxy-7-amido-7-deazaguanosine in enzymatic hydrolysates of DNA extracted from the pathogenic, Gram-negative bacteria Salmonella enterica serovar Montevideo. These modifications were absent in the closely related S. enterica serovar Typhimurium LT2 and from a mutant of S. Montevideo, each lacking the gene cluster. This led us to rename the genes of the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA. Similar gene clusters were analyzed in ?150 phylogenetically diverse bacteria, and the modifications were detected in DNA from other organisms containing these clusters, including Kineococcus radiotolerans, Comamonas testosteroni, and Sphingopyxis alaskensis. Comparative genomic analysis shows that, in Enterobacteriaceae, the cluster is a genomic island integrated at the leuX locus, and the phylogenetic analysis of the TgtA5 family is consistent with widespread horizontal gene transfer. Comparison of transformation efficiencies of modified or unmodified plasmids into isogenic S. Montevideo strains containing or lacking the cluster strongly suggests a restriction–modification role for the cluster in Enterobacteriaceae. Another preQ0 derivative, 2’-deoxy-7-formamidino-7-deazaguanosine, was found in the Escherichia coli bacteriophage 9g, as predicted from the presence of homologs of genes involved in the synthesis of the archaeosine tRNA modification. These results illustrate a deep and unexpected evolutionary connection between DNA and tRNA metabolism.
+ The discovery of ?20-kb gene clusters containing a family of paralogs of tRNA guanosine transglycosylase genes, called tgtA5, alongside 7-cyano-7-deazaguanine (preQ0) synthesis and DNA metabolism genes, led to the hypothesis that 7-deazaguanine derivatives are inserted in DNA. This was established by detecting 2’-deoxy-preQ0 and 2’-deoxy-7-amido-7-deazaguanosine in enzymatic hydrolysates of DNA extracted from the pathogenic, Gram-negative bacteria Salmonella enterica serovar Montevideo. These modifications were absent in the closely related S. enterica serovar Typhimurium LT2 and from a mutant of S. Montevideo, each lacking the gene cluster. This led us to rename the genes of the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA. Similar gene clusters were analyzed in ?150 phylogenetically diverse bacteria, and the modifications were detected in DNA from other organisms containing these clusters, including Kineococcus radiotolerans, Comamonas testosteroni, and Sphingopyxis alaskensis. Comparative genomic analysis shows that, in Enterobacteriaceae, the cluster is a genomic island integrated at the leuX locus, and the phylogenetic analysis of the TgtA5 family is consistent with widespread horizontal gene transfer. Comparison of transformation efficiencies of modified or unmodified plasmids into isogenic S. Montevideo strains containing or lacking the cluster strongly suggests a restriction-modification role for the cluster in Enterobacteriaceae. Another preQ0 derivative, 2’-deoxy-7-formamidino-7-deazaguanosine, was found in the Escherichia coli bacteriophage 9g, as predicted from the presence of homologs of genes involved in the synthesis of the archaeosine tRNA modification. These results illustrate a deep and unexpected evolutionary connection between DNA and tRNA metabolism.
+ PFAM: PF00176, PF00270, PF00271, PF01227, PF01242, PF04055, PF04851, PF06508, PF13091, PF13353, PF13394, PF14072
---
-# Dpd
# Dpd
## Example of genomic structure
@@ -38,3 +38,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/drt.md b/content/2.defense-systems/drt.md
index 1b7ae8106ea9d21beeedbce194e5b27b451f5964..d880cdf39837394191a84b414d0da42f8899e922 100644
--- a/content/2.defense-systems/drt.md
+++ b/content/2.defense-systems/drt.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00078
---
-# DRT
# DRT
## Example of genomic structure
@@ -90,3 +90,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/druantia.md b/content/2.defense-systems/druantia.md
index 80e690cdcc0a9b47f667569b212b124a236a6231..7eaab9cfe2217ce792085dc3e1f8f5da8dc3d8a7 100644
--- a/content/2.defense-systems/druantia.md
+++ b/content/2.defense-systems/druantia.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00145, PF00270, PF00271, PF04851, PF09369, PF14236
---
-# Druantia
# Druantia
## Example of genomic structure
@@ -55,3 +55,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/dsr.md b/content/2.defense-systems/dsr.md
index 908c36bcd8e43e718f98ed57e1fad26f9b95d5f2..165b5832dc7c1de3fa5a1efd242c783c7a8e0dd4 100644
--- a/content/2.defense-systems/dsr.md
+++ b/content/2.defense-systems/dsr.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Sensing phage protein
Activator: Direct
Effector: Nucleotide modifying
+ PFAM: PF13289
---
-# Dsr
# Dsr
## Example of genomic structure
@@ -58,3 +58,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/eleos.md b/content/2.defense-systems/eleos.md
index b9710709ed4706c8e4caa087abccfeb2734c320f..f1738f4dcee24eaee9334b00907d1ea79a8acc28 100644
--- a/content/2.defense-systems/eleos.md
+++ b/content/2.defense-systems/eleos.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00350, PF01926, PF18709
---
-# Eleos
# Eleos
The Eleos system was previously described as the Dynamins-like system in (Millman et al, 2022).
@@ -49,3 +49,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/fs_giy_yig.md b/content/2.defense-systems/fs_giy_yig.md
new file mode 100644
index 0000000000000000000000000000000000000000..5d946fe1bbe40c98bb385700bec9b443d90601fe
--- /dev/null
+++ b/content/2.defense-systems/fs_giy_yig.md
@@ -0,0 +1,21 @@
+---
+title: FS_GIY_YIG
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2022.07.014
+ abstract: |
+ Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+---
+
+# FS_GIY_YIG
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2022.07.014
+
+---
+::
diff --git a/content/2.defense-systems/fs_hepn_tm.md b/content/2.defense-systems/fs_hepn_tm.md
new file mode 100644
index 0000000000000000000000000000000000000000..239eb07f319d77e65904350b3c0dc8d65ebaff11
--- /dev/null
+++ b/content/2.defense-systems/fs_hepn_tm.md
@@ -0,0 +1,21 @@
+---
+title: FS_HEPN_TM
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2022.07.014
+ abstract: |
+ Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+---
+
+# FS_HEPN_TM
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2022.07.014
+
+---
+::
diff --git a/content/2.defense-systems/fs_hp.md b/content/2.defense-systems/fs_hp.md
new file mode 100644
index 0000000000000000000000000000000000000000..7e66e331292194c3a965fd2a1d1c3312beec077f
--- /dev/null
+++ b/content/2.defense-systems/fs_hp.md
@@ -0,0 +1,21 @@
+---
+title: FS_HP
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2022.07.014
+ abstract: |
+ Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+---
+
+# FS_HP
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2022.07.014
+
+---
+::
diff --git a/content/2.defense-systems/fs_hp_sdh_sah.md b/content/2.defense-systems/fs_hp_sdh_sah.md
new file mode 100644
index 0000000000000000000000000000000000000000..7db0ba9c3a3c29092a24fd41816a25aee67cf4eb
--- /dev/null
+++ b/content/2.defense-systems/fs_hp_sdh_sah.md
@@ -0,0 +1,23 @@
+---
+title: FS_HP_SDH_sah
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2022.07.014
+ abstract: |
+ Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+ PFAM: PF01972
+---
+
+# FS_HP_SDH_sah
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2022.07.014
+
+---
+::
+
diff --git a/content/2.defense-systems/fs_hsdr_like.md b/content/2.defense-systems/fs_hsdr_like.md
new file mode 100644
index 0000000000000000000000000000000000000000..3f668c217e7fa8f2ea42ecbec4b0f772deb81132
--- /dev/null
+++ b/content/2.defense-systems/fs_hsdr_like.md
@@ -0,0 +1,21 @@
+---
+title: FS_HsdR_like
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2022.07.014
+ abstract: |
+ Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+---
+
+# FS_HsdR_like
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2022.07.014
+
+---
+::
diff --git a/content/2.defense-systems/fs_sma.md b/content/2.defense-systems/fs_sma.md
new file mode 100644
index 0000000000000000000000000000000000000000..502da1115688ede9959038841aacbd4f88d94be0
--- /dev/null
+++ b/content/2.defense-systems/fs_sma.md
@@ -0,0 +1,23 @@
+---
+title: FS_Sma
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2022.07.014
+ abstract: |
+ Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+ PFAM: PF02452
+---
+
+# FS_Sma
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2022.07.014
+
+---
+::
+
diff --git a/content/2.defense-systems/gabija.md b/content/2.defense-systems/gabija.md
index 2f0dbf0d4f93ede5f1a99b6349ff0ed46a1c1323..5de114e47860d3f65e52b6ef48ddd0fa200c9f79 100644
--- a/content/2.defense-systems/gabija.md
+++ b/content/2.defense-systems/gabija.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Direct
Effector: Degrading nucleic acids
+ PFAM: PF00580, PF11398, PF13175, PF13245, PF13304, PF13361, PF13476
---
-# Gabija
# Gabija
## Description
@@ -62,3 +62,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/gao_ape.md b/content/2.defense-systems/gao_ape.md
index db2e7fc37fd622be9a7ca18b34f025defc2990d6..c104f609e95d84fcf1a450160a6edd41de7a14d8 100644
--- a/content/2.defense-systems/gao_ape.md
+++ b/content/2.defense-systems/gao_ape.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Ape
# Gao_Ape
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_her.md b/content/2.defense-systems/gao_her.md
index 62c7d6db8b56a46fee5f13035f90a2e9c5cb1841..771a2e63272dac957d0e911202200492b369fb89 100644
--- a/content/2.defense-systems/gao_her.md
+++ b/content/2.defense-systems/gao_her.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF01935, PF10412, PF13289
---
-# Gao_Her
# Gao_Her
## Example of genomic structure
@@ -53,3 +53,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/gao_hhe.md b/content/2.defense-systems/gao_hhe.md
index 078ea6d6582e21088cc651dc371b14bc19caf54f..77d1201ad3e96895fc117738bde3c28ae378480f 100644
--- a/content/2.defense-systems/gao_hhe.md
+++ b/content/2.defense-systems/gao_hhe.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF04480, PF13086, PF13087, PF13195, PF18741
---
-# Gao_Hhe
# Gao_Hhe
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/gao_iet.md b/content/2.defense-systems/gao_iet.md
index bf817a950409ff92b12200ea8a0f9bbd57e6d8c2..d618744ebdecb04cc53234f959dab9f73428dff1 100644
--- a/content/2.defense-systems/gao_iet.md
+++ b/content/2.defense-systems/gao_iet.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00004, PF00082
---
-# Gao_Iet
# Gao_Iet
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/gao_mza.md b/content/2.defense-systems/gao_mza.md
index 668ce15d2070c1aaa3047e5b2352634f60796e1e..546f21f6a6a88cb622e59ec67d6812bb6eca5495 100644
--- a/content/2.defense-systems/gao_mza.md
+++ b/content/2.defense-systems/gao_mza.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00023, PF04542, PF04545, PF10592, PF10593, PF13589, PF13606, PF14390
---
-# Gao_Mza
# Gao_Mza
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/gao_ppl.md b/content/2.defense-systems/gao_ppl.md
index 107aaf340df6e4f4960e37ec0830af5bde22db31..068702079641ba082b485ae5e80f8bfa8aa5d4f9 100644
--- a/content/2.defense-systems/gao_ppl.md
+++ b/content/2.defense-systems/gao_ppl.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Ppl
# Gao_Ppl
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_qat.md b/content/2.defense-systems/gao_qat.md
index 131275c5dccc7253176fc3546453117e7453e9af..ad110e3354628b98a72f571010b332c890de1085 100644
--- a/content/2.defense-systems/gao_qat.md
+++ b/content/2.defense-systems/gao_qat.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF01026, PF07693
---
-# Gao_Qat
# Gao_Qat
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/gao_rl.md b/content/2.defense-systems/gao_rl.md
index c639d8243b4445af334721a3012231e312cdec20..76346a1d2025bcf25889ec19863e54720221ba64 100644
--- a/content/2.defense-systems/gao_rl.md
+++ b/content/2.defense-systems/gao_rl.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00176, PF00271, PF04465, PF04851, PF06634, PF12635, PF13091, PF13287, PF13290
---
-# Gao_RL
# Gao_RL
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/gao_tery.md b/content/2.defense-systems/gao_tery.md
index 1c2611ad5639a251c3ecfb14d3645f3e17e02a67..c00fc534ec8bb29c804a0a618eafcb8dd433b82b 100644
--- a/content/2.defense-systems/gao_tery.md
+++ b/content/2.defense-systems/gao_tery.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_TerY
# Gao_TerY
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_tmn.md b/content/2.defense-systems/gao_tmn.md
index bc179c0876e04b0a070bd80797813e30aaf8220e..948e84902afaf93fce27596e11843b98768c1c23 100644
--- a/content/2.defense-systems/gao_tmn.md
+++ b/content/2.defense-systems/gao_tmn.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Tmn
# Gao_Tmn
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_upx.md b/content/2.defense-systems/gao_upx.md
index 4469dd3f89411df7cac04d27c66ea34a9919a252..6380af64eb4242b87c2431076b7c2dbde7a82639 100644
--- a/content/2.defense-systems/gao_upx.md
+++ b/content/2.defense-systems/gao_upx.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Upx
# Gao_Upx
## Example of genomic structure
diff --git a/content/2.defense-systems/gaps1.md b/content/2.defense-systems/gaps1.md
new file mode 100644
index 0000000000000000000000000000000000000000..317126a9db10acc5fef56a3d0ecb802aa01106b4
--- /dev/null
+++ b/content/2.defense-systems/gaps1.md
@@ -0,0 +1,21 @@
+---
+title: GAPS1
+tableColumns:
+ article:
+ 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.
+---
+
+# GAPS1
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.03.28.534373
+
+---
+::
diff --git a/content/2.defense-systems/gaps2.md b/content/2.defense-systems/gaps2.md
new file mode 100644
index 0000000000000000000000000000000000000000..5dda7086fe2efe28368be342e1fa17dfefb43abb
--- /dev/null
+++ b/content/2.defense-systems/gaps2.md
@@ -0,0 +1,23 @@
+---
+title: GAPS2
+tableColumns:
+ article:
+ 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.
+ PFAM: PF00533, PF01653, PF03119, PF03120, PF12826, PF14520
+---
+
+# GAPS2
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.03.28.534373
+
+---
+::
+
diff --git a/content/2.defense-systems/gaps4.md b/content/2.defense-systems/gaps4.md
new file mode 100644
index 0000000000000000000000000000000000000000..982c9a601913e2927e6d05027822906000b07c05
--- /dev/null
+++ b/content/2.defense-systems/gaps4.md
@@ -0,0 +1,21 @@
+---
+title: GAPS4
+tableColumns:
+ article:
+ 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.
+---
+
+# GAPS4
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.03.28.534373
+
+---
+::
diff --git a/content/2.defense-systems/gaps6.md b/content/2.defense-systems/gaps6.md
new file mode 100644
index 0000000000000000000000000000000000000000..36906584cd9f29574c09a095c45e534795f862d8
--- /dev/null
+++ b/content/2.defense-systems/gaps6.md
@@ -0,0 +1,21 @@
+---
+title: GAPS6
+tableColumns:
+ article:
+ 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.
+---
+
+# GAPS6
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.03.28.534373
+
+---
+::
diff --git a/content/2.defense-systems/gasdermin.md b/content/2.defense-systems/gasdermin.md
index 24e06d7844df34a70bb8884fbafd42a2d26d45dc..0f0fa0d5b04617036dc9f9bac469c700911f8687 100644
--- a/content/2.defense-systems/gasdermin.md
+++ b/content/2.defense-systems/gasdermin.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Membrane disrupting
---
-# GasderMIN
# GasderMIN
## Example of genomic structure
diff --git a/content/2.defense-systems/hachiman.md b/content/2.defense-systems/hachiman.md
index f893d7779f2cfb3be9c82350704383315dba0cd3..ef66cd4e3da2601bcbaf542faffc6003f6f6af44 100644
--- a/content/2.defense-systems/hachiman.md
+++ b/content/2.defense-systems/hachiman.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00270, PF00271, PF04851, PF08878, PF14130
---
-# Hachiman
# Hachiman
## Description
@@ -62,3 +62,4 @@ items:
1. Doron S, Melamed S, Ofir G, et al. Systematic discovery of antiphage defense systems in the microbial pangenome. *Science*. 2018;359(6379):eaar4120. doi:10.1126/science.aar4120
2. Payne LJ, Todeschini TC, Wu Y, Perry BJ, Ronson CW, Fineran PC, Nobrega FL, Jackson SA. Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. Nucleic Acids Res. 2021 Nov 8;49(19):10868-10878. doi: 10.1093/nar/gkab883. PMID: 34606606; PMCID: PMC8565338.
+
diff --git a/content/2.defense-systems/hna.md b/content/2.defense-systems/hna.md
new file mode 100644
index 0000000000000000000000000000000000000000..1933e3cef49c1d3597b78f11a326bf235e703005
--- /dev/null
+++ b/content/2.defense-systems/hna.md
@@ -0,0 +1,23 @@
+---
+title: Hna
+tableColumns:
+ article:
+ doi: 10.1016/j.chom.2023.01.010
+ abstract: |
+ There is strong selection for the evolution of systems that protect bacterial populations from viral attack. We report a single phage defense protein, Hna, that provides protection against diverse phages in Sinorhizobium meliloti, a nitrogen-fixing alpha-proteobacterium. Homologs of Hna are distributed widely across bacterial lineages, and a homologous protein from Escherichia coli also confers phage defense. Hna contains superfamily II helicase motifs at its N terminus and a nuclease motif at its C terminus, with mutagenesis of these motifs inactivating viral defense. Hna variably impacts phage DNA replication but consistently triggers an abortive infection response in which infected cells carrying the system die but do not release phage progeny. A similar host cell response is triggered in cells containing Hna upon expression of a phage-encoded single-stranded DNA binding protein (SSB), independent of phage infection. Thus, we conclude that Hna limits phage spread by initiating abortive infection in response to a phage protein.
+ PFAM: PF00270, PF04851, PF13307
+---
+
+# Hna
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.chom.2023.01.010
+
+---
+::
+
diff --git a/content/2.defense-systems/isg15-like.md b/content/2.defense-systems/isg15-like.md
index aac319fdd3022bbe548d4c8c9bcfe24565e1d78c..d5894b86ca712c93733e9549d16448b7496cc79d 100644
--- a/content/2.defense-systems/isg15-like.md
+++ b/content/2.defense-systems/isg15-like.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# ISG15-like
# ISG15-like
## Example of genomic structure
diff --git a/content/2.defense-systems/jukab.md b/content/2.defense-systems/jukab.md
new file mode 100644
index 0000000000000000000000000000000000000000..55295693981ca38468826f78a82c88b5c094d644
--- /dev/null
+++ b/content/2.defense-systems/jukab.md
@@ -0,0 +1,23 @@
+---
+title: JukAB
+tableColumns:
+ article:
+ doi: 10.1101/2022.09.17.508391
+ abstract: |
+ Jumbo bacteriophages of the ?KZ-like family are characterized by large genomes (>200 kb) and the remarkable ability to assemble a proteinaceous nucleus-like structure. The nucleus protects the phage genome from canonical DNA-targeting immune systems, such as CRISPR-Cas and restriction-modification. We hypothesized that the failure of common bacterial defenses creates selective pressure for immune systems that target the unique jumbo phage biology. Here, we identify the "jumbo phage killer"(Juk) immune system that is deployed by a clinical isolate of Pseudomonas aeruginosa to resist PhiKZ. Juk immunity rescues the cell by preventing early phage transcription, DNA replication, and nucleus assembly. Phage infection is first sensed by JukA (formerly YaaW), which localizes rapidly to the site of phage infection at the cell pole, triggered by ejected phage factors. The effector protein JukB is recruited by JukA, which is required to enable immunity and the subsequent degradation of the phage DNA. JukA homologs are found in several bacterial phyla and are associated with numerous other putative effectors, many of which provided specific antiPhiKZ activity when expressed in P. aeruginosa. Together, these data reveal a novel strategy for immunity whereby immune factors are recruited to the site of phage protein and DNA ejection to prevent phage progression and save the cell.
+ PFAM: PF13099
+---
+
+# JukAB
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2022.09.17.508391
+
+---
+::
+
diff --git a/content/2.defense-systems/kiwa.md b/content/2.defense-systems/kiwa.md
index e5826c2847154dcb32d49af70231f16d849b13ce..517226cb0141a297dceb079bdb99ab1806119091 100644
--- a/content/2.defense-systems/kiwa.md
+++ b/content/2.defense-systems/kiwa.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF16162
---
-# Kiwa
# Kiwa
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/lamassu-fam.md b/content/2.defense-systems/lamassu-fam.md
index edf177a6f34c504d7fee673a8f9b19fa2c64a981..436fcca0416284f3796ee031ff8c52d5a0ebef39 100644
--- a/content/2.defense-systems/lamassu-fam.md
+++ b/content/2.defense-systems/lamassu-fam.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Diverse (Nucleic acid degrading (?), Nucleotide modifying (?), Membrane disrupting (?))
+ PFAM: PF00753, PF02463, PF05057, PF12532, PF13175, PF13289, PF13476, PF14130
---
-# Lamassu-Fam
# Lamassu-Fam
## Description
@@ -127,3 +127,4 @@ items:
2. Payne LJ, Todeschini TC, Wu Y, et al. Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. *Nucleic Acids Res*. 2021;49(19):10868-10878. doi:10.1093/nar/gkab883
3. Millman, A., Melamed, S., Leavitt, A., Doron, S., Bernheim, A., Hör, J., Lopatina, A., Ofir, G., Hochhauser, D., Stokar-Avihail, A., Tal, N., Sharir, S., Voichek, M., Erez, Z., Ferrer, J.L.M., Dar, D., Kacen, A., Amitai, G., Sorek, R., 2022. An expanding arsenal of immune systems that protect bacteria from phages. bioRxiv. https://doi.org/10.1101/2022.05.11.491447
+
diff --git a/content/2.defense-systems/lit.md b/content/2.defense-systems/lit.md
index f3b1f40494f066faf821eb8da8341d72eb5ec683..fd7f1c625464bad513593761bb1ef4b74378a4af 100644
--- a/content/2.defense-systems/lit.md
+++ b/content/2.defense-systems/lit.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Monitoring host integrity
Activator: Direct
Effector: Other (Cleaves an elongation factor, inhibiting cellular translation
+ PFAM: PF10463
---
-# Lit
# Lit
## Example of genomic structure
@@ -49,3 +49,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/mads.md b/content/2.defense-systems/mads.md
new file mode 100644
index 0000000000000000000000000000000000000000..ef5756d148a1dbf98af858f8b71f18dc005d902d
--- /dev/null
+++ b/content/2.defense-systems/mads.md
@@ -0,0 +1,23 @@
+---
+title: MADS
+tableColumns:
+ article:
+ doi: 10.1101/2023.03.30.534895
+ abstract: |
+ The constant arms race between bacteria and their phages has resulted in a large diversity of bacterial defence systems1,2, with many bacteria carrying several systems3,4. In response, phages often carry counter-defence genes5-9. If and how bacterial defence mechanisms interact to protect against phages with counter-defence genes remains unclear. Here, we report the existence of a novel defence system, coined MADS (Methylation Associated Defence System), which is located in a strongly conserved genomic defence hotspot in Pseudomonas aeruginosa and distributed across Gram-positive and Gram-negative bacteria. We find that the natural co-existence of MADS and a Type IE CRISPR-Cas adaptive immune system in the genome of P. aeruginosa SMC4386 provides synergistic levels of protection against phage DMS3, which carries an anti-CRISPR (acr) gene. Previous work has demonstrated that Acr-phages need to cooperate to overcome CRISPR immunity, with a first sacrificial phage causing host immunosuppression to enable successful secondary phage infections10,11. Modelling and experiments show that the co-existence of MADS and CRISPR-Cas provides strong and durable protection against Acr-phages by disrupting their cooperation and limiting the spread of mutants that overcome MADS. These data reveal that combining bacterial defences can robustly neutralise phage with counter-defence genes, even if each defence on its own can be readily by-passed, which is key to understanding how selection acts on defence combinations and their coevolutionary consequences.
+ PFAM: PF00069, PF01170, PF02384, PF07714, PF08378, PF12728, PF13304, PF13588
+---
+
+# MADS
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.03.30.534895
+
+---
+::
+
diff --git a/content/2.defense-systems/mazef.md b/content/2.defense-systems/mazef.md
new file mode 100644
index 0000000000000000000000000000000000000000..a9401491f733619a3954371d61da3832493f6e12
--- /dev/null
+++ b/content/2.defense-systems/mazef.md
@@ -0,0 +1,23 @@
+---
+title: MazEF
+tableColumns:
+ article:
+ doi: 10.1007/s00438-004-1048-y
+ abstract: |
+ The Escherichia coli gene pair mazEF is a regulatable chromosomal toxin-antitoxin module: mazF encodes a stable toxin and mazE encodes for a labile antitoxin that overcomes the lethal effect of MazF. Because MazE is labile, inhibition of mazE expression results in cell death. We studied the effect of mazEF on the development of bacteriophage P1 upon thermoinduction of the prophage P1CM c1ts and upon infection with virulent phage particles (P1vir). In several E. coli strains, we showed that the ?mazEF derivative strains produced significantly more phages than did the parent strain. In addition, upon induction of K38(P1CM c1ts), nearly all of the ?mazEF mutant cells lysed; in contrast, very few of the parental mazEF + K38 cells underwent lysis. However, most of these cells did not remain viable. Thus, while the ?mazEF cells die as a result of the lytic action of the phage, most of the mazEF + cells are killed by a different mechanism, apparently through the action of the chromosomal mazEF system itself. Furthermore, the introduction of lysogens into a growing non-lysogenic culture is lethal to ?mazEF but not for mazEF + cultures. Thus, although mazEF action causes individual cells to die, upon phage growth this is generally beneficial to the bacterial culture because it causes P1 phage exclusion from the bacterial population. These results provide additional support for the view that bacterial cultures may share some of the characteristics of multicellular organisms.
+ PFAM: PF02452, PF04014
+---
+
+# MazEF
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1007/s00438-004-1048-y
+
+---
+::
+
diff --git a/content/2.defense-systems/menshen.md b/content/2.defense-systems/menshen.md
index b219cfe8e0afe50b30c038c1b756c7943c7c5d64..06f45bc2d5aa329a39f5fd9b90baeef449e6dbe4 100644
--- a/content/2.defense-systems/menshen.md
+++ b/content/2.defense-systems/menshen.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF03235, PF05973, PF12476, PF13175, PF13304, PF13476
---
-# Menshen
# Menshen
## Example of genomic structure
@@ -49,3 +49,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/mmb_gp29_gp30.md b/content/2.defense-systems/mmb_gp29_gp30.md
new file mode 100644
index 0000000000000000000000000000000000000000..4003dd632eacb44a505d6c70e60406877467e5c6
--- /dev/null
+++ b/content/2.defense-systems/mmb_gp29_gp30.md
@@ -0,0 +1,21 @@
+---
+title: MMB_gp29_gp30
+tableColumns:
+ article:
+ doi: 10.1038/nmicrobiol.2016.251
+ abstract: |
+ Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.
+---
+
+# MMB_gp29_gp30
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1038/nmicrobiol.2016.251
+
+---
+::
diff --git a/content/2.defense-systems/mok_hok_sok.md b/content/2.defense-systems/mok_hok_sok.md
index 414f643a1294fbc42df8613961298c2074637373..4ba47b49bb490c2464f8584e33178db594fbaab9 100644
--- a/content/2.defense-systems/mok_hok_sok.md
+++ b/content/2.defense-systems/mok_hok_sok.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Monitoring of the host cell machinery (?)
Activator: Unknown
Effector: Unknown
+ PFAM: PF01848
---
-# Mok_Hok_Sok
# Mok_Hok_Sok
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/mokosh.md b/content/2.defense-systems/mokosh.md
index e46e8009cb7646414506c2ebb24d039a375c3463..a49346b2d0359d0d3c01092848d6ff6011693b92 100644
--- a/content/2.defense-systems/mokosh.md
+++ b/content/2.defense-systems/mokosh.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00069, PF07714, PF08378, PF13086, PF13087, PF13091, PF13245, PF13604
---
-# Mokosh
# Mokosh
## Example of genomic structure
@@ -53,3 +53,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/mqsrac.md b/content/2.defense-systems/mqsrac.md
index 934810f74c7fafa3caf968b00572a504d8da0eef..a4c93c5c0ac05f6fdef6c9a4f60116147ed5ad19 100644
--- a/content/2.defense-systems/mqsrac.md
+++ b/content/2.defense-systems/mqsrac.md
@@ -7,7 +7,6 @@ tableColumns:
Myriad bacterial anti-phage systems have been described and often the mechanism of programmed cell death is invoked for phage inhibition. However, there is little evidence of ‘suicide’ under physiological conditions for these systems. Instead of death to stop phage propagation, we show here that persister cells, i.e., transiently-tolerant, dormant, antibiotic-insensitive cells, are formed and survive using the Escherichia coli C496_10 tripartite toxin/antitoxin system MqsR/MqsA/MqsC to inhibit T2 phage. Specifically, MqsR/MqsA/MqsC inhibited T2 phage by one million-fold and reduced T2 titers by 500-fold. During T2 phage attack, in the presence of MqsR/MqsA/MqsC, evidence of persistence include the single-cell physiological change of reduced metabolism (via flow cytometry), increased spherical morphology (via transmission electron microscopy), and heterogeneous resuscitation. Critically, we found restriction-modification systems (primarily EcoK McrBC) work in concert with the toxin/antitoxin system to inactivate phage, likely while the cells are in the persister state. Phage attack also induces persistence in Klebsiella and Pseudomonas spp. Hence, phage attack invokes a stress response similar to antibiotics, starvation, and oxidation, which leads to persistence, and this dormant state likely allows restriction/modification systems to clear phage DNA.
---
-# MqsRAC
# MqsRAC
## Example of genomic structure
diff --git a/content/2.defense-systems/nhi.md b/content/2.defense-systems/nhi.md
index d3ed4b73874c4889279504685e66f2213104d140..675aa49a87ea1bc19dc64fef05ae1a7b1cb3a008 100644
--- a/content/2.defense-systems/nhi.md
+++ b/content/2.defense-systems/nhi.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Nucleic acid degrading (?)
+ PFAM: PF01443, PF09848, PF13604
---
-# Nhi
# Nhi
## Example of genomic structure
@@ -55,3 +55,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/nixi.md b/content/2.defense-systems/nixi.md
index 0befa10ab77e6909bd74b7a14984b2a120727e94..5b44630e971a6496d2e68c1ff5c34a5a9fe58fb1 100644
--- a/content/2.defense-systems/nixi.md
+++ b/content/2.defense-systems/nixi.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading
---
-# NixI
# NixI
## Example of genomic structure
diff --git a/content/2.defense-systems/nlr.md b/content/2.defense-systems/nlr.md
index 8b997d621d88c01166e2e0780fca3c52bb493c35..47795fc96ff1eea2f88827fb8e786788cbe2ebb7 100644
--- a/content/2.defense-systems/nlr.md
+++ b/content/2.defense-systems/nlr.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF05729
---
-# NLR
# NLR
## Example of genomic structure
@@ -67,3 +67,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/old_exonuclease.md b/content/2.defense-systems/old_exonuclease.md
index 01c94eb824142b612755ffd0c4eeb65057ddadbe..f87ae962eb4aa67371ae8f1c5aeccee8e03feed9 100644
--- a/content/2.defense-systems/old_exonuclease.md
+++ b/content/2.defense-systems/old_exonuclease.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF13175, PF13304
---
-# Old_exonuclease
# Old_exonuclease
## Example of genomic structure
@@ -43,3 +43,4 @@ A system from *Enterobacteria phage P2* in *Escherichia coli* has an anti-phage
**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.
+
diff --git a/content/2.defense-systems/olokun.md b/content/2.defense-systems/olokun.md
index e3c07e3a266769379a83d284d8caa60cbcdcac92..5b4693f442e5541e286bf01be1c6a9bec5160870 100644
--- a/content/2.defense-systems/olokun.md
+++ b/content/2.defense-systems/olokun.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Olokun
# Olokun
## Example of genomic structure
diff --git a/content/2.defense-systems/pago.md b/content/2.defense-systems/pago.md
index eae655759d495515eec2bd93c05b5ba223c9aed8..b0c6c6cb4f12dc1adeaf9cd546d6643c7ecce4a7 100644
--- a/content/2.defense-systems/pago.md
+++ b/content/2.defense-systems/pago.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Detecting invading nucleic acid
Activator: Direct
Effector: Diverse (Nucleotide modifyingn, Membrane disrupting)
+ PFAM: PF02171, PF13289, PF13676, PF14280, PF18742
---
-# pAgo
# pAgo
## Example of genomic structure
@@ -68,3 +68,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/panchino_gp28.md b/content/2.defense-systems/panchino_gp28.md
new file mode 100644
index 0000000000000000000000000000000000000000..7af6b020d3d24d0512a11775590eabc16f13729e
--- /dev/null
+++ b/content/2.defense-systems/panchino_gp28.md
@@ -0,0 +1,23 @@
+---
+title: Panchino_gp28
+tableColumns:
+ article:
+ doi: 10.1038/nmicrobiol.2016.251
+ abstract: |
+ Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.
+ PFAM: PF01170, PF02384, PF13588
+---
+
+# Panchino_gp28
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1038/nmicrobiol.2016.251
+
+---
+::
+
diff --git a/content/2.defense-systems/rst_paris.md b/content/2.defense-systems/paris.md
similarity index 81%
rename from content/2.defense-systems/rst_paris.md
rename to content/2.defense-systems/paris.md
index d8194bf596ef1dfe85391fdd9b468b2caf4bb411..6a881f784e5fb744e7a579bead124a0fead2694f 100644
--- a/content/2.defense-systems/rst_paris.md
+++ b/content/2.defense-systems/paris.md
@@ -1,5 +1,5 @@
---
-title: Rst_PARIS
+title: Paris
tableColumns:
article:
doi: 10.1016/j.chom.2022.02.018
@@ -10,8 +10,8 @@ tableColumns:
Effector: Unknown
---
-# Rst_PARIS
-# Rst_PARIS
+# Paris
+
## Description
PARIS (for Phage Anti-Restriction-Induced System) is a novel anti-phage system. PARIS is found in 4% of prokaryotic genomes. It comprises an ATPase associated with a DUF4435 protein, which can be found either as a two-gene cassette or a single-gene fusion (1).
@@ -20,39 +20,39 @@ This system relies on an unknown [Abortive infection](/general-concepts/abortive
## Example of genomic structure
-The Rst_PARIS system have been describe in a total of 4 subsystems.
+The Paris system have been describe in a total of 4 subsystems.
Here is some example found in the RefSeq database:
-{max-width=750px}
+{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).
-{max-width=750px}
+{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).
-{max-width=750px}
+{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).
-{max-width=750px}
+{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).
## Distribution of the system among prokaryotes
-The Rst_PARIS system is present in a total of 463 different species.
+The Paris system is present in a total of 463 different species.
Among the 22k complete genomes of RefSeq, this system is present in 1145 genomes (5.0 %).
-{max-width=750px}
+{max-width=750px}
-*Proportion of genome encoding the Rst_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.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.*
## Experimental validation
-Rst_PARIS systems were experimentally validated using:
+Paris systems were experimentally validated using:
Subsystem Paris 1 with a system from *Escherichia coli (P4 loci)* in *Escherichia coli* has an anti-phage effect against Lambda, T4, CLB_P2, LF82_P8, Al505_P2, T7 (Rousset et al., 2022)
diff --git a/content/2.defense-systems/pd-lambda-1.md b/content/2.defense-systems/pd-lambda-1.md
index e0894156a35fdd46bcb4c5ad60c2c027fa1c51ca..2d28cf7113d72403b706ea483d1dfd82284d9dee 100644
--- a/content/2.defense-systems/pd-lambda-1.md
+++ b/content/2.defense-systems/pd-lambda-1.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF10544, PF13250, PF13455
---
-# PD-Lambda-1
# PD-Lambda-1
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-lambda-2.md b/content/2.defense-systems/pd-lambda-2.md
index 063ee69f212deacd5d2e7a0bdad9c97d11762053..15f2f18291b4349c32ac377f5c6ffafc4c367f9a 100644
--- a/content/2.defense-systems/pd-lambda-2.md
+++ b/content/2.defense-systems/pd-lambda-2.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF06114, PF09907, PF14350
---
-# PD-Lambda-2
# PD-Lambda-2
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-lambda-3.md b/content/2.defense-systems/pd-lambda-3.md
index a79919bd35561b5e751f003c06d952887efed984..751423dd7d828f9c0b3d4fce8a7b605c0dd9cfd9 100644
--- a/content/2.defense-systems/pd-lambda-3.md
+++ b/content/2.defense-systems/pd-lambda-3.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF09509
---
-# PD-Lambda-3
# PD-Lambda-3
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-lambda-4.md b/content/2.defense-systems/pd-lambda-4.md
index cbc0f346bcb7711f0ffbabac021955b92e429831..416d993896d9b5308722185df5d4e2fe30ab61e2 100644
--- a/content/2.defense-systems/pd-lambda-4.md
+++ b/content/2.defense-systems/pd-lambda-4.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-Lambda-4
# PD-Lambda-4
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-lambda-5.md b/content/2.defense-systems/pd-lambda-5.md
index a13d1c07beb80c9f811be2b99623870ea78e590c..32604e771b7ae3756653d4a77fe25aac35f5abe4 100644
--- a/content/2.defense-systems/pd-lambda-5.md
+++ b/content/2.defense-systems/pd-lambda-5.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF02086
---
-# PD-Lambda-5
# PD-Lambda-5
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-lambda-6.md b/content/2.defense-systems/pd-lambda-6.md
index 190e8c01a91943ce1ab5d4eb33305e733848404b..6fe30c0b3b07af60c54accfba95ac1e22dbb0d56 100644
--- a/content/2.defense-systems/pd-lambda-6.md
+++ b/content/2.defense-systems/pd-lambda-6.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-Lambda-6
# PD-Lambda-6
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-1.md b/content/2.defense-systems/pd-t4-1.md
index bf19377788bb32a61ae898092ef4e5d5d81e6d01..02a95e9cc53d24d78c7a2ad2a90bd82f3ed281da 100644
--- a/content/2.defense-systems/pd-t4-1.md
+++ b/content/2.defense-systems/pd-t4-1.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF13020
---
-# PD-T4-1
# PD-T4-1
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-t4-10.md b/content/2.defense-systems/pd-t4-10.md
index 30e0935337b416c84524c43e22651a8cbbc69ff6..703a26ad7bc0f5e56ff0b326d348609d3746e5da 100644
--- a/content/2.defense-systems/pd-t4-10.md
+++ b/content/2.defense-systems/pd-t4-10.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-10
# PD-T4-10
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-2.md b/content/2.defense-systems/pd-t4-2.md
index 4c058c11fbb90f4105bf8d5d0348ad2b89cd7dce..ccf93b285f65d4bd7e692220d1ffc3c9dbaf6c15 100644
--- a/content/2.defense-systems/pd-t4-2.md
+++ b/content/2.defense-systems/pd-t4-2.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF03235, PF18735
---
-# PD-T4-2
# PD-T4-2
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-t4-3.md b/content/2.defense-systems/pd-t4-3.md
index c61bcf03247240e41028b754cc5228f68c1ed2cc..49c94b69c65de83fdf47b32e942de047f2c5a754 100644
--- a/content/2.defense-systems/pd-t4-3.md
+++ b/content/2.defense-systems/pd-t4-3.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-3
# PD-T4-3
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-4.md b/content/2.defense-systems/pd-t4-4.md
index 7fafa2ee769bb4c3233061ae4efa1ce8a13c65c3..68953b39261e9bad6c4fa9ed9df04b050bcd0100 100644
--- a/content/2.defense-systems/pd-t4-4.md
+++ b/content/2.defense-systems/pd-t4-4.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF13175, PF13304
---
-# PD-T4-4
# PD-T4-4
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-t4-5.md b/content/2.defense-systems/pd-t4-5.md
index c7e600d2fc136b1babd417394d2ccf167b40d8cc..d64a49331ba86e6a98ddac354eeb8530c91a1ed7 100644
--- a/content/2.defense-systems/pd-t4-5.md
+++ b/content/2.defense-systems/pd-t4-5.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF07751
---
-# PD-T4-5
# PD-T4-5
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-t4-6.md b/content/2.defense-systems/pd-t4-6.md
index 0a63138b84a079364694155a4fac51c28a57b4f9..59f764206671fe3be317753e6024c327a80e844a 100644
--- a/content/2.defense-systems/pd-t4-6.md
+++ b/content/2.defense-systems/pd-t4-6.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00069, PF03793, PF07714
---
-# PD-T4-6
# PD-T4-6
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-t4-7.md b/content/2.defense-systems/pd-t4-7.md
index 7279ce0a4f4fb3fb72ddd1afc353cd26eb934f6f..8042bc4c3469270ada86625f5fd77a213739ffbb 100644
--- a/content/2.defense-systems/pd-t4-7.md
+++ b/content/2.defense-systems/pd-t4-7.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-7
# PD-T4-7
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-8.md b/content/2.defense-systems/pd-t4-8.md
index 99dde5a14d7ae079da7b51f838963cd105c43fa1..d0af03b235bd0189a63d3215b3a400a73b9e601e 100644
--- a/content/2.defense-systems/pd-t4-8.md
+++ b/content/2.defense-systems/pd-t4-8.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF14082
---
-# PD-T4-8
# PD-T4-8
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-t4-9.md b/content/2.defense-systems/pd-t4-9.md
index c7425ba907370a781d481e9cb734a0be989cac5a..e490e0942a920576d55df1224e1fd0bdbd62691f 100644
--- a/content/2.defense-systems/pd-t4-9.md
+++ b/content/2.defense-systems/pd-t4-9.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF02556
---
-# PD-T4-9
# PD-T4-9
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-t7-1.md b/content/2.defense-systems/pd-t7-1.md
index aea267edc4e7e8c435aedca8c3c2800c0a6b9a55..7374c6a0d4e660da7b62e69c57efbdb450bd5989 100644
--- a/content/2.defense-systems/pd-t7-1.md
+++ b/content/2.defense-systems/pd-t7-1.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T7-1
# PD-T7-1
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t7-2.md b/content/2.defense-systems/pd-t7-2.md
index 936f9bd2e704375ff7508701218f23c46f73241f..08b19589cff5c570444dbb381aa70e062e42d359 100644
--- a/content/2.defense-systems/pd-t7-2.md
+++ b/content/2.defense-systems/pd-t7-2.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF01935, PF13289
---
-# PD-T7-2
# PD-T7-2
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-t7-3.md b/content/2.defense-systems/pd-t7-3.md
index 68a80228d9751b6d215f01fbf35d5bc1957988e6..f7451c726d7676563dff39f0bdd699f7bce82158 100644
--- a/content/2.defense-systems/pd-t7-3.md
+++ b/content/2.defense-systems/pd-t7-3.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T7-3
# PD-T7-3
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t7-4.md b/content/2.defense-systems/pd-t7-4.md
index f819d8a29f25753de34a1f53158a5744e8fc23ce..a9e79b6b0783e20d81b39659d252b2e393d6539d 100644
--- a/content/2.defense-systems/pd-t7-4.md
+++ b/content/2.defense-systems/pd-t7-4.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF13643
---
-# PD-T7-4
# PD-T7-4
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-t7-5.md b/content/2.defense-systems/pd-t7-5.md
index 859515e92b53a4049d98e9d668e30032c59542d9..908910e3c9f9abecae778f174b37d6d4aad06bb4 100644
--- a/content/2.defense-systems/pd-t7-5.md
+++ b/content/2.defense-systems/pd-t7-5.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T7-5
# PD-T7-5
## Example of genomic structure
diff --git a/content/2.defense-systems/pfiat.md b/content/2.defense-systems/pfiat.md
index 29b87685f5debcd99780b53b5f7a91264d60a330..c12e0eaa0ae3fed604e0300bd8eb97912740c357 100644
--- a/content/2.defense-systems/pfiat.md
+++ b/content/2.defense-systems/pfiat.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF02604, PF05016
---
-# PfiAT
# PfiAT
## Example of genomic structure
@@ -41,3 +41,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/gp29_gp30.md b/content/2.defense-systems/phrann_gp29_gp30.md
similarity index 68%
rename from content/2.defense-systems/gp29_gp30.md
rename to content/2.defense-systems/phrann_gp29_gp30.md
index 7a5b09378076e60b08e6e30afe7fcb4939881984..a9a676db5b349b0ced5dbc99d3421f813812da71 100644
--- a/content/2.defense-systems/gp29_gp30.md
+++ b/content/2.defense-systems/phrann_gp29_gp30.md
@@ -1,33 +1,34 @@
---
-title: gp29_gp30
+title: Phrann_gp29_gp30
tableColumns:
article:
doi: 10.1038/nmicrobiol.2016.251
abstract: |
- Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host–virus dynamics, and counter-defence promotes phage co-evolution.
+ Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.
+ PFAM: PF04607
---
-# gp29_gp30
-# gp29_gp30
+# Phrann_gp29_gp30
+
## Example of genomic structure
-The gp29_gp30 system is composed of 2 proteins: gp30 and, gp29.
+The phrann_gp29_gp30 system is composed of 2 proteins: gp30 and, gp29.
Here is an example found in the RefSeq database:
-{max-width=750px}
+{max-width=750px}
-gp29_gp30 system in the genome of *Mycobacterium tuberculosis* (GCF_002448055.1) is composed of 2 proteins: gp29 (WP_003407164.1)and, gp30 (WP_003407167.1).
+phrann_gp29_gp30 system in the genome of *Mycobacterium tuberculosis* (GCF_002448055.1) is composed of 2 proteins: gp29 (WP_003407164.1)and, gp30 (WP_003407167.1).
## Distribution of the system among prokaryotes
-The gp29_gp30 system is present in a total of 35 different species.
+The phrann_gp29_gp30 system is present in a total of 35 different species.
Among the 22k complete genomes of RefSeq, this system is present in 314 genomes (1.4 %).
-{max-width=750px}
+{max-width=750px}
-*Proportion of genome encoding the gp29_gp30 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
+*Proportion of genome encoding the phrann_gp29_gp30 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
## Relevant abstracts
@@ -38,3 +39,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pif.md b/content/2.defense-systems/pif.md
index 4c3fbfacd3f1f36f46a97ce604c052c3ced28bff..35f6104de85a6eab8dc36b1686e3f07b13ce7e3e 100644
--- a/content/2.defense-systems/pif.md
+++ b/content/2.defense-systems/pif.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Sensing of phage protein
Activator: Unknown
Effector: Membrane disrupting (?)
+ PFAM: PF07693
---
-# Pif
# Pif
## Example of genomic structure
@@ -49,3 +49,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/prrc.md b/content/2.defense-systems/prrc.md
index 39e3b19c7095128589d3d3b0b0f45587bde43507..2149d38b41670a31ea525d7ffbbec6f1d0dc3d1a 100644
--- a/content/2.defense-systems/prrc.md
+++ b/content/2.defense-systems/prrc.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Monitor the integrity of the bacterial cell machinery
Activator: Direct
Effector: Nucleic acid degrading
+ PFAM: PF00270, PF02384, PF04313, PF04851, PF12008, PF12161, PF13166, PF18766
---
-# PrrC
# PrrC
## Example of genomic structure
@@ -48,3 +48,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/psyrta.md b/content/2.defense-systems/psyrta.md
index 2bba747f3ba4e065aca0d9da4dccf0cf3ffce1e3..57f20a11716effef05b80b3d35d00411b3bbf564 100644
--- a/content/2.defense-systems/psyrta.md
+++ b/content/2.defense-systems/psyrta.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00270, PF00271, PF02481, PF04851, PF18306
---
-# PsyrTA
# PsyrTA
## Example of genomic structure
@@ -48,3 +48,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pycsar.md b/content/2.defense-systems/pycsar.md
index 1bbf925fc36ed282875864872d2bcec7276dad83..14cf01416881ead3a83de41ae0bd5542112a9f0d 100644
--- a/content/2.defense-systems/pycsar.md
+++ b/content/2.defense-systems/pycsar.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Signaling molecules
Effector: Membrane disrupting, Nucleotides modifying
+ PFAM: PF00004, PF00027, PF00211, PF00899, PF01734, PF10137, PF14461, PF14464, PF18145, PF18153, PF18303, PF18967
---
-# Pycsar
# Pycsar
## Example of genomic structure
@@ -49,3 +49,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/radar.md b/content/2.defense-systems/radar.md
index 191d0d5165b96fe19b2b45f23789226c20888327..4305d7154cedd3daadfb15e6b2c13660e0a6a3d0 100644
--- a/content/2.defense-systems/radar.md
+++ b/content/2.defense-systems/radar.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading
---
-# RADAR
# RADAR
## Description
diff --git a/content/2.defense-systems/retron.md b/content/2.defense-systems/retron.md
index 9fd21f64d363b4f87b9c4e781ac8efe04db15380..886992931b235224a309ad23cbd024608b5e263f 100644
--- a/content/2.defense-systems/retron.md
+++ b/content/2.defense-systems/retron.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Monitor the integrity of the bacterial cell machinery
Activator: Unknown
Effector: Diverse
+ PFAM: PF00078, PF00089, PF01381, PF01582, PF12686, PF12844, PF13175, PF13304, PF13365, PF13476, PF13560, PF13676
---
-# Retron
# Retron
## Description
@@ -150,3 +150,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rexab.md b/content/2.defense-systems/rexab.md
index fbc34b388d9ed32c633d3b554e329f88bc338121..23efd871d3ad67eb8488a4ccd53b6f23e095926b 100644
--- a/content/2.defense-systems/rexab.md
+++ b/content/2.defense-systems/rexab.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Sensing of complex phage protein/DNA
Activator: Direct
Effector: Membrane disrupting
+ PFAM: PF15968, PF15969
---
-# RexAB
# RexAB
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rloc.md b/content/2.defense-systems/rloc.md
index 68d1fc32471e6a31772a69ea96dfc3bdf6f7def6..5b7db799e25557bd9f88e9cd7b3caeebf8d0fd3f 100644
--- a/content/2.defense-systems/rloc.md
+++ b/content/2.defense-systems/rloc.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Monitor the integrity of the bacterial cell machinery
Activator: Unknown
Effector: Nucleic acid degrading
+ PFAM: PF13166
---
-# RloC
# RloC
## Example of genomic structure
@@ -48,3 +48,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rm.md b/content/2.defense-systems/rm.md
index 70abce918f14627e978ced621637f6c67bfae8ed..aa4206626acff18fc6f609599e1b9d751abd24ec 100644
--- a/content/2.defense-systems/rm.md
+++ b/content/2.defense-systems/rm.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Detecting invading nucleic acid
Activator: Direct
Effector: Nucleic acid degrading
+ PFAM: PF00270, PF02384, PF04313, PF04851, PF12008, PF12161, PF18766
---
-# RM
# RM
## Example of genomic structure
@@ -57,3 +57,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rnlab.md b/content/2.defense-systems/rnlab.md
index c011da5f5e2a8344efd86b148c7d50caadc7f1f3..19f5afb7ab8d5b71e4e5d978deb9be6d4ac2aab5 100644
--- a/content/2.defense-systems/rnlab.md
+++ b/content/2.defense-systems/rnlab.md
@@ -4,13 +4,13 @@ tableColumns:
article:
doi: 10.1534/genetics.110.121798
abstract: |
- RNase LS was originally identified as a potential antagonist of bacteriophage T4 infection. When T4 dmd is defective, RNase LS activity rapidly increases after T4 infection and cleaves T4 mRNAs to antagonize T4 reproduction. Here we show that rnlA, a structural gene of RNase LS, encodes a novel toxin, and that rnlB (formally yfjO), located immediately downstream of rnlA, encodes an antitoxin against RnlA. Ectopic expression of RnlA caused inhibition of cell growth and rapid degradation of mRNAs in ?rnlAB cells. On the other hand, RnlB neutralized these RnlA effects. Furthermore, overexpression of RnlB in wild-type cells could completely suppress the growth defect of a T4 dmd mutant, that is, excess RnlB inhibited RNase LS activity. Pull-down analysis showed a specific interaction between RnlA and RnlB. Compared to RnlA, RnlB was extremely unstable, being degraded by ClpXP and Lon proteases, and this instability may increase RNase LS activity after T4 infection. All of these results suggested that rnlA–rnlB define a new toxin–antitoxin (TA) system.
+ RNase LS was originally identified as a potential antagonist of bacteriophage T4 infection. When T4 dmd is defective, RNase LS activity rapidly increases after T4 infection and cleaves T4 mRNAs to antagonize T4 reproduction. Here we show that rnlA, a structural gene of RNase LS, encodes a novel toxin, and that rnlB (formally yfjO), located immediately downstream of rnlA, encodes an antitoxin against RnlA. Ectopic expression of RnlA caused inhibition of cell growth and rapid degradation of mRNAs in ?rnlAB cells. On the other hand, RnlB neutralized these RnlA effects. Furthermore, overexpression of RnlB in wild-type cells could completely suppress the growth defect of a T4 dmd mutant, that is, excess RnlB inhibited RNase LS activity. Pull-down analysis showed a specific interaction between RnlA and RnlB. Compared to RnlA, RnlB was extremely unstable, being degraded by ClpXP and Lon proteases, and this instability may increase RNase LS activity after T4 infection. All of these results suggested that rnlA-rnlB define a new toxin-antitoxin (TA) system.
Sensor: Monitor the integrity of the bacterial cell machinery
Activator: Direct
Effector: Nucleic acid degrading
+ PFAM: PF15933, PF15935, PF18869, PF19034
---
-# RnlAB
# RnlAB
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rosmerta.md b/content/2.defense-systems/rosmerta.md
index 89ad12cb9ad75226f67ea5bfb960d40a49b6bc57..8cb81a2e4d25a53c583bdb408b405cf538546b28 100644
--- a/content/2.defense-systems/rosmerta.md
+++ b/content/2.defense-systems/rosmerta.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF01381, PF06114, PF12844, PF13443, PF13560
---
-# RosmerTA
# RosmerTA
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rst_2tm_1tm_tir.md b/content/2.defense-systems/rst_2tm_1tm_tir.md
index bcdaa38960f6864f40bc11512f6a82fbe507b0a4..533f30ce5f9daa8a4e1a3184c312888f9c151ab9 100644
--- a/content/2.defense-systems/rst_2tm_1tm_tir.md
+++ b/content/2.defense-systems/rst_2tm_1tm_tir.md
@@ -5,9 +5,9 @@ tableColumns:
doi: 10.1016/j.chom.2022.02.018
abstract: |
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.
+ PFAM: PF13676
---
-# Rst_2TM_1TM_TIR
# Rst_2TM_1TM_TIR
## Example of genomic structure
@@ -38,3 +38,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rst_3hp.md b/content/2.defense-systems/rst_3hp.md
index c10986546e46dbdacec03d0e691f7c535ce8c83a..b31ab1f89df8f1b96b4e0979738f51ed0a3a7de4 100644
--- a/content/2.defense-systems/rst_3hp.md
+++ b/content/2.defense-systems/rst_3hp.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Rst_3HP
# Rst_3HP
## Example of genomic structure
diff --git a/content/2.defense-systems/rst_duf4238.md b/content/2.defense-systems/rst_duf4238.md
index bb1671511d1c57233aff2837a653f4ec32b62532..95ba0b60c3652d537d73a6934eab4cbf3ab68a87 100644
--- a/content/2.defense-systems/rst_duf4238.md
+++ b/content/2.defense-systems/rst_duf4238.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF14022
---
-# Rst_DUF4238
# Rst_DUF4238
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rst_gop_beta_cll.md b/content/2.defense-systems/rst_gop_beta_cll.md
index c6049f36b62d2c7d11e0bcf53761b9bc3c8504de..3d11950e030ca830dee981e9c091ac44e8bf9536 100644
--- a/content/2.defense-systems/rst_gop_beta_cll.md
+++ b/content/2.defense-systems/rst_gop_beta_cll.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF14350
---
-# Rst_gop_beta_cll
# Rst_gop_beta_cll
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rst_helicaseduf2290.md b/content/2.defense-systems/rst_helicaseduf2290.md
index 51a229be4f321b7d9e1a10198f13f48778da0f55..ed03b13384a1f7f2d6e609ba471329f4c57034fe 100644
--- a/content/2.defense-systems/rst_helicaseduf2290.md
+++ b/content/2.defense-systems/rst_helicaseduf2290.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF10053, PF13538
---
-# Rst_HelicaseDUF2290
# Rst_HelicaseDUF2290
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rst_hydrolase-3tm.md b/content/2.defense-systems/rst_hydrolase-3tm.md
index be86ec803569b9cc0e0cfcce7faf9dc56a84e24c..de56898245dc84222ed34071c22461072e1a42d7 100644
--- a/content/2.defense-systems/rst_hydrolase-3tm.md
+++ b/content/2.defense-systems/rst_hydrolase-3tm.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF13242, PF13419
---
-# Rst_Hydrolase-3Tm
# Rst_Hydrolase-3Tm
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rst_rt-nitrilase-tm.md b/content/2.defense-systems/rst_rt-nitrilase-tm.md
index 5522003e962c147deeb06e1f38556fb843ec8205..fe87e58fa6a488bb14b7787302bdbad81bfa1d8f 100644
--- a/content/2.defense-systems/rst_rt-nitrilase-tm.md
+++ b/content/2.defense-systems/rst_rt-nitrilase-tm.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00078
---
-# Rst_RT-nitrilase-Tm
# Rst_RT-nitrilase-Tm
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rst_tir-nlr.md b/content/2.defense-systems/rst_tir-nlr.md
index 59f5c281415d98e517e5479b338b9505d8630d66..d07a33c7d8f9cc73986260029b99ab42d7184930 100644
--- a/content/2.defense-systems/rst_tir-nlr.md
+++ b/content/2.defense-systems/rst_tir-nlr.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF13676
---
-# Rst_TIR-NLR
# Rst_TIR-NLR
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/sanata.md b/content/2.defense-systems/sanata.md
index 54a92cf671663f04a7da08554f081e7f1984cfd5..d032f25771fdc50fd4a7f09edf691535a7b8b123 100644
--- a/content/2.defense-systems/sanata.md
+++ b/content/2.defense-systems/sanata.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF08843
---
-# SanaTA
# SanaTA
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/sefir.md b/content/2.defense-systems/sefir.md
index e299110e980a2338651e255c224a5291fb4bb2c1..5d3f6d7a0839184aa8d36d12e3877a6519eb8145 100644
--- a/content/2.defense-systems/sefir.md
+++ b/content/2.defense-systems/sefir.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF08357, PF13676
---
-# SEFIR
# SEFIR
## Description
The SEFIR defense system is composed of a single bacterial SEFIR (bSEFIR)-domain protein. bSEFIR-domain genes were identified in bacterial genomes, were shown to be enriched in defense islands and the activity of the defense system was first experimentally validated in *Bacillus sp.* NIO-1130 against phage phi29 [1].
@@ -60,3 +60,4 @@ items:
## References
[1] Millman, A. et al. An expanded arsenal of immune systems that protect bacteria from phages. Cell Host Microbe 30, 1556-1569.e5 (2022).
[2] Novatchkova, M., Leibbrandt, A., Werzowa, J., Neubüser, A., & Eisenhaber, F. (2003). The STIR-domain superfamily in signal transduction, development and immunity. _Trends in biochemical sciences_, _28_(5), 226-229.
+
diff --git a/content/2.defense-systems/septu.md b/content/2.defense-systems/septu.md
index 487f76c7bc296b8e031c79a648eb9728aa48c879..5f7a8218325c7b8a634c137d0f479ea4f965e84f 100644
--- a/content/2.defense-systems/septu.md
+++ b/content/2.defense-systems/septu.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF13175, PF13304, PF13476
---
-# Septu
# Septu
## Example of genomic structure
@@ -51,3 +51,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/shango.md b/content/2.defense-systems/shango.md
index 399734e0eca8a1149130aa6b8d8f684323ca69c0..fd02239b88b9fc19a435ec159a8ba44200cd108f 100644
--- a/content/2.defense-systems/shango.md
+++ b/content/2.defense-systems/shango.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00270, PF00271, PF05099, PF10923, PF13208, PF15615
---
-# Shango
# Shango
## Description
@@ -67,4 +67,5 @@ Shango was discovered in parallel by Adi Millman (Sorek group) and the team of J
[2] Johnson, Matthew, Laderman, Eric, Huiting, Erin, Zhang, Charles, Davidson, Alan, & Bondy-Denomy, Joseph. (2022). _Core Defense Hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems_. [https://doi.org/10.5281/ZENODO.7254690](https://doi.org/10.5281/ZENODO.7254690)
-[3] Alekhina, O., Valkovicova, L., & Turna, J. (2011). Study of membrane attachment and in vivo co-localization of TerB protein from uropathogenic Escherichia coli KL53. _General physiology and biophysics_, _30_(3), 286-292.
\ No newline at end of file
+[3] Alekhina, O., Valkovicova, L., & Turna, J. (2011). Study of membrane attachment and in vivo co-localization of TerB protein from uropathogenic Escherichia coli KL53. _General physiology and biophysics_, _30_(3), 286-292.
+
diff --git a/content/2.defense-systems/shedu.md b/content/2.defense-systems/shedu.md
index d775b45102902e08e3684a0bbe7206060c6bab70..0c365cb36820c98c8af4944e59634e13d98a46ff 100644
--- a/content/2.defense-systems/shedu.md
+++ b/content/2.defense-systems/shedu.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF14082
---
-# Shedu
# Shedu
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/shosta.md b/content/2.defense-systems/shosta.md
index 9c1c779c4ce0db7655d806fe20634609fb7fef90..02640091e6ac4900782e51a9c2681394ccbb8a7a 100644
--- a/content/2.defense-systems/shosta.md
+++ b/content/2.defense-systems/shosta.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF02481
---
-# ShosTA
# ShosTA
## Example of genomic structure
@@ -51,3 +51,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/sofic.md b/content/2.defense-systems/sofic.md
index 3d1ca7e59b480aa165175bd442c4786637084783..a8d3ab5928e4a47dc5946072455a158bd2a6cf7c 100644
--- a/content/2.defense-systems/sofic.md
+++ b/content/2.defense-systems/sofic.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF02661, PF13784
---
-# SoFIC
# SoFIC
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/spbk.md b/content/2.defense-systems/spbk.md
index d7b93c1725028873dd962de0885dab9a54bc52fb..f43df459e39cd982537eca3f1a996263f59525c4 100644
--- a/content/2.defense-systems/spbk.md
+++ b/content/2.defense-systems/spbk.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF13676
---
-# SpbK
# SpbK
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/sspbcde.md b/content/2.defense-systems/sspbcde.md
index fc7e586545095935207fd3ce3f38a495d74f5d0e..c79f2d34ea9dadce2320ca05b3c06573716877bc 100644
--- a/content/2.defense-systems/sspbcde.md
+++ b/content/2.defense-systems/sspbcde.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Detecting invading nucleic acid
Activator: Direct
Effector: Nucleic acid degrading
+ PFAM: PF01507, PF01580, PF03235, PF07510, PF13182
---
-# SspBCDE
# SspBCDE
## Example of genomic structure
@@ -54,3 +54,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/stk2.md b/content/2.defense-systems/stk2.md
index 3a1fa18fbfb474e0aac73a0e622c049871f1a452..e9e59a5d8b184f7f7e522cfb0c40f70f403d2375 100644
--- a/content/2.defense-systems/stk2.md
+++ b/content/2.defense-systems/stk2.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Sensing of phage protein
Activator: Direct
Effector: Other (protein modifying)
+ PFAM: PF00069, PF07714
---
-# Stk2
# Stk2
## Description
@@ -58,3 +58,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/thoeris.md b/content/2.defense-systems/thoeris.md
index 51772f36b9a87283e78b2d742d2d883c36d6b458..be35be5d0868ea4667c5aa7602e85053e1bd687e 100644
--- a/content/2.defense-systems/thoeris.md
+++ b/content/2.defense-systems/thoeris.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Signaling
Effector: Nucleotide modifying
+ PFAM: PF08937, PF13289, PF18185
---
-# Thoeris
# Thoeris
## Example of genomic structure
@@ -56,3 +56,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/tiamat.md b/content/2.defense-systems/tiamat.md
index 169abf12a873e98059be7f959d5dd5c195c20565..bafd49c353b1c7f0afc5544b3d1d615d8eb41e3e 100644
--- a/content/2.defense-systems/tiamat.md
+++ b/content/2.defense-systems/tiamat.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00656, PF13020
---
-# Tiamat
# Tiamat
## Example of genomic structure
@@ -47,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/uzume.md b/content/2.defense-systems/uzume.md
index 167eb495d27e5880fd2b2dc7b8da861ae5bf9ba4..11e72a49b3f82fe039c68673dbf1bd97c6a3e444 100644
--- a/content/2.defense-systems/uzume.md
+++ b/content/2.defense-systems/uzume.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Uzume
# Uzume
## Example of genomic structure
diff --git a/content/2.defense-systems/viperin.md b/content/2.defense-systems/viperin.md
index 8bf85a847b9f1e2e0531d0928c89f8f043e2e6d2..4ac98994c8401a9e1197d0626ed9241e1ea70bff 100644
--- a/content/2.defense-systems/viperin.md
+++ b/content/2.defense-systems/viperin.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Direct
Effector: Nucleotide modifying
+ PFAM: PF04055, PF13353
---
-# Viperin
# Viperin
## Description
@@ -98,3 +98,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/wadjet.md b/content/2.defense-systems/wadjet.md
index 1b77a8a716685a0f3663daa8c56f4d17ff67671a..a6e658107a60b14d8204f55638241b57e6aeaa5d 100644
--- a/content/2.defense-systems/wadjet.md
+++ b/content/2.defense-systems/wadjet.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Detecting invading nucleic acid
Activator: Direct
Effector: Nucleic acid degrading
+ PFAM: PF09660, PF09661, PF09664, PF09983, PF11795, PF11796, PF11855, PF13555, PF13558, PF13835
---
-# Wadjet
# Wadjet
## Example of genomic structure
@@ -49,3 +49,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/zorya.md b/content/2.defense-systems/zorya.md
index f5acde756c7b50e63e2cc655edc598df6458ae12..007f41ab14429154ad26324aae03f988dd5ec4f2 100644
--- a/content/2.defense-systems/zorya.md
+++ b/content/2.defense-systems/zorya.md
@@ -8,9 +8,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00176, PF00271, PF00691, PF04851, PF15611
---
-# Zorya
# Zorya
## Example of genomic structure
@@ -56,3 +56,4 @@ items:
---
::
+
diff --git a/public/avast/AVAST_I,AVAST_I__Avs1A,0,V-plddts_85.07081.pdb b/public/avs/AVAST_I,AVAST_I__Avs1A,0,V-plddts_85.07081.pdb
similarity index 100%
rename from public/avast/AVAST_I,AVAST_I__Avs1A,0,V-plddts_85.07081.pdb
rename to public/avs/AVAST_I,AVAST_I__Avs1A,0,V-plddts_85.07081.pdb
diff --git a/public/avast/AVAST_I,AVAST_I__Avs1B,0,V-plddts_80.96481.pdb b/public/avs/AVAST_I,AVAST_I__Avs1B,0,V-plddts_80.96481.pdb
similarity index 100%
rename from public/avast/AVAST_I,AVAST_I__Avs1B,0,V-plddts_80.96481.pdb
rename to public/avs/AVAST_I,AVAST_I__Avs1B,0,V-plddts_80.96481.pdb
diff --git a/public/avast/AVAST_I,AVAST_I__Avs1C,0,V-plddts_81.74849.pdb b/public/avs/AVAST_I,AVAST_I__Avs1C,0,V-plddts_81.74849.pdb
similarity index 100%
rename from public/avast/AVAST_I,AVAST_I__Avs1C,0,V-plddts_81.74849.pdb
rename to public/avs/AVAST_I,AVAST_I__Avs1C,0,V-plddts_81.74849.pdb
diff --git a/public/avast/AVAST_I.svg b/public/avs/Avs_I.svg
similarity index 100%
rename from public/avast/AVAST_I.svg
rename to public/avs/Avs_I.svg
diff --git a/public/avast/AVAST_II.svg b/public/avs/Avs_II.svg
similarity index 100%
rename from public/avast/AVAST_II.svg
rename to public/avs/Avs_II.svg
diff --git a/public/avast/AVAST_III.svg b/public/avs/Avs_III.svg
similarity index 100%
rename from public/avast/AVAST_III.svg
rename to public/avs/Avs_III.svg
diff --git a/public/avast/AVAST_IV.svg b/public/avs/Avs_IV.svg
similarity index 100%
rename from public/avast/AVAST_IV.svg
rename to public/avs/Avs_IV.svg
diff --git a/public/avast/AVAST_V.svg b/public/avs/Avs_V.svg
similarity index 100%
rename from public/avast/AVAST_V.svg
rename to public/avs/Avs_V.svg
diff --git a/public/avast/Distribution_AVAST.svg b/public/avs/Distribution_Avs.svg
similarity index 100%
rename from public/avast/Distribution_AVAST.svg
rename to public/avs/Distribution_Avs.svg
diff --git a/public/rst_paris/Distribution_Rst_PARIS.svg b/public/paris/Distribution_Paris.svg
similarity index 100%
rename from public/rst_paris/Distribution_Rst_PARIS.svg
rename to public/paris/Distribution_Paris.svg
diff --git a/public/rst_paris/PARIS_I.svg b/public/paris/PARIS_I.svg
similarity index 100%
rename from public/rst_paris/PARIS_I.svg
rename to public/paris/PARIS_I.svg
diff --git a/public/rst_paris/PARIS_II.svg b/public/paris/PARIS_II.svg
similarity index 100%
rename from public/rst_paris/PARIS_II.svg
rename to public/paris/PARIS_II.svg
diff --git a/public/rst_paris/PARIS_II_merge.svg b/public/paris/PARIS_II_merge.svg
similarity index 100%
rename from public/rst_paris/PARIS_II_merge.svg
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