diff --git a/content/3.defense-systems/abia.md b/content/3.defense-systems/abia.md
index 767f5802c40c02fed2e194be8e3acda25c70c482..e0fba523c2727dcf763c753ebcc48e1f624fd104 100644
--- a/content/3.defense-systems/abia.md
+++ b/content/3.defense-systems/abia.md
@@ -44,35 +44,35 @@ The system was detected in 35 different species.
Proportion of genome encoding the AbiA system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### AbiA_large
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abia/AbiA_large__AbiA_large-plddts_90.82916.pdb
+dataUrls:
+ - /abia/AbiA_large__AbiA_large.pdb
+
---
::
-
### AbiA_small
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abia/AbiA_small,AbiA_small__AbiA_SLATT,0,DF-plddts_94.13374.pdb
----
-::
+dataUrls:
+ - /abia/AbiA_small.AbiA_small__AbiA_small.0.DF.pdb
+ - /abia/AbiA_small.AbiA_small__AbiA_SLATT.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /abia/AbiA_small,AbiA_small__AbiA_small,0,DF-plddts_89.82347.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -98,3 +98,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/abib.md b/content/3.defense-systems/abib.md
index 63d2aafc02c6ec40ca8865606669a139eb4e22ff..0b8fb135202cea0924fb3838917ce33b38a29c55 100644
--- a/content/3.defense-systems/abib.md
+++ b/content/3.defense-systems/abib.md
@@ -47,18 +47,22 @@ The system was detected in 5 different species.
Proportion of genome encoding the AbiB system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### AbiB
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abib/AbiB__AbiB-plddts_74.5545.pdb
+dataUrls:
+ - /abib/AbiB__AbiB.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -84,3 +88,4 @@ end
</mermaid>
+
diff --git a/content/3.defense-systems/abic.md b/content/3.defense-systems/abic.md
index aaa95780af0d8dcd6f8cd1c08d54d953d924639b..6876763def56d214f24799d60ee9f2cd50a52b24 100644
--- a/content/3.defense-systems/abic.md
+++ b/content/3.defense-systems/abic.md
@@ -35,18 +35,22 @@ The system was detected in 57 different species.
Proportion of genome encoding the AbiC system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### AbiC
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abic/AbiC__AbiC-plddts_83.80335.pdb
+dataUrls:
+ - /abic/AbiC__AbiC.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
@@ -102,14 +106,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
-
----
-::
diff --git a/content/3.defense-systems/abid.md b/content/3.defense-systems/abid.md
index f41523d23aa0cb0364af67c5c369ee186252b381..6cf817e36c00c87aa6f323b9c2eae022e9242a84 100644
--- a/content/3.defense-systems/abid.md
+++ b/content/3.defense-systems/abid.md
@@ -35,18 +35,22 @@ The system was detected in 964 different species.
Proportion of genome encoding the AbiD system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### AbiD
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abid/AbiD__AbiD-plddts_91.87407.pdb
+dataUrls:
+ - /abid/AbiD__AbiD.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -72,14 +76,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
-
----
-::
diff --git a/content/3.defense-systems/abie.md b/content/3.defense-systems/abie.md
index e8f45950fa498daa52fd7a656174d58710993ccf..706909d8b55d7d12a1bee81b4a70dde9612aaeee 100644
--- a/content/3.defense-systems/abie.md
+++ b/content/3.defense-systems/abie.md
@@ -44,25 +44,23 @@ The system was detected in 1107 different species.
Proportion of genome encoding the AbiE system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### AbiE
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abie/AbiE,AbiE__AbiEi,0,V-plddts_85.81224.pdb
----
-::
+dataUrls:
+ - /abie/AbiE.AbiE__AbiEi.0.V.pdb
+ - /abie/AbiE.AbiE__AbiEii.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /abie/AbiE,AbiE__AbiEii,0,V-plddts_90.73768.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -86,15 +84,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
- - doi: 10.1093/nar/gkt1419
-
----
-::
diff --git a/content/3.defense-systems/abig.md b/content/3.defense-systems/abig.md
index 1d85b256b8ba0480f6f9d088bb7c1da199c3a7c3..87b0b1968205c54dd5d4cb32ff22a7515e3c83fd 100644
--- a/content/3.defense-systems/abig.md
+++ b/content/3.defense-systems/abig.md
@@ -35,25 +35,23 @@ The system was detected in 22 different species.
Proportion of genome encoding the AbiG system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### AbiG
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abig/AbiG,AbiG__AbiGi,0,V-plddts_92.08021.pdb
----
-::
+dataUrls:
+ - /abig/AbiG.AbiG__AbiGi.0.V.pdb
+ - /abig/AbiG.AbiG__AbiGii.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /abig/AbiG,AbiG__AbiGii,0,V-plddts_88.01846.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -79,14 +77,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
-
----
-::
diff --git a/content/3.defense-systems/abih.md b/content/3.defense-systems/abih.md
index 475a4ffd9b910d0ec2db566c1f209ddf26bd5f8e..7b937eff4f742b64172685fd9a7c11ba540664f5 100644
--- a/content/3.defense-systems/abih.md
+++ b/content/3.defense-systems/abih.md
@@ -46,18 +46,22 @@ The system was detected in 439 different species.
Proportion of genome encoding the AbiH system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### AbiH
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abih/AbiH__AbiH-plddts_91.3485.pdb
+dataUrls:
+ - /abih/AbiH__AbiH.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -85,3 +89,4 @@ end
+
diff --git a/content/3.defense-systems/abii.md b/content/3.defense-systems/abii.md
index 6a004f1fc436a9282feedf8e9227e2297469c335..97b709b0c0e0f23f3d0b4e3f32c24f4535c6d59a 100644
--- a/content/3.defense-systems/abii.md
+++ b/content/3.defense-systems/abii.md
@@ -33,18 +33,22 @@ The system was detected in 6 different species.
Proportion of genome encoding the AbiI system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### AbiI
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abii/AbiI__AbiI-plddts_90.31131.pdb
+dataUrls:
+ - /abii/AbiI__AbiI.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -69,13 +73,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
-
----
-::
diff --git a/content/3.defense-systems/abij.md b/content/3.defense-systems/abij.md
index 2a60a05365db4321b54c4e834a854f77a38b724a..03b87ac96c00ce0a485812367d3c79e45d495648 100644
--- a/content/3.defense-systems/abij.md
+++ b/content/3.defense-systems/abij.md
@@ -34,18 +34,22 @@ The system was detected in 261 different species.
Proportion of genome encoding the AbiJ system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### AbiJ
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abij/AbiJ__AbiJ-plddts_85.12535.pdb
+dataUrls:
+ - /abij/AbiJ__AbiJ.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -69,14 +73,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
-
----
-::
diff --git a/content/3.defense-systems/abik.md b/content/3.defense-systems/abik.md
index 284f5d9d62f7bba81268f16380f9bc3bcd652453..607fec7f16eeb11021d1d5eb72831eb1283a2903 100644
--- a/content/3.defense-systems/abik.md
+++ b/content/3.defense-systems/abik.md
@@ -34,18 +34,22 @@ The system was detected in 32 different species.
Proportion of genome encoding the AbiK system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### AbiK
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abik/AbiK__AbiK-plddts_91.42521.pdb
+dataUrls:
+ - /abik/AbiK__AbiK.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -71,15 +75,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
- - doi: 10.1093/nar/gkac467
-
----
-::
diff --git a/content/3.defense-systems/abil.md b/content/3.defense-systems/abil.md
index 5f3fba645e30f51a3cdb466d3c3b03a0e9342d59..c7bc8f3471908b8773c1abeafc0e97d9910cd55f 100644
--- a/content/3.defense-systems/abil.md
+++ b/content/3.defense-systems/abil.md
@@ -49,25 +49,23 @@ The system was detected in 126 different species.
Proportion of genome encoding the AbiL system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### AbiL
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abil/AbiL,AbiL__AbiLi,0,V-plddts_89.17612.pdb
----
-::
+dataUrls:
+ - /abil/AbiL.AbiL__AbiLi.0.V.pdb
+ - /abil/AbiL.AbiL__AbiLii.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /abil/AbiL,AbiL__AbiLii,0,V-plddts_86.69766.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -95,3 +93,4 @@ end
+
diff --git a/content/3.defense-systems/abin.md b/content/3.defense-systems/abin.md
index 2599e99614b10192126c7e1ae9c0601de2e201ed..b803307965f8875850b7d764acc05082934da692 100644
--- a/content/3.defense-systems/abin.md
+++ b/content/3.defense-systems/abin.md
@@ -33,18 +33,22 @@ The system was detected in 52 different species.
Proportion of genome encoding the AbiN system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### AbiN
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abin/AbiN__AbiN-plddts_84.27216.pdb
+dataUrls:
+ - /abin/AbiN__AbiN.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -69,13 +73,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
-
----
-::
diff --git a/content/3.defense-systems/abio.md b/content/3.defense-systems/abio.md
index 88ef25904ea344cb8c22606f2a755893559e3c4e..483e179b8bb53fd36aafed2de493aec25beb7027 100644
--- a/content/3.defense-systems/abio.md
+++ b/content/3.defense-systems/abio.md
@@ -34,18 +34,22 @@ The system was detected in 61 different species.
Proportion of genome encoding the AbiO system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### AbiO
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abio/AbiO__AbiO-plddts_87.43501.pdb
+dataUrls:
+ - /abio/AbiO__AbiO.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -70,14 +74,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
-
----
-::
diff --git a/content/3.defense-systems/abip2.md b/content/3.defense-systems/abip2.md
index 0b4bd61664398adcdb516e1f8dea26caefe62b3b..83840172caca6f29540f49d1d79b65a4a8937bc0 100644
--- a/content/3.defense-systems/abip2.md
+++ b/content/3.defense-systems/abip2.md
@@ -34,18 +34,22 @@ The system was detected in 96 different species.
Proportion of genome encoding the AbiP2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### AbiP2
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abip2/AbiP2__AbiP2-plddts_93.08218.pdb
+dataUrls:
+ - /abip2/AbiP2__AbiP2.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -78,15 +82,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
- - doi: 10.1093/nar/gkac467
-
----
-::
diff --git a/content/3.defense-systems/abiq.md b/content/3.defense-systems/abiq.md
index b9bec1ad48e4788b2e57cfe91d8b3fc945f14a62..2c65ede1732f5049eac58eceab15fd447ce8a64e 100644
--- a/content/3.defense-systems/abiq.md
+++ b/content/3.defense-systems/abiq.md
@@ -34,18 +34,22 @@ The system was detected in 111 different species.
Proportion of genome encoding the AbiQ system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### AbiQ
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abiq/AbiQ__AbiQ-plddts_90.84212.pdb
+dataUrls:
+ - /abiq/AbiQ__AbiQ.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -70,15 +74,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
- - doi: 10.1128/AEM.64.12.4748-4756.1998
-
----
-::
diff --git a/content/3.defense-systems/abir.md b/content/3.defense-systems/abir.md
index 5336f7b18607989eb44908cdfe9b6d0073a0a9f1..7edcc5adfbb0e0880dccff38badd820b6f04abe3 100644
--- a/content/3.defense-systems/abir.md
+++ b/content/3.defense-systems/abir.md
@@ -34,32 +34,24 @@ The system was detected in 28 different species.
Proportion of genome encoding the AbiR system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### AbiR
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abir/AbiR,AbiR__AbiRa,0,V-plddts_88.45598.pdb
----
-::
+dataUrls:
+ - /abir/AbiR.AbiR__AbiRc.0.V.pdb
+ - /abir/AbiR.AbiR__AbiRb.0.V.pdb
+ - /abir/AbiR.AbiR__AbiRa.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /abir/AbiR,AbiR__AbiRb,0,V-plddts_92.82829.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /abir/AbiR,AbiR__AbiRc,0,V-plddts_86.60767.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -84,14 +76,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
-
----
-::
diff --git a/content/3.defense-systems/abit.md b/content/3.defense-systems/abit.md
index 943c0852f427dc08332d359f85cd3c234e134d65..6e79b4a15afb9f39555134f7d06504a9672b54a2 100644
--- a/content/3.defense-systems/abit.md
+++ b/content/3.defense-systems/abit.md
@@ -34,25 +34,23 @@ The system was detected in 6 different species.
Proportion of genome encoding the AbiT system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### AbiT
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abit/AbiT,AbiT__AbiTi,0,V-plddts_81.84478.pdb
----
-::
+dataUrls:
+ - /abit/AbiT.AbiT__AbiTi.0.V.pdb
+ - /abit/AbiT.AbiT__AbiTii.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /abit/AbiT,AbiT__AbiTii,0,V-plddts_88.46375.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -77,14 +75,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
-
----
-::
diff --git a/content/3.defense-systems/abiu.md b/content/3.defense-systems/abiu.md
index a94e3073128f47dfaa63a20a0941705a49f2b63a..d8b3722bd877390044747c9a37c5a4f7d2bace3f 100644
--- a/content/3.defense-systems/abiu.md
+++ b/content/3.defense-systems/abiu.md
@@ -47,18 +47,22 @@ The system was detected in 389 different species.
Proportion of genome encoding the AbiU system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### AbiU
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abiu/AbiU__AbiU-plddts_84.61928.pdb
+dataUrls:
+ - /abiu/AbiU__AbiU.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -84,3 +88,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/abiv.md b/content/3.defense-systems/abiv.md
index 050846424fec937a27a4fb04b7f0bddb19b9d8c9..db4169184408357fd1e0bc22c6a5b4106b936ca5 100644
--- a/content/3.defense-systems/abiv.md
+++ b/content/3.defense-systems/abiv.md
@@ -34,18 +34,22 @@ The system was detected in 61 different species.
Proportion of genome encoding the AbiV system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### AbiV
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abiv/AbiV__AbiV-plddts_93.56204.pdb
+dataUrls:
+ - /abiv/AbiV__AbiV.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Haaber_2008[<a href='https://doi.org/10.1128/AEM.00780-08'>Haaber et al., 2008</a>] --> Origin_0
@@ -77,14 +81,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1128/AEM.00780-08
-
----
-::
diff --git a/content/3.defense-systems/abiz.md b/content/3.defense-systems/abiz.md
index 5bfcd31da00c160430dec3bbe335bc5fe0e84d12..aa18e65a9d86b328c0e57127972f5ac33bc6482a 100644
--- a/content/3.defense-systems/abiz.md
+++ b/content/3.defense-systems/abiz.md
@@ -33,18 +33,22 @@ The system was detected in 97 different species.
Proportion of genome encoding the AbiZ system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### AbiZ
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /abiz/AbiZ__AbiZ-plddts_78.85683.pdb
+dataUrls:
+ - /abiz/AbiZ__AbiZ.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Durmaz_2007[<a href='https://doi.org/10.1128/JB.00904-06'>Durmaz and Klaenhammer, 2007</a>] --> Origin_0
@@ -77,13 +81,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1128/JB.00904-06
-
----
-::
diff --git a/content/3.defense-systems/aditi.md b/content/3.defense-systems/aditi.md
index ff6c7c2c79c93ee578b4391f283a35c36075d88d..452259dceaad96b73967aaef9cbbe683613a5c6a 100644
--- a/content/3.defense-systems/aditi.md
+++ b/content/3.defense-systems/aditi.md
@@ -34,25 +34,23 @@ The system was detected in 19 different species.
Proportion of genome encoding the Aditi system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Aditi
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /aditi/Aditi,Aditi__DitA,0,V-plddts_93.42072.pdb
----
-::
+dataUrls:
+ - /aditi/Aditi.Aditi__DitB.0.V.pdb
+ - /aditi/Aditi.Aditi__DitA.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /aditi/Aditi,Aditi__DitB,0,V-plddts_90.75274.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -78,13 +76,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
diff --git a/content/3.defense-systems/avs.md b/content/3.defense-systems/avs.md
index 16d148c54e76e95d4748e9f835aeebd72d8bc645..ceed506756276b7fe8740f3f01e7f72036bbdcfc 100644
--- a/content/3.defense-systems/avs.md
+++ b/content/3.defense-systems/avs.md
@@ -65,24 +65,70 @@ The system was detected in 366 different species.
Proportion of genome encoding the Avs system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
## Structure
+### AVAST_I
+##### Example 1
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrls:
+ - /avs/AVAST_I.AVAST_I__Avs1A.0.V.pdb
+ - /avs/AVAST_I.AVAST_I__Avs1C.0.V.pdb
+ - /avs/AVAST_I.AVAST_I__Avs1B.0.V.pdb
-### Avs_I
+---
+::
+### AVAST_II
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrls:
- - /avs/AVAST_I,AVAST_I__Avs1B,0,V-plddts_80.96481.pdb
- - /avs/AVAST_I,AVAST_I__Avs1A,0,V-plddts_85.07081.pdb
- - /avs/AVAST_I,AVAST_I__Avs1C,0,V-plddts_81.74849.pdb
+dataUrls:
+ - /avs/AVAST_II__Avs2A.pdb
+
---
::
+### AVAST_III
+##### Example 1
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrls:
+ - /avs/AVAST_III.AVAST_III__Avs3B.0.V.pdb
+ - /avs/AVAST_III.AVAST_III__Avs3A.0.V.pdb
+
+---
+::
+### AVAST_IV
+##### Example 1
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrls:
+ - /avs/AVAST_IV__Avs4A.pdb
+
+---
+::
+### AVAST_V
+##### Example 1
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrls:
+ - /avs/AVAST_V__Avs5A.pdb
+
+---
+::
## Experimental validation
+
<mermaid>
graph LR;
Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
@@ -284,3 +330,4 @@ end
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/azaca.md b/content/3.defense-systems/azaca.md
index 87bb9fd3296b3bc889eec4f3e733b314c4d18103..15ae31cbf5f5ba9c1edb66605c6434f02fb5fae8 100644
--- a/content/3.defense-systems/azaca.md
+++ b/content/3.defense-systems/azaca.md
@@ -34,32 +34,24 @@ The system was detected in 166 different species.
Proportion of genome encoding the Azaca system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Azaca
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /azaca/Azaca,Azaca__ZacA,0,V-plddts_85.13072.pdb
----
-::
+dataUrls:
+ - /azaca/Azaca.Azaca__ZacA.0.V.pdb
+ - /azaca/Azaca.Azaca__ZacB.0.V.pdb
+ - /azaca/Azaca.Azaca__ZacC.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /azaca/Azaca,Azaca__ZacB,0,V-plddts_87.34712.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /azaca/Azaca,Azaca__ZacC,0,V-plddts_86.69875.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -94,13 +86,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
diff --git a/content/3.defense-systems/borvo.md b/content/3.defense-systems/borvo.md
index 9cd6a0646ba259b179e35d700f42bcce6f17d199..457341c1adbb388067905ea0e9fd17c25dd9fef2 100644
--- a/content/3.defense-systems/borvo.md
+++ b/content/3.defense-systems/borvo.md
@@ -48,18 +48,22 @@ The system was detected in 79 different species.
Proportion of genome encoding the Borvo system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Borvo
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /borvo/Borvo__BovA-plddts_90.79263.pdb
+dataUrls:
+ - /borvo/Borvo__BovA.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -87,3 +91,4 @@ end
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/brex.md b/content/3.defense-systems/brex.md
index 15d782af27b34d7cfbf68b64403a40441291e294..7b3a1e2b14c3a57bba8f2dc5804309c756142a41 100644
--- a/content/3.defense-systems/brex.md
+++ b/content/3.defense-systems/brex.md
@@ -84,223 +84,81 @@ The system was detected in 888 different species.
Proportion of genome encoding the BREX system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### BREX_II
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /brex/BREX_II,BREX__brxD,0,DF-plddts_88.40179.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_II,BREX__pglW,0,DF-plddts_77.91126.pdb
----
-::
+dataUrls:
+ - /brex/BREX_VI.BREX__brxHI.0.DF.pdb
+ - /brex/BREX_VI.BREX__brxD.0.DF.pdb
+ - /brex/BREX_II.BREX__pglY.0.DF.pdb
+ - /brex/BREX_II.BREX__pglX2.0.DF.pdb
+ - /brex/BREX_II.BREX__pglW.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_II,BREX__pglX2,0,DF-plddts_87.98644.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_II,BREX__pglY,0,DF-plddts_83.07386.pdb
---
::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_II,BREX__pglZ2,0,DF-plddts_86.2672.pdb
----
-::
-
### BREX_III
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /brex/BREX_III,BREX__brxA,0,DF-plddts_92.03753.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_III,BREX__brxC,0,DF-plddts_85.62129.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_III,BREX__brxF,0,DF-plddts_95.59973.pdb
----
-::
+dataUrls:
+ - /brex/BREX_III.BREX__brxF.0.DF.pdb
+ - /brex/BREX_III.BREX__pglXI.0.DF.pdb
+ - /brex/BREX_V.BREX__brxHII.0.DF.pdb
+ - /brex/BREX_III.BREX__pglZ3.0.DF.pdb
+ - /brex/BREX_III.BREX__brxA.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_III,BREX__brxHII,0,DF-plddts_82.85526.pdb
---
::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_III,BREX__pglXI,0,DF-plddts_86.98487.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_III,BREX__pglZ3,0,DF-plddts_89.03152.pdb
----
-::
-
### BREX_IV
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /brex/BREX_IV,BREX__PglZ,0,DF-plddts_86.90171.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_IV,BREX__brxC,0,DF-plddts_85.82022.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_IV,BREX__brxL,0,DF-plddts_92.06923.pdb
----
-::
+dataUrls:
+ - /brex/BREX_IV.BREX__brxP.0.DF.pdb
+ - /brex/BREX_IV.BREX__PglZ.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_IV,BREX__brxP,0,DF-plddts_88.53431.pdb
---
::
-
### BREX_V
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /brex/BREX_V,BREX__brxA_DUF1819,0,DF-plddts_96.04893.pdb
----
-::
+dataUrls:
+ - /brex/BREX_V.BREX__brxHII.0.DF.pdb
+ - /brex/BREX_VI.BREX__pglZA.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_V,BREX__brxB_DUF1788,0,DF-plddts_90.45365.pdb
---
::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_V,BREX__brxC,0,DF-plddts_82.61479.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_V,BREX__brxHII,0,DF-plddts_83.9134.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_V,BREX__pglX1,0,DF-plddts_92.49306.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_V,BREX__pglZA,0,DF-plddts_92.2016.pdb
----
-::
-
### BREX_VI
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /brex/BREX_VI,BREX__brxB_DUF1788,0,DF-plddts_91.60152.pdb
----
-::
+dataUrls:
+ - /brex/BREX_VI.BREX__brxHI.0.DF.pdb
+ - /brex/BREX_VI.BREX__brxD.0.DF.pdb
+ - /brex/BREX_VI.BREX__pglZA.0.DF.pdb
+ - /brex/BREX_VI.BREX_brxA.0.DF.pdb
+ - /brex/BREX_VI.BREX__brxE.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_VI,BREX__brxC,0,DF-plddts_86.1139.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_VI,BREX__brxD,0,DF-plddts_90.67427.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_VI,BREX__brxE,0,DF-plddts_90.30329.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_VI,BREX__brxHI,0,DF-plddts_87.87451.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_VI,BREX__pglX1,0,DF-plddts_78.09923.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_VI,BREX__pglZA,0,DF-plddts_88.59061.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /brex/BREX_VI,BREX_brxA,0,DF-plddts_93.93224.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -347,3 +205,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/bsta.md b/content/3.defense-systems/bsta.md
index 3f005e1090152424d3cae50a6bb33fc717b136b2..58ea6fcc54c645f42d19b1c8ca7c33c9a76bf014 100644
--- a/content/3.defense-systems/bsta.md
+++ b/content/3.defense-systems/bsta.md
@@ -43,32 +43,24 @@ The system was detected in 88 different species.
Proportion of genome encoding the BstA system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### BstA
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /bsta/BstA__BstA-plddts_84.76542.pdb
----
-::
+dataUrls:
+ - /bsta/BstA__BstA.pdb
+ - /bsta/BstA__BstA1.pdb
+ - /bsta/BstA__BstA2.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /bsta/BstA__BstA1-plddts_85.78689.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /bsta/BstA__BstA2-plddts_92.11235.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Owen_2021[<a href='https://doi.org/10.1016/j.chom.2021.09.002'>Owen et al., 2021</a>] --> Origin_0
@@ -127,17 +119,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2021.09.002
-
----
-::
-
-
-## References
-1. Owen SV, Wenner N, Dulberger CL, Rodwell EV, Bowers-Barnard A, Quinones-Olvera N, Rigden DJ, Rubin EJ, Garner EC, Baym M, Hinton JCD. Prophages encode phage-defense systems with cognate self-immunity. Cell Host Microbe. 2021 Nov 10;29(11):1620-1633.e8. doi: 10.1016/j.chom.2021.09.002. Epub 2021 Sep 30. PMID: 34597593; PMCID: PMC8585504.
diff --git a/content/3.defense-systems/bunzi.md b/content/3.defense-systems/bunzi.md
index 1a28925d41ff2aeb9b085477832ca402a1f45784..95b0915b725d8efc7e0b86661615c29f8a6460de 100644
--- a/content/3.defense-systems/bunzi.md
+++ b/content/3.defense-systems/bunzi.md
@@ -45,25 +45,23 @@ The system was detected in 58 different species.
Proportion of genome encoding the Bunzi system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Bunzi
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /bunzi/Bunzi,Bunzi__BnzA,0,V-plddts_83.13475.pdb
----
-::
+dataUrls:
+ - /bunzi/Bunzi.Bunzi__BnzB.0.V.pdb
+ - /bunzi/Bunzi.Bunzi__BnzA.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /bunzi/Bunzi,Bunzi__BnzB,0,V-plddts_86.79774.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -89,3 +87,4 @@ end
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/butters_gp30_gp31.md b/content/3.defense-systems/butters_gp30_gp31.md
index 6794f44db70bc52394b550c638b8effcd2441561..87963a3b83a21457e79023bfa2ddd4880bf3e681 100644
--- a/content/3.defense-systems/butters_gp30_gp31.md
+++ b/content/3.defense-systems/butters_gp30_gp31.md
@@ -33,25 +33,23 @@ The system was detected in 34 different species.
Proportion of genome encoding the Butters_gp30_gp31 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Butters_gp30_gp31
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /butters_gp30_gp31/Butters_gp30_gp31__Butters_gp30-plddts_79.33298.pdb
----
-::
+dataUrls:
+ - /butters_gp30_gp31/Butters_gp30_gp31__Butters_gp30.pdb
+ - /butters_gp30_gp31/Butters_gp30_gp31__Butters_gp31.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /butters_gp30_gp31/Butters_gp30_gp31__Butters_gp31-plddts_84.75463.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Mageeney_2020[<a href='https://doi.org/10.1128/mSystems.00534-20'>Mageeney et al., 2020</a>] --> Origin_0
@@ -75,11 +73,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1128/mSystems.00534-20
----
-::
diff --git a/content/3.defense-systems/butters_gp57r.md b/content/3.defense-systems/butters_gp57r.md
index 2e6e5d61436c3ccd1ab8aec56808cf8911458e66..7279df464b42dbcb86acb3b09d9f7034698140b6 100644
--- a/content/3.defense-systems/butters_gp57r.md
+++ b/content/3.defense-systems/butters_gp57r.md
@@ -33,18 +33,22 @@ The system was detected in 7 different species.
Proportion of genome encoding the Butters_gp57r system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Butters_gp57r
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /butters_gp57r/Butters_gp57r__gp57r-plddts_90.7432.pdb
+dataUrls:
+ - /butters_gp57r/Butters_gp57r__gp57r.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Mohammed_2023[<a href='https://doi.org/10.1101/2023.01.03.522681'>Mohammed et al., 2023</a>] --> Origin_0
@@ -75,11 +79,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1101/2023.01.03.522681
----
-::
diff --git a/content/3.defense-systems/caprel.md b/content/3.defense-systems/caprel.md
index b57785361cfc1adf41432d9eb9b8a40b80ad910b..63938fddc0006c6cff53de6df9e05ec78149f3f7 100644
--- a/content/3.defense-systems/caprel.md
+++ b/content/3.defense-systems/caprel.md
@@ -46,18 +46,22 @@ The system was detected in 217 different species.
Proportion of genome encoding the CapRel system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### CapRel
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /caprel/CapRel__CapRel-plddts_90.09132.pdb
+dataUrls:
+ - /caprel/CapRel__CapRel.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Zhang_2022[<a href='https://doi.org/10.1038/s41586-022-05444-z'>Zhang et al., 2022</a>] --> Origin_0
@@ -99,17 +103,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41586-022-05444-z
-
----
-::
-
-
-## 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/3.defense-systems/cbass.md b/content/3.defense-systems/cbass.md
index 06c6bcfcd1d6fb7e7de4c9e6881399b1a5046141..3981e2578f8972f18cd65dd92f02410628eb608d 100644
--- a/content/3.defense-systems/cbass.md
+++ b/content/3.defense-systems/cbass.md
@@ -46,129 +46,67 @@ The system was detected in 1290 different species.
Proportion of genome encoding the CBASS system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### CBASS_I
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /cbass/CBASS_I,CBASS__Cyclase_II,0,V-plddts_92.48144.pdb
----
-::
+dataUrls:
+ - /cbass/CBASS_I.CBASS__Cyclase_II.0.V.pdb
+ - /cbass/CBASS_I.CBASS__TM.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /cbass/CBASS_I,CBASS__TM,0,V-plddts_91.45177.pdb
---
::
-
### CBASS_II
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /cbass/CBASS_II,CBASS__AG_E2_Prok-E2,0,V-plddts_89.8018.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /cbass/CBASS_II,CBASS__Cyclase_II,0,V-plddts_89.65358.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /cbass/CBASS_II,CBASS__Jab,0,V-plddts_95.53434.pdb
----
-::
+dataUrls:
+ - /cbass/CBASS_II.CBASS__Phospholipase.0.V.pdb
+ - /cbass/CBASS_II.CBASS__AG_E2_Prok-E2.0.V.pdb
+ - /cbass/CBASS_I.CBASS__Cyclase_II.0.V.pdb
+ - /cbass/CBASS_II.CBASS__Jab.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /cbass/CBASS_II,CBASS__Phospholipase,0,V-plddts_89.1622.pdb
---
::
-
### CBASS_III
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /cbass/CBASS_III,CBASS__Cyclase_II,0,V-plddts_97.70389.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /cbass/CBASS_III,CBASS__Endonuc_small,0,V-plddts_97.03481.pdb
----
-::
+dataUrls:
+ - /cbass/CBASS_III.CBASS__Endonuc_small.0.V.pdb
+ - /cbass/CBASS_I.CBASS__Cyclase_II.0.V.pdb
+ - /cbass/CBASS_III.CBASS__bacHORMA_2.0.V.pdb
+ - /cbass/CBASS_III.CBASS__HORMA.0.V.pdb
+ - /cbass/CBASS_III.CBASS__TRIP13.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /cbass/CBASS_III,CBASS__HORMA,0,V-plddts_89.50696.pdb
---
::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /cbass/CBASS_III,CBASS__TRIP13,0,V-plddts_89.6492.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /cbass/CBASS_III,CBASS__bacHORMA_2,0,V-plddts_84.43633.pdb
----
-::
-
### CBASS_IV
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /cbass/CBASS_IV,CBASS__2TM_type_IV,0,DF-plddts_87.89742.pdb
----
-::
+dataUrls:
+ - /cbass/CBASS_IV.CBASS__QueC.0.DF.pdb
+ - /cbass/CBASS_IV.CBASS__TGT.0.DF.pdb
+ - /cbass/CBASS_IV.CBASS__Cyclase_SMODS.0.DF.pdb
+ - /cbass/CBASS_IV.CBASS__2TM_type_IV.0.DF.pdb
+ - /cbass/CBASS_IV.CBASS__OGG.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /cbass/CBASS_IV,CBASS__Cyclase_SMODS,0,DF-plddts_87.98201.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /cbass/CBASS_IV,CBASS__OGG,0,DF-plddts_95.21551.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /cbass/CBASS_IV,CBASS__QueC,0,DF-plddts_93.98141.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /cbass/CBASS_IV,CBASS__TGT,0,DF-plddts_93.84001.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Cohen_2019[<a href='https://doi.org/10.1038/s41586-019-1605-5'>Cohen et al., 2019</a>] --> Origin_0
@@ -225,17 +163,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.molcel.2019.12.009
- - doi: 10.1016/j.molcel.2021.10.020
- - doi: 10.1038/s41564-020-0777-y
- - doi: 10.1038/s41586-019-1605-5
- - doi: 10.1038/s41586-020-2719-5
-
----
-::
diff --git a/content/3.defense-systems/charlie_gp32.md b/content/3.defense-systems/charlie_gp32.md
index 04aa34b16682cd8d8264636d41a83cb293d7c759..397b2562cc09a84ceca033b50f08e5f0f02fdd22 100644
--- a/content/3.defense-systems/charlie_gp32.md
+++ b/content/3.defense-systems/charlie_gp32.md
@@ -33,18 +33,22 @@ The system was detected in 47 different species.
Proportion of genome encoding the Charlie_gp32 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Charlie_gp32
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /charlie_gp32/Charlie_gp32__gp32-plddts_82.99758.pdb
+dataUrls:
+ - /charlie_gp32/Charlie_gp32__gp32.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Dedrick_2017[<a href='https://doi.org/10.1038/nmicrobiol.2016.251'>Dedrick et al., 2017</a>] --> Origin_0
@@ -68,11 +72,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1038/nmicrobiol.2016.251
----
-::
diff --git a/content/3.defense-systems/dartg.md b/content/3.defense-systems/dartg.md
index 89bf5e39c58c26ba20f0fcc40c980d6c42eb9339..7b8a0e291eee26d8e6bed8a5d9981d03beb7f458 100644
--- a/content/3.defense-systems/dartg.md
+++ b/content/3.defense-systems/dartg.md
@@ -50,25 +50,23 @@ The system was detected in 386 different species.
Proportion of genome encoding the DarTG system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### DarTG
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /dartg/DarTG,DarTG_DarG,0,DF-plddts_94.40611.pdb
----
-::
+dataUrls:
+ - /dartg/DarTG.DarTG_DarT.0.DF.pdb
+ - /dartg/DarTG.DarTG_DarG.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dartg/DarTG,DarTG_DarT,0,DF-plddts_94.62475.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Leroux_2022[<a href='https://doi.org/10.1038/s41564-022-01153-5'>LeRoux et al., 2022</a>] --> Origin_0
@@ -96,3 +94,4 @@ end
</mermaid>
::
+
diff --git a/content/3.defense-systems/dazbog.md b/content/3.defense-systems/dazbog.md
index 83f019ea58577af990784b6c5c554e93e8ba4269..6060fa8f1adcbbc6cd1f04255c5686343b5f1643 100644
--- a/content/3.defense-systems/dazbog.md
+++ b/content/3.defense-systems/dazbog.md
@@ -45,41 +45,34 @@ The system was detected in 50 different species.
Proportion of genome encoding the Dazbog system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Dazbog
+##### Example 1
-Example 1:
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /dazbog/Dazbog,Dazbog__DzbA,0,V-plddts_87.87307.pdb
----
-::
+dataUrls:
+ - /dazbog/Dazbog.Dazbog__DzbA.1.V.pdb
+ - /dazbog/Dazbog.Dazbog__DzbB.1.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dazbog/Dazbog,Dazbog__DzbB,0,V-plddts_93.82789.pdb
---
::
+##### Example 2
-Example 2:
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /dazbog/Dazbog,Dazbog__DzbA,0,V-plddts_87.87307.pdb
----
-::
+dataUrls:
+ - /dazbog/Dazbog.Dazbog__DzbA.1.V.pdb
+ - /dazbog/Dazbog.Dazbog__DzbB.1.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dazbog/Dazbog,Dazbog__DzbB,0,V-plddts_93.82789.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -117,3 +110,4 @@ end
</mermaid>
+
diff --git a/content/3.defense-systems/dctpdeaminase.md b/content/3.defense-systems/dctpdeaminase.md
index 6cca2256d706b3599a98c22a37866956c52b054f..4f0235f7645f6c2df04486dc3d6caa91973e1f67 100644
--- a/content/3.defense-systems/dctpdeaminase.md
+++ b/content/3.defense-systems/dctpdeaminase.md
@@ -50,18 +50,22 @@ The system was detected in 294 different species.
Proportion of genome encoding the dCTPdeaminase system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### dCTPdeaminase
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /dctpdeaminase/dCTPdeaminase__dCTPdeaminase-plddts_91.37723.pdb
+dataUrls:
+ - /dctpdeaminase/dCTPdeaminase__dCTPdeaminase.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Tal_2022[<a href='https://doi.org/10.1038/s41564-022-01158-0'>Tal et al., 2022</a>] --> Origin_0
@@ -134,3 +138,4 @@ end
</mermaid>
+
diff --git a/content/3.defense-systems/ddmde.md b/content/3.defense-systems/ddmde.md
index d09c53d7669792ad7b3db40161d18a552b351069..9f9fe28f4b904838152513001ce9ef52fc1afd54 100644
--- a/content/3.defense-systems/ddmde.md
+++ b/content/3.defense-systems/ddmde.md
@@ -30,30 +30,17 @@ The system was detected in 50 different species.
Proportion of genome encoding the DdmDE system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### DdmDE
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /dmdde/DdmDE,DdmDE__DdmD,0,V-plddts_86.22213.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dmdde/DdmDE,DdmDE__DdmE,0,V-plddts_90.70804.pdb
----
-::
-
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41586-022-04546-y
+dataUrls:
+ - /ddmde/DdmDE.DdmDE__DdmD.0.V.pdb
+ - /ddmde/DdmDE.DdmDE__DdmE.0.V.pdb
---
::
diff --git a/content/3.defense-systems/detocs.md b/content/3.defense-systems/detocs.md
index 5a9a42d35cc06d89f0969f9ebd64bedd3fa94f1a..3ddb8843ec1f94a94588edd4a906fee88ddc2de7 100644
--- a/content/3.defense-systems/detocs.md
+++ b/content/3.defense-systems/detocs.md
@@ -65,55 +65,37 @@ The system was detected in 128 different species.
Proportion of genome encoding the Detocs system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Detocs
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /detocs/Detocs__dtcA-plddts_86.06608.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /detocs/Detocs__dtcB-plddts_95.55971.pdb
----
-::
+dataUrls:
+ - /detocs/Detocs__dtcC.pdb
+ - /detocs/Detocs__dtcB.pdb
+ - /detocs/Detocs__dtcA.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /detocs/Detocs__dtcC-plddts_94.54261.pdb
---
::
-
### Detocs_hydrolase
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /detocs/Detocs_hydrolase__dtcA-plddts_85.48132.pdb
----
-::
+dataUrls:
+ - /detocs/Detocs_hydrolase__dtcC.pdb
+ - /detocs/Detocs_hydrolase__dtcB.pdb
+ - /detocs/Detocs_hydrolase__dtcA.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /detocs/Detocs_hydrolase__dtcB-plddts_93.6662.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /detocs/Detocs_hydrolase__dtcC-plddts_89.47253.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Rousset_2023[<a href='https://doi.org/10.1016/j.cell.2023.07.020'>Rousset et al., 2023</a>] --> Origin_0
@@ -163,3 +145,4 @@ end
=======
</mermaid>
>>>>>>> content/3.defense-systems/detocs.md
+
diff --git a/content/3.defense-systems/dgtpase.md b/content/3.defense-systems/dgtpase.md
index 6e19ae2a1d6e3456fac0fb78a2078478947b8d37..55ce9aafc69672a437bc8cde57c49ec4a95d07d4 100644
--- a/content/3.defense-systems/dgtpase.md
+++ b/content/3.defense-systems/dgtpase.md
@@ -45,18 +45,22 @@ The system was detected in 449 different species.
Proportion of genome encoding the dGTPase system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### dGTPase
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /dgtpase/dGTPase__Sp_dGTPase-plddts_94.35719.pdb
+dataUrls:
+ - /dgtpase/dGTPase__Sp_dGTPase.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Tal_2022[<a href='https://doi.org/10.1038/s41564-022-01158-0'>Tal et al., 2022</a>] --> Origin_0
@@ -123,3 +127,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/disarm.md b/content/3.defense-systems/disarm.md
index 99b73d5e08c3ebe4fd0c11c5a91a88a3dbdc60f6..a1d2d80212ad0e186cb9deb473ee74a44b445fc7 100644
--- a/content/3.defense-systems/disarm.md
+++ b/content/3.defense-systems/disarm.md
@@ -58,10 +58,41 @@ The system was detected in 201 different species.
Proportion of genome encoding the DISARM system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
## Structure
+### DISARM_1
+##### Example 1
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrls:
+ - /disarm/DISARM_2.DISARM__drmC.0.V.pdb
+ - /disarm/DISARM_2.DISARM__drmB.0.V.pdb
+ - /disarm/DISARM_1.DISARM__drmA.0.DF.pdb
+ - /disarm/DISARM_1.DISARM_1__drmMI.0.DF.pdb
+ - /disarm/DISARM_1.DISARM_1__drmD.0.DF.pdb
+
+---
+::
+### DISARM_2
+##### Example 1
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrls:
+ - /disarm/DISARM_1.DISARM__drmA.0.DF.pdb
+ - /disarm/DISARM_2.DISARM__drmC.0.V.pdb
+ - /disarm/DISARM_2.DISARM_2__drmMII.0.V.pdb
+ - /disarm/DISARM_2.DISARM__drmB.0.V.pdb
+ - /disarm/DISARM_2.DISARM_2__drmE.0.V.pdb
+
+---
+::
## Experimental validation
+
<mermaid>
graph LR;
Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
@@ -122,3 +153,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/dnd.md b/content/3.defense-systems/dnd.md
index d6f1900275f5c0a0613e5033a59ddf1efc8294ef..2e06e4faea2e151c5f7f2aaf67ada2b136a02973 100644
--- a/content/3.defense-systems/dnd.md
+++ b/content/3.defense-systems/dnd.md
@@ -38,104 +38,45 @@ The system was detected in 237 different species.
Proportion of genome encoding the Dnd system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Dnd_ABCDE
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /dnd/Dnd_ABCDE,Dnd__DndA,0,DF-plddts_93.47347.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dnd/Dnd_ABCDE,Dnd__DndB,0,DF-plddts_92.88424.pdb
----
-::
+dataUrls:
+ - /dnd/Dnd_ABCDE.Dnd__DndD.0.DF.pdb
+ - /dnd/Dnd_ABCDE.Dnd__DndE.0.DF.pdb
+ - /dnd/Dnd_ABCDE.Dnd__DndD.0.DF.pdb
+ - /dnd/Dnd_ABCDE.Dnd__DndC.0.DF.pdb
+ - /dnd/Dnd_ABCDEFGH.Dnd__DndB.0.DF.pdb
+ - /dnd/Dnd_ABCDE.Dnd__DndA.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dnd/Dnd_ABCDE,Dnd__DndC,0,DF-plddts_88.29934.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dnd/Dnd_ABCDE,Dnd__DndD,0,DF-plddts_86.40104.pdb
---
::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dnd/Dnd_ABCDE,Dnd__DndE,0,DF-plddts_94.0153.pdb
----
-::
-
### Dnd_ABCDEFGH
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /dnd/Dnd_ABCDEFGH,Dnd_ABCDEFGH__DptF,0,DF-plddts_90.5398.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dnd/Dnd_ABCDEFGH,Dnd_ABCDEFGH__DptG,0,DF-plddts_92.29053.pdb
----
-::
+dataUrls:
+ - /dnd/Dnd_ABCDE.Dnd__DndA.0.DF.pdb
+ - /dnd/Dnd_ABCDEFGH.Dnd__DndB.0.DF.pdb
+ - /dnd/Dnd_ABCDE.Dnd__DndC.0.DF.pdb
+ - /dnd/Dnd_ABCDE.Dnd__DndD.0.DF.pdb
+ - /dnd/Dnd_ABCDE.Dnd__DndE.0.DF.pdb
+ - /dnd/Dnd_ABCDEFGH.Dnd_ABCDEFGH__DptH.0.DF.pdb
+ - /dnd/Dnd_ABCDEFGH.Dnd_ABCDEFGH__DptG.0.DF.pdb
+ - /dnd/Dnd_ABCDEFGH.Dnd_ABCDEFGH__DptF.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dnd/Dnd_ABCDEFGH,Dnd_ABCDEFGH__DptH,0,DF-plddts_83.00895.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dnd/Dnd_ABCDEFGH,Dnd__DndA,0,DF-plddts_95.7234.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dnd/Dnd_ABCDEFGH,Dnd__DndB,0,DF-plddts_94.63597.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dnd/Dnd_ABCDEFGH,Dnd__DndC,0,DF-plddts_90.06321.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dnd/Dnd_ABCDEFGH,Dnd__DndD,0,DF-plddts_85.70431.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dnd/Dnd_ABCDEFGH,Dnd__DndE,0,DF-plddts_95.24932.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Xiong_2019[<a href='https://doi.org/10.1038/s41467-019-09390-9'>Xiong et al., 2019</a>] --> Origin_0
@@ -159,14 +100,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/nchembio.2007.39
- - doi: 10.1038/s41467-019-09390-9
-
----
-::
diff --git a/content/3.defense-systems/dodola.md b/content/3.defense-systems/dodola.md
index 15002c7c112d92e025dc4ce9911a9d7f4311bcaa..a7c02de810cb57b03dc918fcfa25621ba7cb449e 100644
--- a/content/3.defense-systems/dodola.md
+++ b/content/3.defense-systems/dodola.md
@@ -47,25 +47,23 @@ The system was detected in 91 different species.
Proportion of genome encoding the Dodola system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Dodola
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /dodola/Dodola,Dodola__DolA,0,V-plddts_78.91796.pdb
----
-::
+dataUrls:
+ - /dodola/Dodola.Dodola__DolB.0.V.pdb
+ - /dodola/Dodola.Dodola__DolA.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dodola/Dodola,Dodola__DolB,0,V-plddts_92.53304.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -91,3 +89,4 @@ end
</mermaid>
+
diff --git a/content/3.defense-systems/dpd.md b/content/3.defense-systems/dpd.md
index efa443fa4bc5bfdcf1a469ee9cc737228420869c..2301fb984a643fe9b817078786373b055ed63fe4 100644
--- a/content/3.defense-systems/dpd.md
+++ b/content/3.defense-systems/dpd.md
@@ -31,103 +31,27 @@ The system was detected in 103 different species.
Proportion of genome encoding the Dpd system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Dpd
-
-Example 1:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dpd/Dpd.Dpd__DpdF.0.DF-plddts_89.51241.pdb
----
-::
-
-Example 2:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dpd/Dpd.Dpd__DpdF.0.DF-plddts_89.51241.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dpd/Dpd,Dpd__DpdA,0,DF-plddts_94.55021.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dpd/Dpd,Dpd__DpdB,0,DF-plddts_93.00056.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dpd/Dpd,Dpd__DpdC,0,DF-plddts_93.71712.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dpd/Dpd,Dpd__DpdD,0,DF-plddts_85.62349.pdb
----
-::
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /dpd/Dpd,Dpd__DpdE,0,DF-plddts_88.00382.pdb
----
-::
+dataUrls:
+ - /dpd/Dpd.Dpd__QueD.0.DF.pdb
+ - /dpd/Dpd.Dpd__DpdD.0.DF.pdb
+ - /dpd/Dpd.Dpd__DpdK.0.DF.pdb
+ - /dpd/Dpd.Dpd__DpdJ.0.DF.pdb
+ - /dpd/Dpd.Dpd__DpdI.0.DF.pdb
+ - /dpd/Dpd.Dpd__DpdH.0.DF.pdb
+ - /dpd/Dpd.Dpd__DpdG.0.DF.pdb
+ - /dpd/Dpd.Dpd__DpdF.0.DF.pdb
+ - /dpd/Dpd.Dpd__DpdE.0.DF.pdb
+ - /dpd/Dpd.Dpd__DpdB.0.DF.pdb
+ - /dpd/Dpd.Dpd__DpdA.0.DF.pdb
+ - /dpd/Dpd.Dpd__DpdC.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dpd/Dpd,Dpd__DpdG,0,DF-plddts_91.59671.pdb
---
::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dpd/Dpd,Dpd__DpdH,0,DF-plddts_85.20178.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dpd/Dpd,Dpd__DpdI,0,DF-plddts_83.71254.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dpd/Dpd,Dpd__DpdJ,0,DF-plddts_89.00672.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /dpd/Dpd,Dpd__DpdK,0,DF-plddts_93.96529.pdb
----
-::
-
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1073/pnas.1518570113
-
----
-::
-
diff --git a/content/3.defense-systems/drt.md b/content/3.defense-systems/drt.md
index 4297087b3f5db4bd9507e9fdb777c0920136c903..20be54dfb9fad3f4b68735eee1e623505ef35b69 100644
--- a/content/3.defense-systems/drt.md
+++ b/content/3.defense-systems/drt.md
@@ -94,104 +94,112 @@ The system was detected in 577 different species.
Proportion of genome encoding the DRT system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### DRT6
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /drt/DRT6__DRT6-plddts_92.73056.pdb
+dataUrls:
+ - /drt/DRT6__DRT6.pdb
+
---
::
-
### DRT7
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /drt/DRT7__DRT7-plddts_85.85621.pdb
+dataUrls:
+ - /drt/DRT7__DRT7.pdb
+
---
::
-
### DRT8
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /drt/DRT8__DRT8-plddts_92.44735.pdb
+dataUrls:
+ - /drt/DRT8__DRT8.pdb
+
---
::
-
### DRT9
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /drt/DRT9__DRT9-plddts_91.47402.pdb
+dataUrls:
+ - /drt/DRT9__DRT9.pdb
+
---
::
-
### DRT_1
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /drt/DRT_1,DRT_1__drt1a,0,V-plddts_88.59974.pdb
----
-::
+dataUrls:
+ - /drt/DRT_1.DRT_1__drt1b.0.V.pdb
+ - /drt/DRT_1.DRT_1__drt1a.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /drt/DRT_1,DRT_1__drt1b,0,V-plddts_92.26985.pdb
---
::
-
### DRT_2
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /drt/DRT_2__drt2-plddts_95.09027.pdb
+dataUrls:
+ - /drt/DRT_2__drt2.pdb
+
---
::
-
### DRT_3
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /drt/DRT_3,DRT_3__drt3a,0,V-plddts_91.16835.pdb
----
-::
+dataUrls:
+ - /drt/DRT_3.DRT_3__drt3b.0.V.pdb
+ - /drt/DRT_3.DRT_3__drt3a.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /drt/DRT_3,DRT_3__drt3b,0,V-plddts_87.11665.pdb
---
::
-
### DRT_4
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /drt/DRT_4__drt4-plddts_92.79751.pdb
+dataUrls:
+ - /drt/DRT_4__drt4.pdb
+
---
::
-
### DRT_5
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /drt/DRT_5__drt5-plddts_90.89502.pdb
+dataUrls:
+ - /drt/DRT_5__drt5.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -302,3 +310,4 @@ end
</mermaid>
+
diff --git a/content/3.defense-systems/druantia.md b/content/3.defense-systems/druantia.md
index 6179376f5aadde4254af71b0fa4a4c96be8ea46a..835f6555141898e3ba9915a5b0724d616743c1a1 100644
--- a/content/3.defense-systems/druantia.md
+++ b/content/3.defense-systems/druantia.md
@@ -42,92 +42,52 @@ The system was detected in 303 different species.
Proportion of genome encoding the Druantia system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Druantia_I
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /druantia/Druantia_I,Druantia_I__DruA,0,V-plddts_88.89293.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /druantia/Druantia_I,Druantia_I__DruB,0,V-plddts_82.83057.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /druantia/Druantia_I,Druantia_I__DruC,0,V-plddts_85.18836.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /druantia/Druantia_I,Druantia_I__DruD,0,V-plddts_91.26112.pdb
----
-::
+dataUrls:
+ - /druantia/Druantia_I.Druantia_I__DruA.0.V.pdb
+ - /druantia/Druantia_I.Druantia_I__DruB.0.V.pdb
+ - /druantia/Druantia_I.Druantia_I__DruC.0.V.pdb
+ - /druantia/Druantia_I.Druantia_I__DruD.0.V.pdb
+ - /druantia/Druantia_I.Druantia__DruE.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /druantia/Druantia_I,Druantia__DruE,0,V-plddts_86.11628.pdb
---
::
-
### Druantia_II
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /druantia/Druantia_II,Druantia_II__DruF,0,DF-plddts_86.11001.pdb
----
-::
+dataUrls:
+ - /druantia/Druantia_II.Druantia_II__DruM.0.DF.pdb
+ - /druantia/Druantia_II.Druantia_II__DruF.0.DF.pdb
+ - /druantia/Druantia_II.Druantia_II__DruG.0.DF.pdb
+ - /druantia/Druantia_II.Druantia__DruE_2.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /druantia/Druantia_II,Druantia_II__DruG,0,DF-plddts_80.40261.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /druantia/Druantia_II,Druantia_II__DruM,0,DF-plddts_90.00131.pdb
---
::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /druantia/Druantia_II,Druantia__DruE_2,0,DF-plddts_84.77074.pdb
----
-::
-
### Druantia_III
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /druantia/Druantia_III,Druantia_III__DruH,0,DF-plddts_82.87318.pdb
----
-::
+dataUrls:
+ - /druantia/Druantia_III.Druantia_III__DruH.0.DF.pdb
+ - /druantia/Druantia_III.Druantia__DruE_3.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /druantia/Druantia_III,Druantia__DruE_3,0,DF-plddts_83.26091.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -178,13 +138,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aar4120
-
----
-::
diff --git a/content/3.defense-systems/dsr.md b/content/3.defense-systems/dsr.md
index 0c90ee007d37334378a5cfe2c606ec9a557dfc3b..03e3cf2348473bebc0764183dea1e5ab1da55b71 100644
--- a/content/3.defense-systems/dsr.md
+++ b/content/3.defense-systems/dsr.md
@@ -38,27 +38,33 @@ The system was detected in 162 different species.
Proportion of genome encoding the Dsr system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Dsr_I
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /dsr/Dsr_I__Dsr1-plddts_87.99578.pdb
+dataUrls:
+ - /dsr/Dsr_I__Dsr1.pdb
+
---
::
-
### Dsr_II
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /dsr/Dsr_II__Dsr2-plddts_86.62203.pdb
+dataUrls:
+ - /dsr/Dsr_II__Dsr2.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -110,14 +116,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01207-8
- - doi: 10.1126/science.aba0372
-
----
-::
diff --git a/content/3.defense-systems/eleos.md b/content/3.defense-systems/eleos.md
index ebd6dde80091004b02bf92c55f6a2cd01e561a06..8220a15c63a07b32db6a3197320ac7b98737237d 100644
--- a/content/3.defense-systems/eleos.md
+++ b/content/3.defense-systems/eleos.md
@@ -36,25 +36,23 @@ The system was detected in 223 different species.
Proportion of genome encoding the Eleos system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Eleos
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /eleos/Eleos,Eleos__LeoA,0,V-plddts_81.66314.pdb
----
-::
+dataUrls:
+ - /eleos/Eleos.Eleos__LeoBC.0.V.pdb
+ - /eleos/Eleos.Eleos__LeoA.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /eleos/Eleos,Eleos__LeoBC,0,V-plddts_83.32056.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -79,13 +77,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
diff --git a/content/3.defense-systems/fs_giy_yig.md b/content/3.defense-systems/fs_giy_yig.md
index 7a8084b660a75fb1926719609f08e110109fac0f..210603c67b063638b59b35126e6e9d74f0dea9ca 100644
--- a/content/3.defense-systems/fs_giy_yig.md
+++ b/content/3.defense-systems/fs_giy_yig.md
@@ -33,18 +33,22 @@ The system was detected in 87 different species.
Proportion of genome encoding the FS_GIY_YIG system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### FS_GIY_YIG
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /fs_giy_yig/FS_GIY_YIG__GIY_YIG-plddts_93.05664.pdb
+dataUrls:
+ - /fs_giy_yig/FS_GIY_YIG__GIY_YIG.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
@@ -77,11 +81,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.cell.2022.07.014
----
-::
diff --git a/content/3.defense-systems/fs_hepn_tm.md b/content/3.defense-systems/fs_hepn_tm.md
index f6d2095eb362adad388028d525520acb614acc08..c53fc9ffd300d52ef86cf507f2dec4dbcc66b71e 100644
--- a/content/3.defense-systems/fs_hepn_tm.md
+++ b/content/3.defense-systems/fs_hepn_tm.md
@@ -12,25 +12,23 @@ tableColumns:
## To do
-## Structure
+## Structure
### FS_HEPN_TM
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /fs_hepn_tm/FS_HEPN_TM__HEPN-plddts_69.12248.pdb
----
-::
+dataUrls:
+ - /fs_hepn_tm/FS_HEPN_TM__TM.pdb
+ - /fs_hepn_tm/FS_HEPN_TM__HEPN.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /fs_hepn_tm/FS_HEPN_TM__TM-plddts_90.28126.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
@@ -56,11 +54,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.cell.2022.07.014
----
-::
diff --git a/content/3.defense-systems/fs_hp.md b/content/3.defense-systems/fs_hp.md
index b256ce11251b3d89348f2d319e33f6fe6c670d37..e78e56584a8aff428ce114bf3a245fa719724665 100644
--- a/content/3.defense-systems/fs_hp.md
+++ b/content/3.defense-systems/fs_hp.md
@@ -43,18 +43,22 @@ The system was detected in 29 different species.
Proportion of genome encoding the FS_HP system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### FS_HP
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /fs_hp/FS_HP__HP-plddts_94.44828.pdb
+dataUrls:
+ - /fs_hp/FS_HP__HP.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
@@ -86,3 +90,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/fs_hp_sdh_sah.md b/content/3.defense-systems/fs_hp_sdh_sah.md
index 335c2cddafbdb147d99a20030d4b06404de41f72..0334531ae5b8655fddd2b865d97ffff7a409daba 100644
--- a/content/3.defense-systems/fs_hp_sdh_sah.md
+++ b/content/3.defense-systems/fs_hp_sdh_sah.md
@@ -34,25 +34,23 @@ The system was detected in 3 different species.
Proportion of genome encoding the FS_HP_SDH_sah system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### FS_HP_SDH_sah
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /fs_hp_sdh_sah/FS_HP_SDH_sah__HP-plddts_58.30935.pdb
----
-::
+dataUrls:
+ - /fs_hp_sdh_sah/FS_HP_SDH_sah__SDH_sah.pdb
+ - /fs_hp_sdh_sah/FS_HP_SDH_sah__HP.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /fs_hp_sdh_sah/FS_HP_SDH_sah__SDH_sah-plddts_95.32024.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
@@ -76,12 +74,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.cell.2022.07.014
-
----
-::
diff --git a/content/3.defense-systems/fs_hsdr_like.md b/content/3.defense-systems/fs_hsdr_like.md
index 0da466dd98fdc2fdf6bfd44a1cda572ec6a9d99a..90d07a4a27393c65038599a9201a1fb46adede9c 100644
--- a/content/3.defense-systems/fs_hsdr_like.md
+++ b/content/3.defense-systems/fs_hsdr_like.md
@@ -33,25 +33,33 @@ The system was detected in 15 different species.
Proportion of genome encoding the FS_HsdR_like system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
-### FS_HsdR_like
+## Structure
+### FS_HsdR_like_HP-plddts_74.75219.html
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /fs_hsdr_like/FS_HsdR_like__HP-plddts_74.75219.pdb
+dataUrls:
+ - /fs_hsdr_like/FS_HsdR_like_HP.pdb
+
---
::
+### FS_HsdR_like_HdrR-plddts_88.7069.html
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /fs_hsdr_like/FS_HsdR_like__HdrR-plddts_88.7069.pdb
+dataUrls:
+ - /fs_hsdr_like/FS_HsdR_like_HdrR.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
@@ -90,11 +98,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.cell.2022.07.014
----
-::
diff --git a/content/3.defense-systems/fs_sma.md b/content/3.defense-systems/fs_sma.md
index 037cf211cda99af1385c0e5d203af7cf67e24c82..9931ce08c9a82384bd6087d061fb143d0c9f0757 100644
--- a/content/3.defense-systems/fs_sma.md
+++ b/content/3.defense-systems/fs_sma.md
@@ -34,18 +34,22 @@ The system was detected in 20 different species.
Proportion of genome encoding the FS_Sma system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### FS_Sma
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /fs_sma/FS_Sma__Sma-plddts_94.14969.pdb
+dataUrls:
+ - /fs_sma/FS_Sma__Sma.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
@@ -86,12 +90,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.cell.2022.07.014
-
----
-::
diff --git a/content/3.defense-systems/gabija.md b/content/3.defense-systems/gabija.md
index 5c18050cbb47378f9f096e1626fee426e6f1b219..d255ba39de99668111223960feb0fc84e49f10fd 100644
--- a/content/3.defense-systems/gabija.md
+++ b/content/3.defense-systems/gabija.md
@@ -54,25 +54,23 @@ The system was detected in 1375 different species.
Proportion of genome encoding the Gabija system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Gabija
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /gabija/Gabija,Gabija_GajB,0,V-plddts_91.3911.pdb
----
-::
+dataUrls:
+ - /gabija/Gabija.Gabija__GajA.0.V.pdb
+ - /gabija/Gabija.Gabija_GajB.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gabija/Gabija,Gabija__GajA,0,V-plddts_86.08162.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
@@ -116,3 +114,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/gao_ape.md b/content/3.defense-systems/gao_ape.md
index a371e7c602abffe9e619179148ff07319221bd0b..a5da96e75d0148911731ee809a3c9568fbd66797 100644
--- a/content/3.defense-systems/gao_ape.md
+++ b/content/3.defense-systems/gao_ape.md
@@ -47,18 +47,22 @@ The system was detected in 45 different species.
Proportion of genome encoding the Gao_Ape system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Gao_Ape
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /gao_ape/Gao_Ape__ApeA-plddts_90.44181.pdb
+dataUrls:
+ - /gao_ape/Gao_Ape__ApeA.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -87,3 +91,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/gao_her.md b/content/3.defense-systems/gao_her.md
index e3f668fb8ac7d8ba17cadff61c1365504b6ebb53..c942058db40bcb5f9b2bad14e4c80bd871670536 100644
--- a/content/3.defense-systems/gao_her.md
+++ b/content/3.defense-systems/gao_her.md
@@ -38,41 +38,35 @@ The system was detected in 134 different species.
Proportion of genome encoding the Gao_Her system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Gao_Her_DUF
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /gao_her/Gao_Her_DUF,Gao_Her_DUF__DUF4297,0,V-plddts_91.87572.pdb
----
-::
+dataUrls:
+ - /gao_her/Gao_Her_DUF.Gao_Her_DUF__DUF4297.0.V.pdb
+ - /gao_her/Gao_Her_DUF.Gao_Her_DUF__HerA_DUF.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_her/Gao_Her_DUF,Gao_Her_DUF__HerA_DUF,0,V-plddts_88.91697.pdb
---
::
-
### Gao_Her_SIR
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /gao_her/Gao_Her_SIR,Gao_Her_SIR__HerA_SIR2,0,V-plddts_86.52691.pdb
----
-::
+dataUrls:
+ - /gao_her/Gao_Her_SIR.Gao_Her_SIR__HerA_SIR2.0.V.pdb
+ - /gao_her/Gao_Her_SIR.Gao_Her_SIR__SIR2.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_her/Gao_Her_SIR,Gao_Her_SIR__SIR2,0,V-plddts_87.76893.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -112,13 +106,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aba0372
-
----
-::
diff --git a/content/3.defense-systems/gao_hhe.md b/content/3.defense-systems/gao_hhe.md
index e39c90a5c35bd5d565dbafc5432128b5d316f428..9d6f96e55a1c23e87c0886f70bd5654ece79965d 100644
--- a/content/3.defense-systems/gao_hhe.md
+++ b/content/3.defense-systems/gao_hhe.md
@@ -45,18 +45,22 @@ The system was detected in 56 different species.
Proportion of genome encoding the Gao_Hhe system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Gao_Hhe
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /gao_hhe/Gao_Hhe__HheA-plddts_81.41701.pdb
+dataUrls:
+ - /gao_hhe/Gao_Hhe__HheA.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -85,3 +89,4 @@ end
</mermaid>
+
diff --git a/content/3.defense-systems/gao_iet.md b/content/3.defense-systems/gao_iet.md
index 92f0e5cfb8613aa2c2e0f9999ce973f00c498fd9..5c0f1dd38492774a05b3d3db2dc6f216cc2fbb61 100644
--- a/content/3.defense-systems/gao_iet.md
+++ b/content/3.defense-systems/gao_iet.md
@@ -34,25 +34,23 @@ The system was detected in 185 different species.
Proportion of genome encoding the Gao_Iet system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Gao_Iet
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /gao_iet/Gao_Iet,Gao_Iet__IetA,0,V-plddts_85.57017.pdb
----
-::
+dataUrls:
+ - /gao_iet/Gao_Iet.Gao_Iet__IetA.0.V.pdb
+ - /gao_iet/Gao_Iet.Gao_Iet__IetS.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_iet/Gao_Iet,Gao_Iet__IetS,0,V-plddts_90.4167.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -79,13 +77,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aba0372
-
----
-::
diff --git a/content/3.defense-systems/gao_mza.md b/content/3.defense-systems/gao_mza.md
index 837f52188a2ad4eaa5ac06b61bf41846db13f20f..738774165381629a50c335ae49a3c04d60202ec2 100644
--- a/content/3.defense-systems/gao_mza.md
+++ b/content/3.defense-systems/gao_mza.md
@@ -45,46 +45,26 @@ The system was detected in 32 different species.
Proportion of genome encoding the Gao_Mza system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Gao_Mza
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /gao_mza/Gao_Mza,Gao_Mza__MzaA,0,V-plddts_73.82237.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_mza/Gao_Mza,Gao_Mza__MzaB,0,V-plddts_88.82333.pdb
----
-::
+dataUrls:
+ - /gao_mza/Gao_Mza.Gao_Mza__MzaE.0.V.pdb
+ - /gao_mza/Gao_Mza.Gao_Mza__MzaD.0.V.pdb
+ - /gao_mza/Gao_Mza.Gao_Mza__MzaC.0.V.pdb
+ - /gao_mza/Gao_Mza.Gao_Mza__MzaB.0.V.pdb
+ - /gao_mza/Gao_Mza.Gao_Mza__MzaA.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_mza/Gao_Mza,Gao_Mza__MzaC,0,V-plddts_83.55691.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_mza/Gao_Mza,Gao_Mza__MzaD,0,V-plddts_88.07953.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_mza/Gao_Mza,Gao_Mza__MzaE,0,V-plddts_87.92462.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -115,3 +95,4 @@ end
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/gao_ppl.md b/content/3.defense-systems/gao_ppl.md
index 036156d0503de82bb793c2d5c68fa9d05ac94fcd..a5aa0cc2e4cb907e7f0f92933c45b54f74212fb9 100644
--- a/content/3.defense-systems/gao_ppl.md
+++ b/content/3.defense-systems/gao_ppl.md
@@ -33,18 +33,22 @@ The system was detected in 104 different species.
Proportion of genome encoding the Gao_Ppl system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Gao_Ppl
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /gao_ppl/Gao_Ppl__PplA-plddts_89.89639.pdb
+dataUrls:
+ - /gao_ppl/Gao_Ppl__PplA.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -71,12 +75,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aba0372
-
----
-::
diff --git a/content/3.defense-systems/gao_qat.md b/content/3.defense-systems/gao_qat.md
index 9c3da94fa8d5fea677547cca683f35acd58a71dc..c0129613a55f0e273e3afcb7c6ba7a21d59bfec9 100644
--- a/content/3.defense-systems/gao_qat.md
+++ b/content/3.defense-systems/gao_qat.md
@@ -34,39 +34,25 @@ The system was detected in 267 different species.
Proportion of genome encoding the Gao_Qat system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Gao_Qat
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /gao_qat/Gao_Qat,Gao_Qat__QatA,0,V-plddts_81.28827.pdb
----
-::
+dataUrls:
+ - /gao_qat/Gao_Qat.Gao_Qat__QatA.0.V.pdb
+ - /gao_qat/Gao_Qat.Gao_Qat__QatB.0.V.pdb
+ - /gao_qat/Gao_Qat.Gao_Qat__QatC.0.V.pdb
+ - /gao_qat/Gao_Qat.Gao_Qat__QatD.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_qat/Gao_Qat,Gao_Qat__QatB,0,V-plddts_86.3728.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_qat/Gao_Qat,Gao_Qat__QatC,0,V-plddts_93.16811.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_qat/Gao_Qat,Gao_Qat__QatD,0,V-plddts_94.78681.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -92,13 +78,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aba0372
-
----
-::
diff --git a/content/3.defense-systems/gao_rl.md b/content/3.defense-systems/gao_rl.md
index 06631e1bbaca644e5425a10acae3088f4a2305ca..5f77504e503a5d0ed23d7e7265e1c5532d1bb6c3 100644
--- a/content/3.defense-systems/gao_rl.md
+++ b/content/3.defense-systems/gao_rl.md
@@ -47,39 +47,25 @@ The system was detected in 74 different species.
Proportion of genome encoding the Gao_RL system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Gao_RL
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /gao_rl/Gao_RL,Gao_RL__RL_A,0,V-plddts_87.81206.pdb
----
-::
+dataUrls:
+ - /gao_rl/Gao_RL.Gao_RL__RL_A.0.V.pdb
+ - /gao_rl/Gao_RL.Gao_RL__RL_D.0.V.pdb
+ - /gao_rl/Gao_RL.Gao_RL__RL_B.0.V.pdb
+ - /gao_rl/Gao_RL.Gao_RL__RL_C.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_rl/Gao_RL,Gao_RL__RL_B,0,V-plddts_87.72993.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_rl/Gao_RL,Gao_RL__RL_C,0,V-plddts_90.086.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_rl/Gao_RL,Gao_RL__RL_D,0,V-plddts_85.47115.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -106,3 +92,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/gao_tery.md b/content/3.defense-systems/gao_tery.md
index 42bf18b177ffff35836be9dcf51cf732b770329b..21910352ef09258b1fdc817a41f404d705982b62 100644
--- a/content/3.defense-systems/gao_tery.md
+++ b/content/3.defense-systems/gao_tery.md
@@ -33,32 +33,24 @@ The system was detected in 74 different species.
Proportion of genome encoding the Gao_TerY system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Gao_TerY
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /gao_tery/Gao_TerY,Gao_TerY__TerYA,0,V-plddts_91.43497.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_tery/Gao_TerY,Gao_TerY__TerYB,0,V-plddts_95.75285.pdb
----
-::
+dataUrls:
+ - /gao_tery/Gao_TerY.Gao_TerY__TerYA.0.V.pdb
+ - /gao_tery/Gao_TerY.Gao_TerY__TerYB.0.V.pdb
+ - /gao_tery/Gao_TerY.Gao_TerY__TerYC.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_tery/Gao_TerY,Gao_TerY__TerYC,0,V-plddts_81.328.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -85,12 +77,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aba0372
-
----
-::
diff --git a/content/3.defense-systems/gao_tmn.md b/content/3.defense-systems/gao_tmn.md
index c7511731b11b6df8b5008f64ed79f2a66feaebd0..d4cc024cd703979a1485f22e0085ff5f482b0745 100644
--- a/content/3.defense-systems/gao_tmn.md
+++ b/content/3.defense-systems/gao_tmn.md
@@ -46,18 +46,22 @@ The system was detected in 84 different species.
Proportion of genome encoding the Gao_Tmn system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Gao_Tmn
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /gao_tmn/Gao_Tmn__TmnA-plddts_82.0142.pdb
+dataUrls:
+ - /gao_tmn/Gao_Tmn__TmnA.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -84,3 +88,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/gao_upx.md b/content/3.defense-systems/gao_upx.md
index 9bdf3daaa92f37433665883b633121130967f095..f83ae2c2270e6cab79bde6d7554461681efb67cb 100644
--- a/content/3.defense-systems/gao_upx.md
+++ b/content/3.defense-systems/gao_upx.md
@@ -41,18 +41,22 @@ The system was detected in 33 different species.
Proportion of genome encoding the Gao_Upx system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Gao_Upx
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /gao_upx/Gao_Upx__UpxA-plddts_90.66658.pdb
+dataUrls:
+ - /gao_upx/Gao_Upx__UpxA.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -77,3 +81,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/gaps1.md b/content/3.defense-systems/gaps1.md
index c7eb1ed59a5c3cd8a85b38f9df9218ec9cb85895..14b2de5033401b04ad33ec437076a23d5203899d 100644
--- a/content/3.defense-systems/gaps1.md
+++ b/content/3.defense-systems/gaps1.md
@@ -45,18 +45,22 @@ The system was detected in 56 different species.
Proportion of genome encoding the GAPS1 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### GAPS1
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /gaps1/GAPS1__GAPS1-plddts_91.57482.pdb
+dataUrls:
+ - /gaps1/GAPS1__GAPS1.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0
@@ -82,3 +86,4 @@ end
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/gaps2.md b/content/3.defense-systems/gaps2.md
index 8eb3e73cbbaeaff2df4cf9b98b23a2c242047da9..46a20217bf3ab2516143bf2daa92ab9939bd5415 100644
--- a/content/3.defense-systems/gaps2.md
+++ b/content/3.defense-systems/gaps2.md
@@ -34,18 +34,22 @@ The system was detected in 208 different species.
Proportion of genome encoding the GAPS2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### GAPS2
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /gaps2/GAPS2__GAPS2-plddts_87.94657.pdb
+dataUrls:
+ - /gaps2/GAPS2__GAPS2.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0
@@ -70,12 +74,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1101/2023.03.28.534373
-
----
-::
diff --git a/content/3.defense-systems/gaps4.md b/content/3.defense-systems/gaps4.md
index a926ef527ba8f2fc886a22ee0810baa5b3701de3..4fe4db652d5136337a87b0f74828f84525eef384 100644
--- a/content/3.defense-systems/gaps4.md
+++ b/content/3.defense-systems/gaps4.md
@@ -33,25 +33,23 @@ The system was detected in 74 different species.
Proportion of genome encoding the GAPS4 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### GAPS4
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /gaps4/GAPS4__GAPS4a-plddts_91.74015.pdb
----
-::
+dataUrls:
+ - /gaps4/GAPS4__GAPS4a.pdb
+ - /gaps4/GAPS4__GAPS4b.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gaps4/GAPS4__GAPS4b-plddts_86.45931.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0
@@ -78,11 +76,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1101/2023.03.28.534373
----
-::
diff --git a/content/3.defense-systems/gaps6.md b/content/3.defense-systems/gaps6.md
index 2a8e424130e828dfef31448ed6a200f84cc52ee1..3b218b601ae0e4eee18c3490a24af308afb8fcfe 100644
--- a/content/3.defense-systems/gaps6.md
+++ b/content/3.defense-systems/gaps6.md
@@ -33,25 +33,23 @@ The system was detected in 33 different species.
Proportion of genome encoding the GAPS6 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### GAPS6
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /gaps6/GAPS6__GAPS6a-plddts_82.29413.pdb
----
-::
+dataUrls:
+ - /gaps6/GAPS6__GAPS6a.pdb
+ - /gaps6/GAPS6__GAPS6b.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gaps6/GAPS6__GAPS6b-plddts_90.04892.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0
@@ -78,11 +76,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1101/2023.03.28.534373
----
-::
diff --git a/content/3.defense-systems/gasdermin.md b/content/3.defense-systems/gasdermin.md
index 13302581c2bee8ca9e889a6bb37c8af363ad3be6..64bd8d76d2e3b9e55e0ad75a7950446e626378c2 100644
--- a/content/3.defense-systems/gasdermin.md
+++ b/content/3.defense-systems/gasdermin.md
@@ -48,53 +48,27 @@ The system was detected in 26 different species.
Proportion of genome encoding the GasderMIN system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### GasderMIN
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /gasdermin/GasderMIN__ATPase-plddts_79.44181.pdb
----
-::
+dataUrls:
+ - /gasdermin/GasderMIN__bGSDM.pdb
+ - /gasdermin/GasderMIN__Protease1.pdb
+ - /gasdermin/GasderMIN__Protease2.pdb
+ - /gasdermin/GasderMIN__ATPase.pdb
+ - /gasdermin/GasderMIN__Protease.pdb
+ - /gasdermin/GasderMIN__bGSDM1.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gasdermin/GasderMIN__Protease-plddts_85.56354.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gasdermin/GasderMIN__Protease1-plddts_86.2054.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gasdermin/GasderMIN__Protease2-plddts_85.10965.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gasdermin/GasderMIN__bGSDM-plddts_83.88977.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gasdermin/GasderMIN__bGSDM1-plddts_65.95252.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Johnson_2022[<a href='https://doi.org/10.1371/journal.pgen.1010065'>Johnson et al., 2022</a>] --> Origin_0
@@ -122,3 +96,4 @@ end
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/hachiman.md b/content/3.defense-systems/hachiman.md
index 4d52aee37f49295e02b01de533297f44f08c209e..5a8515cf333d53b71414d4a4fbcff7e5ce09f034 100644
--- a/content/3.defense-systems/hachiman.md
+++ b/content/3.defense-systems/hachiman.md
@@ -40,27 +40,23 @@ The system was detected in 541 different species.
Proportion of genome encoding the Hachiman system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Hachiman
+##### Example 1
-Example 1:
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /hachiman/Hachiman.Hachiman__HamB.0.V-plddts_88.00493.pdb
----
-::
+dataUrls:
+ - /hachiman/Hachiman.Hachiman__HamB.0.V.pdb
+ - /hachiman/Hachiman.Hachiman__HamA.0.V.pdb
-Example 2:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /hachiman/Hachiman.Hachiman__HamB.0.V-plddts_88.00493.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
@@ -101,20 +97,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aar4120
-
----
-::
-
-
-## References
-
-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/3.defense-systems/hna.md b/content/3.defense-systems/hna.md
index 82d73c2d23255f35eb49be021fd63421ec9b774a..56a84f17e58ce9fbde520a4cd0d9ca856558a056 100644
--- a/content/3.defense-systems/hna.md
+++ b/content/3.defense-systems/hna.md
@@ -34,18 +34,22 @@ The system was detected in 305 different species.
Proportion of genome encoding the Hna system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Hna
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /hna/Hna__Hna-plddts_91.2064.pdb
+dataUrls:
+ - /hna/Hna__Hna.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
@@ -81,12 +85,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2023.01.010
-
----
-::
diff --git a/content/3.defense-systems/isg15-like.md b/content/3.defense-systems/isg15-like.md
index 7b71a70c7d73f7142c20bdd054bdce868339e369..314be5d18fa45b18e939f4baaee844e578035f6b 100644
--- a/content/3.defense-systems/isg15-like.md
+++ b/content/3.defense-systems/isg15-like.md
@@ -33,156 +33,77 @@ The system was detected in 39 different species.
Proportion of genome encoding the ISG15-like system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### ISG15-like
+##### Example 1
-Example 1:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilA,0,V-plddts_93.65636.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilB,0,V-plddts_95.49136.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilC,0,V-plddts_92.06734.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilD,0,V-plddts_93.10226.pdb
----
-::
-
-Example 2:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilA,0,V-plddts_93.65636.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilB,0,V-plddts_95.49136.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilC,0,V-plddts_92.06734.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilD,0,V-plddts_93.10226.pdb
----
-::
-
-Example 3:
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilA,0,V-plddts_93.65636.pdb
----
-::
+dataUrls:
+ - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.pdb
+ - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.pdb
+ - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.pdb
+ - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilB,0,V-plddts_95.49136.pdb
---
::
+##### Example 2
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilC,0,V-plddts_92.06734.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilD,0,V-plddts_93.10226.pdb
----
-::
-
-Example 4:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilA,0,V-plddts_93.65636.pdb
----
-::
+dataUrls:
+ - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.pdb
+ - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.pdb
+ - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.pdb
+ - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilB,0,V-plddts_95.49136.pdb
---
::
+##### Example 3
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilC,0,V-plddts_92.06734.pdb
----
-::
+dataUrls:
+ - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.pdb
+ - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.pdb
+ - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.pdb
+ - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilD,0,V-plddts_93.10226.pdb
---
::
+##### Example 4
-Example 5:
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilA,0,V-plddts_93.65636.pdb
----
-::
+dataUrls:
+ - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.pdb
+ - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.pdb
+ - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.pdb
+ - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilB,0,V-plddts_95.49136.pdb
---
::
+##### Example 5
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilC,0,V-plddts_92.06734.pdb
----
-::
+dataUrls:
+ - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.pdb
+ - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.pdb
+ - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.pdb
+ - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /isg15-like/ISG15-like,ISG15-like__BilD,0,V-plddts_93.10226.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -264,12 +185,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
----
-::
diff --git a/content/3.defense-systems/jukab.md b/content/3.defense-systems/jukab.md
index 54409b2137bdfcd56e1b58aacaa955f21238024b..b650585efd48ec979a2d95efa78768dec9e2a9c3 100644
--- a/content/3.defense-systems/jukab.md
+++ b/content/3.defense-systems/jukab.md
@@ -34,25 +34,23 @@ The system was detected in 50 different species.
Proportion of genome encoding the JukAB system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### JukAB
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /jukab/JukAB__JukA-plddts_77.76916.pdb
----
-::
+dataUrls:
+ - /jukab/JukAB__JukB.pdb
+ - /jukab/JukAB__JukA.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /jukab/JukAB__JukB-plddts_67.28863.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Li_2022[<a href='https://doi.org/10.1101/2022.09.17.508391'>Li et al., 2022</a>] --> Origin_0
@@ -76,12 +74,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1101/2022.09.17.508391
-
----
-::
diff --git a/content/3.defense-systems/kiwa.md b/content/3.defense-systems/kiwa.md
index 7e83855f46d24981711f7f5f1ad80a40ade38eee..87a2bc70071a7fbfeaecfe26db24876c3d67e8a4 100644
--- a/content/3.defense-systems/kiwa.md
+++ b/content/3.defense-systems/kiwa.md
@@ -47,25 +47,23 @@ The system was detected in 382 different species.
Proportion of genome encoding the Kiwa system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Kiwa
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /kiwa/Kiwa,Kiwa__KwaA,0,V-plddts_86.99693.pdb
----
-::
+dataUrls:
+ - /kiwa/Kiwa.Kiwa__KwaB.0.V.pdb
+ - /kiwa/Kiwa.Kiwa__KwaA.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /kiwa/Kiwa,Kiwa__KwaB,0,V-plddts_93.65136.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
@@ -91,3 +89,4 @@ end
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/lamassu-fam.md b/content/3.defense-systems/lamassu-fam.md
index 3fcb7cea7856512f76dfc66ed9b81933e4facc9b..8b5be3196a2c3b784279a92401f060687b9471d3 100644
--- a/content/3.defense-systems/lamassu-fam.md
+++ b/content/3.defense-systems/lamassu-fam.md
@@ -96,239 +96,143 @@ The system was detected in 1220 different species.
Proportion of genome encoding the Lamassu-Fam system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Lamassu-Amidase
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /lamassu-fam/Lamassu-Amidase,Lamassu-Fam__LmuA_effector_Amidase,0,DF-plddts_93.15132.pdb
----
-::
+dataUrls:
+ - /lamassu-fam/Lamassu-Amidase.Lamassu-Fam__LmuA_effector_Amidase.0.DF.pdb
+ - /lamassu-fam/Lamassu-Amidase.Lamassu-Fam__LmuB_SMC_Amidase.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Amidase,Lamassu-Fam__LmuB_SMC_Amidase,0,DF-plddts_83.58631.pdb
---
::
-
### Lamassu-Cap4_nuclease
+##### Example 1
-Example 1:
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /lamassu-fam/Lamassu-Cap4_nuclease,Lamassu-Fam__LmuA_effector_Cap4_nuclease_II,0,DF-plddts_93.57957.pdb
----
-::
+dataUrls:
+ - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuA_effector_Cap4_nuclease_II.0.DF.pdb
+ - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuC_acc_Cap4_nuclease.0.DF.pdb
+ - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Cap4_nuclease,Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II,0,DF-plddts_90.05853.pdb
---
::
+##### Example 2
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /lamassu-fam/Lamassu-Cap4_nuclease,Lamassu-Fam__LmuC_acc_Cap4_nuclease,0,DF-plddts_91.47415.pdb
----
-::
+dataUrls:
+ - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuA_effector_Cap4_nuclease.1.DF.pdb
+ - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam_undetected_LmuC.1.DF.pdb
+ - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuB_SMC_Cap4_nuclease.1.DF.pdb
-Example 2:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Cap4_nuclease,Lamassu-Fam__LmuA_effector_Cap4_nuclease_II,0,DF-plddts_93.57957.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Cap4_nuclease,Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II,0,DF-plddts_90.05853.pdb
---
::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Cap4_nuclease,Lamassu-Fam__LmuC_acc_Cap4_nuclease,0,DF-plddts_91.47415.pdb
----
-::
-
### Lamassu-FMO
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /lamassu-fam/Lamassu-FMO,Lamassu-Fam__LmuA_effector_FMO,0,DF-plddts_90.83272.pdb
----
-::
+dataUrls:
+ - /lamassu-fam/Lamassu-FMO.Lamassu-Fam__LmuB_SMC_FMO.0.DF.pdb
+ - /lamassu-fam/Lamassu-FMO.Lamassu-Fam__LmuC_acc_FMO.0.DF.pdb
+ - /lamassu-fam/Lamassu-FMO.Lamassu-Fam__LmuA_effector_FMO.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-FMO,Lamassu-Fam__LmuB_SMC_FMO,0,DF-plddts_83.19523.pdb
---
::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-FMO,Lamassu-Fam__LmuC_acc_FMO,0,DF-plddts_89.32543.pdb
----
-::
-
### Lamassu-Fam_Hydrolase_Protease
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /lamassu-fam/Lamassu-Fam_Hydrolase_Protease,Lamassu-Fam__LmuA_effector_Hydrolase,0,V-plddts_93.45211.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Fam_Hydrolase_Protease,Lamassu-Fam__LmuA_effector_Protease,0,V-plddts_90.19112.pdb
----
-::
+dataUrls:
+ - /lamassu-fam/Lamassu-Fam_Hydrolase_Protease.Lamassu-Fam__LmuA_effector_Hydrolase.0.V.pdb
+ - /lamassu-fam/Lamassu-Fam_Hydrolase_Protease.Lamassu-Fam__LmuA_effector_Protease.0.V.pdb
+ - /lamassu-fam/Lamassu-Fam_Hydrolase_Protease.Lamassu-Fam__LmuC_acc_hydrolase_protease.0.V.pdb
+ - /lamassu-fam/Lamassu-Fam_Hydrolase_Protease.Lamassu-Fam__LmuB_SMC_Hydrolase_protease.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Fam_Hydrolase_Protease,Lamassu-Fam__LmuB_SMC_Hydrolase_protease,0,V-plddts_80.40324.pdb
---
::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Fam_Hydrolase_Protease,Lamassu-Fam__LmuC_acc_hydrolase_protease,0,V-plddts_89.02396.pdb
----
-::
-
### Lamassu-Fam_Mrr
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /lamassu-fam/Lamassu-Fam_Mrr,Lamassu-Fam__LmuA_effector_Mrr,0,V-plddts_84.76528.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Fam_Mrr,Lamassu-Fam__LmuB_SMC_Mrr,0,V-plddts_85.79974.pdb
----
-::
+dataUrls:
+ - /lamassu-fam/Lamassu-Fam_Mrr.Lamassu-Fam__LmuA_effector_Mrr.0.V.pdb
+ - /lamassu-fam/Lamassu-Fam_Mrr.Lamassu-Fam__LmuC_acc_Mrr.0.V.pdb
+ - /lamassu-fam/Lamassu-Fam_Mrr.Lamassu-Fam__LmuB_SMC_Mrr.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Fam_Mrr,Lamassu-Fam__LmuC_acc_Mrr,0,V-plddts_86.75101.pdb
---
::
-
### Lamassu-Fam_PDDEXK
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /lamassu-fam/Lamassu-Fam_PDDEXK,Lamassu-Fam__LmuA_effector_PDDEXK,0,V-plddts_90.62277.pdb
----
-::
+dataUrls:
+ - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuA_effector_PDDEXK.0.V.pdb
+ - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuB_SMC_PDDEXK.0.V.pdb
+ - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuC_acc_PDDEXK.0.V.pdb
+ - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuC_acc_PDDEXK.0.V.pdb
+ - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuB_SMC_PDDEXK.0.V.pdb
+ - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuA_effector_PDDEXK.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Fam_PDDEXK,Lamassu-Fam__LmuB_SMC_PDDEXK,0,V-plddts_83.57058.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Fam_PDDEXK,Lamassu-Fam__LmuC_acc_PDDEXK,0,V-plddts_93.07571.pdb
---
::
-
### Lamassu-Hypothetical
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /lamassu-fam/Lamassu-Hypothetical,Lamassu-Fam__LmuA_effector_hypothetical,0,DF-plddts_87.29909.pdb
----
-::
+dataUrls:
+ - /lamassu-fam/Lamassu-Hypothetical.Lamassu-Fam__LmuB_SMC_hypothetical.0.DF.pdb
+ - /lamassu-fam/Lamassu-Hypothetical.Lamassu-Fam__LmuC_acc_hypothetical.0.DF.pdb
+ - /lamassu-fam/Lamassu-Hypothetical.Lamassu-Fam__LmuA_effector_hypothetical.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Hypothetical,Lamassu-Fam__LmuB_SMC_hypothetical,0,DF-plddts_90.35013.pdb
---
::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Hypothetical,Lamassu-Fam__LmuC_acc_hypothetical,0,DF-plddts_90.49821.pdb
----
-::
-
### Lamassu-Lipase
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /lamassu-fam/Lamassu-Lipase,Lamassu-Fam__LmuA_effector_Lipase,0,DF-plddts_86.47244.pdb
----
-::
+dataUrls:
+ - /lamassu-fam/Lamassu-Lipase.Lamassu-Fam__LmuB_SMC_Lipase.0.DF.pdb
+ - /lamassu-fam/Lamassu-Lipase.Lamassu-Fam__LmuC_acc_Lipase.0.DF.pdb
+ - /lamassu-fam/Lamassu-Lipase.Lamassu-Fam__LmuA_effector_Lipase.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Lipase,Lamassu-Fam__LmuB_SMC_Lipase,0,DF-plddts_89.07634.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Lipase,Lamassu-Fam__LmuC_acc_Lipase,0,DF-plddts_86.70507.pdb
---
::
-
### Lamassu-Sir2
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /lamassu-fam/Lamassu-Sir2,Lamassu-Fam__LmuA_effector_Sir2,0,DF-plddts_89.3866.pdb
----
-::
+dataUrls:
+ - /lamassu-fam/Lamassu-Sir2.Lamassu-Fam__LmuB_SMC_Sir2.0.DF.pdb
+ - /lamassu-fam/Lamassu-Sir2.Lamassu-Fam__LmuC_acc_Sir2.0.DF.pdb
+ - /lamassu-fam/Lamassu-Sir2.Lamassu-Fam__LmuA_effector_Sir2.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Sir2,Lamassu-Fam__LmuB_SMC_Sir2,0,DF-plddts_86.39095.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /lamassu-fam/Lamassu-Sir2,Lamassu-Fam__LmuC_acc_Sir2,0,DF-plddts_85.94734.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
@@ -437,3 +341,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/lit.md b/content/3.defense-systems/lit.md
index 701cbb9005c5c290890bf1cc0696c73452564f1a..55de976804c1e74c357977070ee3039f78ae196c 100644
--- a/content/3.defense-systems/lit.md
+++ b/content/3.defense-systems/lit.md
@@ -51,18 +51,22 @@ The system was detected in 78 different species.
Proportion of genome encoding the Lit system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Lit
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /lit/Lit__Lit-plddts_91.19971.pdb
+dataUrls:
+ - /lit/Lit__Lit.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Yu_1994[<a href='https://doi.org/10.1073/pnas.91.2.802'>Yu and Snyder, 1994</a>] --> Origin_0
@@ -86,3 +90,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/mads.md b/content/3.defense-systems/mads.md
index c9ba94ff00a1a624aab4c0d1d705c274ea128a37..e13fcc404f870026c9f1484c67af2e611998b6a4 100644
--- a/content/3.defense-systems/mads.md
+++ b/content/3.defense-systems/mads.md
@@ -34,60 +34,28 @@ The system was detected in 63 different species.
Proportion of genome encoding the MADS system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### MADS
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /mads/MADS__mad1-plddts_82.3118.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /mads/MADS__mad2-plddts_87.54253.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /mads/MADS__mad3-plddts_93.27207.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /mads/MADS__mad4-plddts_92.44061.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /mads/MADS__mad5-plddts_93.90587.pdb
----
-::
+dataUrls:
+ - /mads/MADS__mad8.pdb
+ - /mads/MADS__mad7.pdb
+ - /mads/MADS__mad4.pdb
+ - /mads/MADS__mad3.pdb
+ - /mads/MADS__mad1.pdb
+ - /mads/MADS__mad5.pdb
+ - /mads/MADS__mad2.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /mads/MADS__mad7-plddts_91.54141.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /mads/MADS__mad8-plddts_82.23514.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Maestri_2023[<a href='https://doi.org/10.1101/2023.03.30.534895'>Maestri et al., 2023</a>] --> Origin_0
@@ -114,12 +82,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1101/2023.03.30.534895
-
----
-::
diff --git a/content/3.defense-systems/menshen.md b/content/3.defense-systems/menshen.md
index 536decd91221c5bcfb17fb9dd2b0501e6c8acced..6678c81f9b1b900d1f9c93b7c420a997073f7063 100644
--- a/content/3.defense-systems/menshen.md
+++ b/content/3.defense-systems/menshen.md
@@ -47,32 +47,24 @@ The system was detected in 263 different species.
Proportion of genome encoding the Menshen system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Menshen
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /menshen/Menshen,Menshen__NsnA,0,V-plddts_87.39628.pdb
----
-::
+dataUrls:
+ - /menshen/Menshen.Menshen__NsnA.0.V.pdb
+ - /menshen/Menshen.Menshen__NsnB.0.V.pdb
+ - /menshen/Menshen.Menshen__NsnC.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /menshen/Menshen,Menshen__NsnB,0,V-plddts_89.66947.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /menshen/Menshen,Menshen__NsnC,0,V-plddts_91.07244.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -107,3 +99,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/mmb_gp29_gp30.md b/content/3.defense-systems/mmb_gp29_gp30.md
index 1669c5f9dc9c4be30718e680a02da41f78cd523c..1985314ee990107d1e7284628f9535b8546d9366 100644
--- a/content/3.defense-systems/mmb_gp29_gp30.md
+++ b/content/3.defense-systems/mmb_gp29_gp30.md
@@ -41,25 +41,23 @@ The system was detected in 4 different species.
Proportion of genome encoding the MMB_gp29_gp30 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### MMB_gp29_gp30
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /mmb_gp29_gp30/MMB_gp29_gp30__gp29-plddts_82.71079.pdb
----
-::
+dataUrls:
+ - /mmb_gp29_gp30/MMB_gp29_gp30__gp29.pdb
+ - /mmb_gp29_gp30/MMB_gp29_gp30__gp30.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /mmb_gp29_gp30/MMB_gp29_gp30__gp30-plddts_65.6043.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Dedrick_2017[<a href='https://doi.org/10.1038/nmicrobiol.2016.251'>Dedrick et al., 2017</a>] --> Origin_0
@@ -85,3 +83,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/mok_hok_sok.md b/content/3.defense-systems/mok_hok_sok.md
index a7bc48e602010cf139920842f9cbcdd000bd9cd1..ddcf152d7224dc55a5c06c39387f9e28f7b064b8 100644
--- a/content/3.defense-systems/mok_hok_sok.md
+++ b/content/3.defense-systems/mok_hok_sok.md
@@ -51,18 +51,22 @@ The system was detected in 83 different species.
Proportion of genome encoding the Mok_Hok_Sok system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Mok_Hok_Sok
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /mok_hok_sok/Mok_Hok_Sok__Hok-plddts_80.98652.pdb
+dataUrls:
+ - /mok_hok_sok/Mok_Hok_Sok__Hok.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Pecota_1996[<a href='https://doi.org/10.1128/jb.178.7.2044-2050.1996'>Pecota and Wood, 1996</a>] --> Origin_0
@@ -87,3 +91,4 @@ end
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/mokosh.md b/content/3.defense-systems/mokosh.md
index 15224c64e08a160b61c1ace2eb6108d81d100b4e..0c365bcb7d2633c4e48b2c1acee33a64ea6ead56 100644
--- a/content/3.defense-systems/mokosh.md
+++ b/content/3.defense-systems/mokosh.md
@@ -66,50 +66,43 @@ The system was detected in 577 different species.
Proportion of genome encoding the Mokosh system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Mokosh_TypeI
+##### Example 1
-Example 1:
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /mokosh/Mokosh_TypeI,Mokosh_TypeI__MkoA,0,V-plddts_81.37154.pdb
----
-::
+dataUrls:
+ - /mokosh/Mokosh_TypeI.Mokosh_TypeI__MkoB.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /mokosh/Mokosh_TypeI,Mokosh_TypeI__MkoB,0,V-plddts_91.10094.pdb
---
::
+##### Example 2
-Example 2:
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /mokosh/Mokosh_TypeI,Mokosh_TypeI__MkoA,0,V-plddts_81.37154.pdb
----
-::
+dataUrls:
+ - /mokosh/Mokosh_TypeI.Mokosh_TypeI__MkoB.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /mokosh/Mokosh_TypeI,Mokosh_TypeI__MkoB,0,V-plddts_91.10094.pdb
---
::
-
### Mokosh_TypeII
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /mokosh/Mokosh_TypeII__MkoC-plddts_90.69139.pdb
+dataUrls:
+ - /mokosh/Mokosh_TypeII__MkoC.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -157,3 +150,4 @@ end
</mermaid>
+
diff --git a/content/3.defense-systems/nhi.md b/content/3.defense-systems/nhi.md
index 3c1dc2e5c7722507041bf90e8da75a4ae868a39e..08d379f4c97ff3a865bf990ad11d882eb9f7e08b 100644
--- a/content/3.defense-systems/nhi.md
+++ b/content/3.defense-systems/nhi.md
@@ -48,18 +48,22 @@ The system was detected in 61 different species.
Proportion of genome encoding the Nhi system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Nhi
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /nhi/Nhi__Nhi-plddts_83.89425.pdb
+dataUrls:
+ - /nhi/Nhi__Nhi.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -123,3 +127,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/nixi.md b/content/3.defense-systems/nixi.md
index 3f115bb76f8329b78a58ff12ebdceae294804168..ac4971e617461adf3981e2049f1a90b26c806488 100644
--- a/content/3.defense-systems/nixi.md
+++ b/content/3.defense-systems/nixi.md
@@ -43,18 +43,22 @@ The system was detected in 5 different species.
Proportion of genome encoding the NixI system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### NixI
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /nixi/NixI__NixI-plddts_92.38782.pdb
+dataUrls:
+ - /nixi/NixI__NixI.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Legault_2022[<a href='https://doi.org/10.1093/nar/gkac002'>LeGault et al., 2022</a>] --> Origin_0
@@ -78,3 +82,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/nlr.md b/content/3.defense-systems/nlr.md
index 311bef418ea278a88dfe16aa42a9ac6f53b53e16..c463d48387b602d9ead55c76a8446b5cb0163a1f 100644
--- a/content/3.defense-systems/nlr.md
+++ b/content/3.defense-systems/nlr.md
@@ -38,27 +38,33 @@ The system was detected in 205 different species.
Proportion of genome encoding the NLR system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### NLR_like_bNACHT01
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /nlr/NLR_like_bNACHT01__NLR_like_bNACHT01-plddts_87.90581.pdb
+dataUrls:
+ - /nlr/NLR_like_bNACHT01__NLR_like_bNACHT01.pdb
+
---
::
-
### NLR_like_bNACHT09
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /nlr/NLR_like_bNACHT09__NLR_like_bNACHT09-plddts_85.63627.pdb
+dataUrls:
+ - /nlr/NLR_like_bNACHT09__NLR_like_bNACHT09.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Kibby_2022[<a href='https://doi.org/10.1101/2022.07.19.500537'>Kibby et al., 2022</a>] --> Origin_0
@@ -170,13 +176,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1101/2022.07.19.500537
-
----
-::
diff --git a/content/3.defense-systems/old_exonuclease.md b/content/3.defense-systems/old_exonuclease.md
index e438b40a99a021c69904f48fe5214f70cad6511d..8359ab39edf16a7e7034e67eeb1483ca735c335a 100644
--- a/content/3.defense-systems/old_exonuclease.md
+++ b/content/3.defense-systems/old_exonuclease.md
@@ -46,18 +46,22 @@ The system was detected in 56 different species.
Proportion of genome encoding the Old_exonuclease system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Old_exonuclease
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /old_exonuclease/Old_exonuclease__Old_exonuclease-plddts_88.62156.pdb
+dataUrls:
+ - /old_exonuclease/Old_exonuclease__Old_exonuclease.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0
@@ -84,3 +88,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/olokun.md b/content/3.defense-systems/olokun.md
index 390ba0afed9dde50e4b30a056e455e723f4ea8c2..4b48a3299328033b4b6ae275475b6c85a0d1b029 100644
--- a/content/3.defense-systems/olokun.md
+++ b/content/3.defense-systems/olokun.md
@@ -52,25 +52,23 @@ The system was detected in 137 different species.
Proportion of genome encoding the Olokun system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Olokun
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /olokun/Olokun,Olokun__OloA,0,V-plddts_89.84697.pdb
----
-::
+dataUrls:
+ - /olokun/Olokun.Olokun__OloA.0.V.pdb
+ - /olokun/Olokun.Olokun__OloB.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /olokun/Olokun,Olokun__OloB,0,V-plddts_85.67714.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -95,3 +93,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/pago.md b/content/3.defense-systems/pago.md
index 7028073c44274bcd28fc38775cfe0063145692ed..86caf2b4d68c8abbfa26c5b55fc2e837de149cbf 100644
--- a/content/3.defense-systems/pago.md
+++ b/content/3.defense-systems/pago.md
@@ -99,80 +99,30 @@ The system was detected in 464 different species.
Proportion of genome encoding the pAgo system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### pAgo
+##### Example 1
-Example 1:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pago/pAgo__pAgo_LongA-plddts_90.01396.pdb
----
-::
-
-Example 2:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pago/pAgo__pAgo_LongA-plddts_90.01396.pdb
----
-::
-
-Example 3:
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pago/pAgo__pAgo_LongA-plddts_90.01396.pdb
----
-::
+dataUrls:
+ - /pago/pAgo__pAgo_LongA.pdb
+ - /pago/pAgo__pAgo_LongB.pdb
+ - /pago/pAgo__pAgo_S1A.pdb
+ - /pago/pAgo__SIR2APAZ.pdb
+ - /pago/pAgo__pAgo_S1B.pdb
+ - /pago/pAgo__XAPAZ.pdb
+ - /pago/pAgo__pAgo_S2B.pdb
+ - /pago/pAgo__TIRAPAZ.pdb
+ - /pago/pAgo__pAgo_SPARTA.pdb
-Example 4:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pago/pAgo__pAgo_LongA-plddts_90.01396.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pago/pAgo__pAgo_LongB-plddts_92.47739.pdb
----
-::
-
-Example 5:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pago/pAgo__pAgo_LongA-plddts_90.01396.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pago/pAgo__pAgo_LongB-plddts_92.47739.pdb
----
-::
-
-Example 6:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pago/pAgo__pAgo_LongA-plddts_90.01396.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pago/pAgo__pAgo_LongB-plddts_92.47739.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Kuzmenko_2020[<a href='https://doi.org/10.1038/s41586-020-2605-1'>Kuzmenko et al., 2020</a>] --> Origin_0
@@ -270,3 +220,4 @@ end
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/panchino_gp28.md b/content/3.defense-systems/panchino_gp28.md
index 0535dd85a03891b8d1a73a27dc3ae39703b7a79c..e197f1d87baefa57d3020bd5b25d6d474d4050a9 100644
--- a/content/3.defense-systems/panchino_gp28.md
+++ b/content/3.defense-systems/panchino_gp28.md
@@ -34,18 +34,22 @@ The system was detected in 5 different species.
Proportion of genome encoding the Panchino_gp28 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Panchino_gp28
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /panchino_gp28/Panchino_gp28__gp28-plddts_90.80762.pdb
+dataUrls:
+ - /panchino_gp28/Panchino_gp28__gp28.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Dedrick_2017[<a href='https://doi.org/10.1038/nmicrobiol.2016.251'>Dedrick et al., 2017</a>] --> Origin_0
@@ -73,12 +77,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1038/nmicrobiol.2016.251
-
----
-::
diff --git a/content/3.defense-systems/paris.md b/content/3.defense-systems/paris.md
index 5a2f7ab743cb5eaa7d114859816a6b890285576b..c9b25cc499eb0aab115c307360cd175036aabe83 100644
--- a/content/3.defense-systems/paris.md
+++ b/content/3.defense-systems/paris.md
@@ -45,59 +45,57 @@ The system was detected in 518 different species.
Proportion of genome encoding the Paris system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PARIS_I
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /paris/PARIS_I,PARIS_I__AAA_15,0,V-plddts_82.06453.pdb
----
-::
+dataUrls:
+ - /paris/PARIS_I.PARIS_I__AAA_15.0.V.pdb
+ - /paris/PARIS_I.Rst_PARIS__DUF4435.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /paris/PARIS_I,Rst_PARIS__DUF4435,0,V-plddts_91.32921.pdb
---
::
-
### PARIS_II
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /paris/PARIS_II,PARIS_II__AAA_21,0,V-plddts_81.78189.pdb
----
-::
+dataUrls:
+ - /paris/PARIS_I.Rst_PARIS__DUF4435.0.V.pdb
+ - /paris/PARIS_II.PARIS_II__AAA_21.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /paris/PARIS_II,Rst_PARIS__DUF4435,0,V-plddts_95.50028.pdb
---
::
-
### PARIS_II_merge
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /paris/PARIS_II_merge__AAA_21_DUF4435-plddts_93.06529.pdb
+dataUrls:
+ - /paris/PARIS_II_merge__AAA_21_DUF4435.pdb
+
---
::
-
### PARIS_I_merge
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /paris/PARIS_I_merge__AAA_15_DUF4435-plddts_85.1867.pdb
+dataUrls:
+ - /paris/PARIS_I_merge__AAA_15_DUF4435.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0
@@ -139,13 +137,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.02.018
-
-
----
-::
diff --git a/content/3.defense-systems/pd-lambda-1.md b/content/3.defense-systems/pd-lambda-1.md
index 45179650be0119d192f3cb5d8a6ad8b25cd20f25..b09ecd2877fc075140e559bf53df7ab8d7e57fc7 100644
--- a/content/3.defense-systems/pd-lambda-1.md
+++ b/content/3.defense-systems/pd-lambda-1.md
@@ -48,18 +48,22 @@ The system was detected in 483 different species.
Proportion of genome encoding the PD-Lambda-1 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-Lambda-1
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-lambda-1/PD-Lambda-1__PD-Lambda-1-plddts_85.64965.pdb
+dataUrls:
+ - /pd-lambda-1/PD-Lambda-1__PD-Lambda-1.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -85,3 +89,4 @@ end
</mermaid>
+
diff --git a/content/3.defense-systems/pd-lambda-2.md b/content/3.defense-systems/pd-lambda-2.md
index c8f1704987b75c87633621716d1fa3291acbdc27..a6d47cfc8ab135029cf7a37d05a7e9ebadc9d1a3 100644
--- a/content/3.defense-systems/pd-lambda-2.md
+++ b/content/3.defense-systems/pd-lambda-2.md
@@ -34,32 +34,24 @@ The system was detected in 59 different species.
Proportion of genome encoding the PD-Lambda-2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-Lambda-2
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-lambda-2/PD-Lambda-2,PD-Lambda-2__PD-Lambda-2_A,0,V-plddts_84.87041.pdb
----
-::
+dataUrls:
+ - /pd-lambda-2/PD-Lambda-2.PD-Lambda-2__PD-Lambda-2_C.0.V.pdb
+ - /pd-lambda-2/PD-Lambda-2.PD-Lambda-2__PD-Lambda-2_B.0.V.pdb
+ - /pd-lambda-2/PD-Lambda-2.PD-Lambda-2__PD-Lambda-2_A.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pd-lambda-2/PD-Lambda-2,PD-Lambda-2__PD-Lambda-2_B,0,V-plddts_82.06596.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pd-lambda-2/PD-Lambda-2,PD-Lambda-2__PD-Lambda-2_C,0,V-plddts_94.25495.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -88,13 +80,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
diff --git a/content/3.defense-systems/pd-lambda-3.md b/content/3.defense-systems/pd-lambda-3.md
index 00b4eea3ff56c669b7369278bff6c8e5c70f6c46..06508b699c61a0709ad3cf49ce1c723bbb0bc6fe 100644
--- a/content/3.defense-systems/pd-lambda-3.md
+++ b/content/3.defense-systems/pd-lambda-3.md
@@ -45,32 +45,24 @@ The system was detected in 28 different species.
Proportion of genome encoding the PD-Lambda-3 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-Lambda-3
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-lambda-3/PD-Lambda-3,PD-Lambda-3__PD-Lambda-3_A,0,V-plddts_93.15726.pdb
----
-::
+dataUrls:
+ - /pd-lambda-3/PD-Lambda-3.PD-Lambda-3__PD-Lambda-3_A.0.V.pdb
+ - /pd-lambda-3/PD-Lambda-3.PD-Lambda-3__PD-Lambda-3_B.0.V.pdb
+ - /pd-lambda-3/PD-Lambda-3.PD-Lambda-3__PD-Lambda-3_C.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pd-lambda-3/PD-Lambda-3,PD-Lambda-3__PD-Lambda-3_B,0,V-plddts_92.44549.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pd-lambda-3/PD-Lambda-3,PD-Lambda-3__PD-Lambda-3_C,0,V-plddts_92.92218.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -96,3 +88,4 @@ end
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/pd-lambda-4.md b/content/3.defense-systems/pd-lambda-4.md
index 2ec229f2f4a7b56737b47b85bad21465676c0e4a..2890057bdf19a6939dedc0ef6e4dbe31c105871a 100644
--- a/content/3.defense-systems/pd-lambda-4.md
+++ b/content/3.defense-systems/pd-lambda-4.md
@@ -33,25 +33,23 @@ The system was detected in 14 different species.
Proportion of genome encoding the PD-Lambda-4 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-Lambda-4
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-lambda-4/PD-Lambda-4,PD-Lambda-4__PD-Lambda-4_A,0,V-plddts_84.51259.pdb
----
-::
+dataUrls:
+ - /pd-lambda-4/PD-Lambda-4.PD-Lambda-4__PD-Lambda-4_B.0.V.pdb
+ - /pd-lambda-4/PD-Lambda-4.PD-Lambda-4__PD-Lambda-4_A.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pd-lambda-4/PD-Lambda-4,PD-Lambda-4__PD-Lambda-4_B,0,V-plddts_81.06371.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -78,12 +76,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
----
-::
diff --git a/content/3.defense-systems/pd-lambda-5.md b/content/3.defense-systems/pd-lambda-5.md
index b18ff6c2642eb95be173e5456f7041a08be3f3b8..e19d460d57b2382f8e2933495b6ef58424236cea 100644
--- a/content/3.defense-systems/pd-lambda-5.md
+++ b/content/3.defense-systems/pd-lambda-5.md
@@ -44,25 +44,23 @@ The system was detected in 186 different species.
Proportion of genome encoding the PD-Lambda-5 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-Lambda-5
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-lambda-5/PD-Lambda-5,PD-Lambda-5__PD-Lambda-5_A,0,V-plddts_83.30421.pdb
----
-::
+dataUrls:
+ - /pd-lambda-5/PD-Lambda-5.PD-Lambda-5__PD-Lambda-5_A.0.V.pdb
+ - /pd-lambda-5/PD-Lambda-5.PD-Lambda-5__PD-Lambda-5_B.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pd-lambda-5/PD-Lambda-5,PD-Lambda-5__PD-Lambda-5_B,0,V-plddts_90.05221.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -94,3 +92,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/pd-lambda-6.md b/content/3.defense-systems/pd-lambda-6.md
index 19b5a462428547f7845062f82c7f48622fe9f5ae..70128d2a8b5dfbfe2e228d06e8162331366de4a3 100644
--- a/content/3.defense-systems/pd-lambda-6.md
+++ b/content/3.defense-systems/pd-lambda-6.md
@@ -33,18 +33,22 @@ The system was detected in 11 different species.
Proportion of genome encoding the PD-Lambda-6 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-Lambda-6
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-lambda-6/PD-Lambda-6__PD-Lambda-6-plddts_89.62781.pdb
+dataUrls:
+ - /pd-lambda-6/PD-Lambda-6__PD-Lambda-6.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -69,12 +73,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
diff --git a/content/3.defense-systems/pd-t4-1.md b/content/3.defense-systems/pd-t4-1.md
index 9d41d4a2fc9120a285ecc546a67f004dad51b271..5f5d9c36abbac78f58a73265553fa81be3433f9a 100644
--- a/content/3.defense-systems/pd-t4-1.md
+++ b/content/3.defense-systems/pd-t4-1.md
@@ -34,18 +34,22 @@ The system was detected in 38 different species.
Proportion of genome encoding the PD-T4-1 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-T4-1
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-t4-1/PD-T4-1__PD-T4-1-plddts_87.89553.pdb
+dataUrls:
+ - /pd-t4-1/PD-T4-1__PD-T4-1.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -71,13 +75,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1371/journal.pgen.1010065
-
----
-::
diff --git a/content/3.defense-systems/pd-t4-10.md b/content/3.defense-systems/pd-t4-10.md
index 4c479ab12ee83fac585fe59551411a46e77730d6..18d40210275a1825e442407464b5510a3ee9a03b 100644
--- a/content/3.defense-systems/pd-t4-10.md
+++ b/content/3.defense-systems/pd-t4-10.md
@@ -45,25 +45,23 @@ The system was detected in 23 different species.
Proportion of genome encoding the PD-T4-10 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-T4-10
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-t4-10/PD-T4-10,PD-T4-10__PD-T4-10_A,0,V-plddts_88.65128.pdb
----
-::
+dataUrls:
+ - /pd-t4-10/PD-T4-10.PD-T4-10__PD-T4-10_B.0.V.pdb
+ - /pd-t4-10/PD-T4-10.PD-T4-10__PD-T4-10_A.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pd-t4-10/PD-T4-10,PD-T4-10__PD-T4-10_B,0,V-plddts_88.59779.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -91,3 +89,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/pd-t4-2.md b/content/3.defense-systems/pd-t4-2.md
index 2e094b66702c47e23e5c3e90c80f7459329405fa..289fd9cb051b252de5c3a7ffb5f182bd3059c763 100644
--- a/content/3.defense-systems/pd-t4-2.md
+++ b/content/3.defense-systems/pd-t4-2.md
@@ -34,25 +34,23 @@ The system was detected in 28 different species.
Proportion of genome encoding the PD-T4-2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-T4-2
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-t4-2/PD-T4-2,PD-T4-2__PD-T4-2_A,0,DF-plddts_90.58136.pdb
----
-::
+dataUrls:
+ - /pd-t4-2/PD-T4-2.PD-T4-2__PD-T4-2_A.0.DF.pdb
+ - /pd-t4-2/PD-T4-2.PD-T4-2__PD-T4-2_B.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pd-t4-2/PD-T4-2,PD-T4-2__PD-T4-2_B,0,DF-plddts_93.48773.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -79,13 +77,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
diff --git a/content/3.defense-systems/pd-t4-3.md b/content/3.defense-systems/pd-t4-3.md
index 9d2ac0923215a6e18a1add3a62cfd528182c57d5..ea87f4c9edab550159f7d94772d0c5cdb21e99ab 100644
--- a/content/3.defense-systems/pd-t4-3.md
+++ b/content/3.defense-systems/pd-t4-3.md
@@ -46,18 +46,22 @@ The system was detected in 172 different species.
Proportion of genome encoding the PD-T4-3 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-T4-3
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-t4-3/PD-T4-3__PD-T4-3-plddts_88.02514.pdb
+dataUrls:
+ - /pd-t4-3/PD-T4-3__PD-T4-3.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -85,3 +89,4 @@ end
</mermaid>
---
::
+
diff --git a/content/3.defense-systems/pd-t4-4.md b/content/3.defense-systems/pd-t4-4.md
index 6821b9a38a19d550849ff04840fba0e4abae7563..b7693c80be195ef3813a2a1dc55c1d4d79058695 100644
--- a/content/3.defense-systems/pd-t4-4.md
+++ b/content/3.defense-systems/pd-t4-4.md
@@ -44,25 +44,23 @@ The system was detected in 37 different species.
Proportion of genome encoding the PD-T4-4 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-T4-4
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-t4-4/PD-T4-4,PD-T4-4__PD-T4-4_A,0,V-plddts_89.6125.pdb
----
-::
+dataUrls:
+ - /pd-t4-4/PD-T4-4.PD-T4-4__PD-T4-4_B.0.V.pdb
+ - /pd-t4-4/PD-T4-4.PD-T4-4__PD-T4-4_A.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pd-t4-4/PD-T4-4,PD-T4-4__PD-T4-4_B,0,V-plddts_92.18973.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -90,3 +88,4 @@ end
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/pd-t4-5.md b/content/3.defense-systems/pd-t4-5.md
index bb7b919e7770e2f42d54134e2ec8ecfcbab37bec..dd2b311865fc0c68b99a7bdd67e104a2d6df1147 100644
--- a/content/3.defense-systems/pd-t4-5.md
+++ b/content/3.defense-systems/pd-t4-5.md
@@ -34,18 +34,22 @@ The system was detected in 128 different species.
Proportion of genome encoding the PD-T4-5 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-T4-5
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-t4-5/PD-T4-5__PD-T4-5-plddts_94.58803.pdb
+dataUrls:
+ - /pd-t4-5/PD-T4-5__PD-T4-5.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -72,13 +76,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
diff --git a/content/3.defense-systems/pd-t4-6.md b/content/3.defense-systems/pd-t4-6.md
index 9ead59fa61d0cd8868e1859a92541a391e44a9d4..6c419ca3c3e0d9faab432357d41bedffa3dbd3d8 100644
--- a/content/3.defense-systems/pd-t4-6.md
+++ b/content/3.defense-systems/pd-t4-6.md
@@ -45,18 +45,22 @@ The system was detected in 18 different species.
Proportion of genome encoding the PD-T4-6 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-T4-6
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-t4-6/PD-T4-6__PD-T4-6-plddts_84.95824.pdb
+dataUrls:
+ - /pd-t4-6/PD-T4-6__PD-T4-6.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -82,3 +86,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/pd-t4-7.md b/content/3.defense-systems/pd-t4-7.md
index e60b1dd2ef5650f2d6f4c3b1a78decb03fa91d96..0cb3aa714bd2dcae7f343b64229b09d2ddd75bbc 100644
--- a/content/3.defense-systems/pd-t4-7.md
+++ b/content/3.defense-systems/pd-t4-7.md
@@ -47,18 +47,22 @@ The system was detected in 100 different species.
Proportion of genome encoding the PD-T4-7 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-T4-7
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-t4-7/PD-T4-7__PD-T4-7-plddts_91.28596.pdb
+dataUrls:
+ - /pd-t4-7/PD-T4-7__PD-T4-7.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -84,3 +88,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/pd-t4-8.md b/content/3.defense-systems/pd-t4-8.md
index b1cd9b9cbfb0763509558dfa612d5c833e703fb1..dbc3b0c15f129f179d0bdf692438272f59ec64b9 100644
--- a/content/3.defense-systems/pd-t4-8.md
+++ b/content/3.defense-systems/pd-t4-8.md
@@ -45,18 +45,22 @@ The system was detected in 50 different species.
Proportion of genome encoding the PD-T4-8 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-T4-8
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-t4-8/PD-T4-8__PD-T4-8-plddts_91.39016.pdb
+dataUrls:
+ - /pd-t4-8/PD-T4-8__PD-T4-8.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -84,3 +88,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/pd-t4-9.md b/content/3.defense-systems/pd-t4-9.md
index 56c98f5736a442f5cbeb4f02f58f876e4339658d..8a6b8a36cb7a5e1ea5827c4afeb19a235b82aaae 100644
--- a/content/3.defense-systems/pd-t4-9.md
+++ b/content/3.defense-systems/pd-t4-9.md
@@ -34,32 +34,24 @@ The system was detected in 88 different species.
Proportion of genome encoding the PD-T4-9 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-T4-9
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-t4-9/PD-T4-9,PD-T4-9__PD-T4-9_A,0,V-plddts_93.71807.pdb
----
-::
+dataUrls:
+ - /pd-t4-9/PD-T4-9.PD-T4-9__PD-T4-9_A.0.V.pdb
+ - /pd-t4-9/PD-T4-9.PD-T4-9__PD-T4-9_B.0.V.pdb
+ - /pd-t4-9/PD-T4-9.PD-T4-9__PD-T4-9_C.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pd-t4-9/PD-T4-9,PD-T4-9__PD-T4-9_B,0,V-plddts_71.02357.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pd-t4-9/PD-T4-9,PD-T4-9__PD-T4-9_C,0,V-plddts_93.05735.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -86,13 +78,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
diff --git a/content/3.defense-systems/pd-t7-1.md b/content/3.defense-systems/pd-t7-1.md
index b7085c3e435c288da876ae7448fd233b9cd750ae..c095375395a96419c6de8468bf501925b3b89e6f 100644
--- a/content/3.defense-systems/pd-t7-1.md
+++ b/content/3.defense-systems/pd-t7-1.md
@@ -33,18 +33,22 @@ The system was detected in 146 different species.
Proportion of genome encoding the PD-T7-1 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-T7-1
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-t7-1/PD-T7-1__PD-T7-1-plddts_93.91174.pdb
+dataUrls:
+ - /pd-t7-1/PD-T7-1__PD-T7-1.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -68,12 +72,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
diff --git a/content/3.defense-systems/pd-t7-2.md b/content/3.defense-systems/pd-t7-2.md
index fcc69e05dbeb4e7c1239d0b273af312608a70914..bd62bba08dd1a0016816b8e66a31d4b827f3c262 100644
--- a/content/3.defense-systems/pd-t7-2.md
+++ b/content/3.defense-systems/pd-t7-2.md
@@ -34,25 +34,23 @@ The system was detected in 667 different species.
Proportion of genome encoding the PD-T7-2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-T7-2
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-t7-2/PD-T7-2,PD-T7-2__PD-T7-2_A,0,V-plddts_90.8134.pdb
----
-::
+dataUrls:
+ - /pd-t7-2/PD-T7-2.PD-T7-2__PD-T7-2_B.0.V.pdb
+ - /pd-t7-2/PD-T7-2.PD-T7-2__PD-T7-2_A.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pd-t7-2/PD-T7-2,PD-T7-2__PD-T7-2_B,0,V-plddts_86.88934.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -84,13 +82,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
diff --git a/content/3.defense-systems/pd-t7-3.md b/content/3.defense-systems/pd-t7-3.md
index 469689e5a171f1eb74068a43e6adbc007ca09a68..7ff456880e326c1614610a8838b15ba1ef2dcbf5 100644
--- a/content/3.defense-systems/pd-t7-3.md
+++ b/content/3.defense-systems/pd-t7-3.md
@@ -45,18 +45,22 @@ The system was detected in 130 different species.
Proportion of genome encoding the PD-T7-3 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-T7-3
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-t7-3/PD-T7-3__PD-T7-3-plddts_89.74752.pdb
+dataUrls:
+ - /pd-t7-3/PD-T7-3__PD-T7-3.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -87,3 +91,4 @@ end
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/pd-t7-4.md b/content/3.defense-systems/pd-t7-4.md
index 9a17b14236530f17434bbf9cbb9b962a29e08074..6658dba56df3154a728f3c8d7b5cf085c4126439 100644
--- a/content/3.defense-systems/pd-t7-4.md
+++ b/content/3.defense-systems/pd-t7-4.md
@@ -34,18 +34,22 @@ The system was detected in 218 different species.
Proportion of genome encoding the PD-T7-4 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-T7-4
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-t7-4/PD-T7-4__PD-T7-4-plddts_93.28251.pdb
+dataUrls:
+ - /pd-t7-4/PD-T7-4__PD-T7-4.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -72,13 +76,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
diff --git a/content/3.defense-systems/pd-t7-5.md b/content/3.defense-systems/pd-t7-5.md
index 22c4aff5bf40c067ad54a2ba50cb4a605ae10829..564c4bfebfdf1ed74109857b46cca7e2058f7d39 100644
--- a/content/3.defense-systems/pd-t7-5.md
+++ b/content/3.defense-systems/pd-t7-5.md
@@ -33,18 +33,22 @@ The system was detected in 129 different species.
Proportion of genome encoding the PD-T7-5 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PD-T7-5
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pd-t7-5/PD-T7-5__PD-T7-5-plddts_92.01228.pdb
+dataUrls:
+ - /pd-t7-5/PD-T7-5__PD-T7-5.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -70,12 +74,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
diff --git a/content/3.defense-systems/pfiat.md b/content/3.defense-systems/pfiat.md
index a29dab0372b1f8aa4f48669c34894276b5882b16..c21eec60e2a709f9ce05347f0e50b29c84ec41d2 100644
--- a/content/3.defense-systems/pfiat.md
+++ b/content/3.defense-systems/pfiat.md
@@ -34,31 +34,17 @@ The system was detected in 308 different species.
Proportion of genome encoding the PfiAT system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PfiAT
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pfiat/PfiAT,PfiAT__PfiA,0,V-plddts_95.62475.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pfiat/PfiAT,PfiAT__PfiT,0,V-plddts_94.1034.pdb
----
-::
-
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1111/1751-7915.13570
+dataUrls:
+ - /pfiat/PfiAT.PfiAT__PfiA.0.V.pdb
+ - /pfiat/PfiAT.PfiAT__PfiT.0.V.pdb
---
::
-
diff --git a/content/3.defense-systems/pif.md b/content/3.defense-systems/pif.md
index 8279c80fe49c99f3da4eaf1f7b7a9adf82ee3c07..0785faf05c6861d2859f15714acbb9b659a8b3f7 100644
--- a/content/3.defense-systems/pif.md
+++ b/content/3.defense-systems/pif.md
@@ -50,25 +50,23 @@ The system was detected in 25 different species.
Proportion of genome encoding the Pif system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Pif
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pif/Pif,Pif__PifA,0,V-plddts_83.95828.pdb
----
-::
+dataUrls:
+ - /pif/Pif.Pif__PifA.0.V.pdb
+ - /pif/Pif.Pif__PifC.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pif/Pif,Pif__PifC,0,V-plddts_91.50188.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Cheng_2004[<a href='https://doi.org/10.1016/j.virol.2004.06.001'>Cheng et al., 2004</a>] --> Origin_0
@@ -92,3 +90,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/prrc.md b/content/3.defense-systems/prrc.md
index 09da95b9186a5fbd48e9e31181806b274edca33a..8e7517d5b2ef542595c1500ae9e30cf5984b84b1 100644
--- a/content/3.defense-systems/prrc.md
+++ b/content/3.defense-systems/prrc.md
@@ -50,25 +50,35 @@ The system was detected in 309 different species.
Proportion of genome encoding the PrrC system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PrrC
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /prrc/PrrC__EcoprrI-plddts_91.30003.pdb
+dataUrls:
+ - /prrc/PrrC__EcoprrI.pdb
+ - /prrc/PrrC__PrrC.pdb
+
---
::
+### RM
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /prrc/PrrC__PrrC-plddts_86.4815.pdb
+dataUrls:
+ - /prrc/RM__Type_I_S.pdb
+ - /prrc/RM__Type_I_REases.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Jabbar_1984[<a href='https://doi.org/10.1128/JVI.51.2.522-529.1984'>Jabbar and Snyder, 1984</a>] --> Origin_0
@@ -95,3 +105,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/psyrta.md b/content/3.defense-systems/psyrta.md
index cd7deb73f2e1ab96c4fe28d124a8779a40055c0a..6e1d4fa90cb02b37ae2040ea07575b1c98f28ee8 100644
--- a/content/3.defense-systems/psyrta.md
+++ b/content/3.defense-systems/psyrta.md
@@ -66,25 +66,23 @@ The system was detected in 132 different species.
Proportion of genome encoding the PsyrTA system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### PsyrTA
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /psyrta/PsyrTA,PsyrTA__PsyrA,0,V-plddts_88.4921.pdb
----
-::
+dataUrls:
+ - /psyrta/PsyrTA.PsyrTA__PsyrT.0.V.pdb
+ - /psyrta/PsyrTA.PsyrTA__PsyrA.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /psyrta/PsyrTA,PsyrTA__PsyrT,0,V-plddts_88.00999.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -112,3 +110,4 @@ end
</mermaid>
::
+
diff --git a/content/3.defense-systems/pycsar.md b/content/3.defense-systems/pycsar.md
index dde91165b646dca6cfeae2105cbd299358b8af83..f33d2091cc6e175b093a927815bc25a576573496 100644
--- a/content/3.defense-systems/pycsar.md
+++ b/content/3.defense-systems/pycsar.md
@@ -36,41 +36,34 @@ The system was detected in 295 different species.
Proportion of genome encoding the Pycsar system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Pycsar
+##### Example 1
-Example 1:
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pycsar/Pycsar,CBASS__TIR,0,V-plddts_90.36719.pdb
----
-::
+dataUrls:
+ - /pycsar/Pycsar.Pycsar__AG_cyclase.1.V.pdb
+ - /pycsar/Pycsar.CBASS__TIR.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pycsar/Pycsar,Pycsar__AG_cyclase,0,V-plddts_94.90778.pdb
---
::
+##### Example 2
-Example 2:
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /pycsar/Pycsar,CBASS__TIR,0,V-plddts_90.36719.pdb
----
-::
+dataUrls:
+ - /pycsar/Pycsar.CBASS_TM.1.V.pdb
+ - /pycsar/Pycsar.Pycsar__AG_cyclase.1.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pycsar/Pycsar,Pycsar__AG_cyclase,0,V-plddts_94.90778.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Tal_2021[<a href='https://doi.org/10.1016/j.cell.2021.09.031'>Tal et al., 2021</a>] --> Origin_0
@@ -104,13 +97,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.cell.2021.09.031
-
----
-::
diff --git a/content/3.defense-systems/radar.md b/content/3.defense-systems/radar.md
index 3af879dc13165bcb8237a515d4d8e30cb047804d..11aae90b7a3cce23dadacc6ddd98b3b33b35704f 100644
--- a/content/3.defense-systems/radar.md
+++ b/content/3.defense-systems/radar.md
@@ -46,48 +46,36 @@ The system was detected in 44 different species.
Proportion of genome encoding the RADAR system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### radar_I
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /radar/radar_I,radar_I__rdrA_I,0,V-plddts_84.65854.pdb
----
-::
+dataUrls:
+ - /radar/radar_I.radar_I__rdrB_I.0.V.pdb
+ - /radar/radar_I.radar_I__rdrA_I.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /radar/radar_I,radar_I__rdrB_I,0,V-plddts_87.10562.pdb
---
::
-
### radar_II
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /radar/radar_II,radar_II__rdrA_II,0,V-plddts_84.35322.pdb
----
-::
+dataUrls:
+ - /radar/radar_II.radar_II__rdrC_II.0.V.pdb
+ - /radar/radar_II.radar_II__rdrB_II.0.V.pdb
+ - /radar/radar_II.radar_II__rdrA_II.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /radar/radar_II,radar_II__rdrB_II,0,V-plddts_86.83828.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /radar/radar_II,radar_II__rdrC_II,0,V-plddts_75.42507.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -143,17 +131,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aba0372
-
----
-::
-
-
-## References
-1. Gao L, Altae-Tran H, Böhning F, et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. *Science*. 2020;369(6507):1077-1084. doi:10.1126/science.aba0372
diff --git a/content/3.defense-systems/retron.md b/content/3.defense-systems/retron.md
index be5a790d79ac6781586da2e050ef654e48c02b11..a9daa09d4f12b765cae926ddddeac12a81e19ed9 100644
--- a/content/3.defense-systems/retron.md
+++ b/content/3.defense-systems/retron.md
@@ -123,205 +123,143 @@ The system was detected in 840 different species.
Proportion of genome encoding the Retron system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
-### Retron_II
+## Structure
+### RT_Ec67_SLATT
+##### Example Ec57
-Example 1:
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /retron/Retron_II,Retron_II__NDT,Ec73,V-plddts_91.19742.pdb
----
-::
+dataUrls:
+ - /retron/RT_Ec67_SLATT.AbiA__AbiA_small_SLATT.Ec57.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_II,Retron__RT_Tot,Ec73,V-plddts_94.26558.pdb
---
::
+##### Example Ec67
-Example 2:
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /retron/Retron_II,Retron_II__NDT,Ec73,V-plddts_91.19742.pdb
----
-::
+dataUrls:
+ - /retron/DRT_3.DRT_3__drt3a.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_II,Retron__RT_Tot,Ec73,V-plddts_94.26558.pdb
---
::
+### Retron_II
+##### Example Ec73
-### Retron_III
-
-Example 1:
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /retron/Retron_III,Retron_III__PRTase,0,DF-plddts_93.05385.pdb
----
-::
+dataUrls:
+ - /retron/Retron_II.Retron_II__NDT.Ec73.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_III,Retron_III__WH,0,DF-plddts_81.40731.pdb
---
::
+##### Example Ec86
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /retron/Retron_III,Retron__RT_Tot,0,DF-plddts_95.80558.pdb
----
-::
+dataUrls:
+ - /retron/Retron_II.Retron_II__NDT.Ec73.V.pdb
-Example 2:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_III,Retron_III__PRTase,0,DF-plddts_93.05385.pdb
---
::
+### Retron_III
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /retron/Retron_III,Retron_III__WH,0,DF-plddts_81.40731.pdb
----
-::
+dataUrls:
+ - /retron/Retron_III.Retron_III__PRTase.0.DF.pdb
+ - /retron/Retron_III.Retron_III__WH.0.DF.pdb
-### Retron_IV
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_IV,Retron_IV__2TM,Ec48,V-plddts_90.18352.pdb
---
::
+##### Example 2
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /retron/Retron_IV,Retron__RT_Tot,Ec48,V-plddts_92.96552.pdb
----
-::
-
-### Retron_I_A
+dataUrls:
+ - /retron/Retron_III.Retron_III__PRTase_WH.1.DF.pdb
-Example 1:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_I_A.Retron_I_A__HNH_TIGR02646.Ec78.V-plddts_94.92113.pdb
---
::
+### Retron_IV
+##### Example Ec48
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /retron/Retron_I_A.Retron_I_A__HNH_TIGR02646.Ec83.V-plddts_95.89569.pdb
----
-::
+dataUrls:
+ - /retron/Retron_IV.Retron_IV__2TM.Ec48.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_I_A.Retron_I_A__HNH_TIGR02646.Vc95.V-plddts_96.13478.pdb
---
::
+### Retron_I_A
+##### Example Ec83
-Example 2:
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /retron/Retron_I_A.Retron_I_A__HNH_TIGR02646.Ec78.V-plddts_94.92113.pdb
----
-::
+dataUrls:
+ - /retron/Retron_I_A.Retron__RT_Tot.Ec83.V.pdb
+ - /retron/Retron_I_A.Retron_I_A__ATPase_TypeIA.Vc95.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_I_A.Retron_I_A__HNH_TIGR02646.Ec83.V-plddts_95.89569.pdb
---
::
+##### Example Vc95
-Example 3:
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /retron/Retron_I_A.Retron_I_A__HNH_TIGR02646.Ec78.V-plddts_94.92113.pdb
----
-::
+dataUrls:
+ - /retron/Retron_I_A.Retron_I_A__ATPase_TypeIA.Vc95.V.pdb
+ - /retron/Retron_I_A.Retron__RT_Tot.Ec83.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_I_A.Retron_I_A__HNH_TIGR02646.Ec83.V-plddts_95.89569.pdb
---
::
-
### Retron_I_B
+##### Example Eco8
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /retron/Retron_I_B,Retron_I_B__ATPase_TOPRIM_COG3593,Eco8,V-plddts_86.92789.pdb
----
-::
+dataUrls:
+ - /retron/Retron_I_B.Retron_I_B__ATPase_TOPRIM_COG3593.Eco8.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_I_B,Retron__RT_Tot,Eco8,V-plddts_93.00774.pdb
---
::
-
### Retron_VI
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /retron/Retron_VI,Possible_Retron_VI__SP,0,DF-plddts_81.90355.pdb
----
-::
+dataUrls:
+ - /retron/Retron_VI.Retron_VI__HTH.0.DF.pdb
+ - /retron/Retron_VI.Possible_Retron_VI__SP.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_VI,Retron_VI__HTH,0,DF-plddts_86.36271.pdb
---
::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_VI,Retron__RT_Tot,0,DF-plddts_95.37927.pdb
----
-::
-
### Retron_VII_2
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /retron/Retron_VII_2,Retron_VII_2__DUF3800,0,DF-plddts_91.55254.pdb
----
-::
+dataUrls:
+ - /retron/Retron_VII_2.Retron_VII_2__DUF3800.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_VII_2,Retron__RT_Tot,0,DF-plddts_95.60845.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
@@ -566,3 +504,4 @@ end
</mermaid>
+
diff --git a/content/3.defense-systems/rexab.md b/content/3.defense-systems/rexab.md
index 06ccbd3a851b1051c19554acd82d637478a1ef2f..ee6c0c51a5bbd9dca8c47bb82d71650efe17669b 100644
--- a/content/3.defense-systems/rexab.md
+++ b/content/3.defense-systems/rexab.md
@@ -34,25 +34,23 @@ The system was detected in 18 different species.
Proportion of genome encoding the RexAB system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### RexAB
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /rexab/RexAB,RexAB_RexA,0,V-plddts_80.37265.pdb
----
-::
+dataUrls:
+ - /rexab/RexAB.RexAB_RexB.0.V.pdb
+ - /rexab/RexAB.RexAB_RexA.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rexab/RexAB,RexAB_RexB,0,V-plddts_87.11344.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Parma_1992[<a href='https://doi.org/10.1101/gad.6.3.497'>Parma et al., 1992</a>] --> Origin_0
@@ -77,13 +75,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1101/gad.6.3.497
-
----
-::
diff --git a/content/3.defense-systems/rloc.md b/content/3.defense-systems/rloc.md
index 798e25f99970b3f8b2beeb9185658b05a4e65934..3bb3916436b9e52a41283a33aaba629df8903923 100644
--- a/content/3.defense-systems/rloc.md
+++ b/content/3.defense-systems/rloc.md
@@ -34,18 +34,22 @@ The system was detected in 919 different species.
Proportion of genome encoding the RloC system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### RloC
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /rloc/RloC__RloC-plddts_86.73175.pdb
+dataUrls:
+ - /rloc/RloC__RloC.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Penner_1995[<a href='https://doi.org/10.1006/jmbi.1995.0343'>Penner et al., 1995</a>] --> Origin_0
@@ -68,14 +72,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1111/j.1365-2958.2008.06387.x
- - doi: 10.1111/mmi.13074
-
----
-::
diff --git a/content/3.defense-systems/rnlab.md b/content/3.defense-systems/rnlab.md
index 9bff2f857e4832067549e9c2478926d4f7371af7..7aec609fe786fe8cc90dd07dfa36f4a002d9bfd9 100644
--- a/content/3.defense-systems/rnlab.md
+++ b/content/3.defense-systems/rnlab.md
@@ -34,25 +34,23 @@ The system was detected in 68 different species.
Proportion of genome encoding the RnlAB system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### RnlAB
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /rnlab/RnlAB,RnlAB__RnlA,0,DF-plddts_91.3649.pdb
----
-::
+dataUrls:
+ - /rnlab/RnlAB.RnlAB__RnlA.0.DF.pdb
+ - /rnlab/RnlAB.RnlAB__RnlB.0.DF.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rnlab/RnlAB,RnlAB__RnlB,0,DF-plddts_92.42543.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Koga_2011[<a href='https://doi.org/10.1534/genetics.110.121798'>Koga et al., 2011</a>] --> Origin_0
@@ -75,13 +73,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1534/genetics.110.121798
-
----
-::
diff --git a/content/3.defense-systems/rosmerta.md b/content/3.defense-systems/rosmerta.md
index cca150e7cb982623f3b606d9bb2d8d6244256d88..c59f85c1215e335f5bce2abcbd097ca247d210b3 100644
--- a/content/3.defense-systems/rosmerta.md
+++ b/content/3.defense-systems/rosmerta.md
@@ -34,25 +34,23 @@ The system was detected in 613 different species.
Proportion of genome encoding the RosmerTA system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### RosmerTA
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /rosmerta/RosmerTA,RosmerTA__RmrA,0,V-plddts_88.40961.pdb
----
-::
+dataUrls:
+ - /rosmerta/RosmerTA.RosmerTA__RmrA.0.V.pdb
+ - /rosmerta/RosmerTA.RosmerTA__RmrT.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rosmerta/RosmerTA,RosmerTA__RmrT,0,V-plddts_84.3404.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -77,13 +75,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
diff --git a/content/3.defense-systems/rst_2tm_1tm_tir.md b/content/3.defense-systems/rst_2tm_1tm_tir.md
index a616b1772d99291a86a9c935d2bd0dbc903e1fc3..7865f437d7da80f470c21b3d7cb7ed6a5cb37ed6 100644
--- a/content/3.defense-systems/rst_2tm_1tm_tir.md
+++ b/content/3.defense-systems/rst_2tm_1tm_tir.md
@@ -31,38 +31,18 @@ The system was detected in 1 different species.
Proportion of genome encoding the Rst_2TM_1TM_TIR system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Rst_2TM_1TM_TIR
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /rst_2tm_1tm_tir/Rst_2TM_1TM_TIR,Rst_2TM_1TM_TIR__Rst_1TM_TIR,0,V-plddts_90.66226.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rst_2tm_1tm_tir/Rst_2TM_1TM_TIR,Rst_2TM_1TM_TIR__Rst_2TM_TIR,0,V-plddts_78.12882.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rst_2tm_1tm_tir/Rst_2TM_1TM_TIR,Rst_2TM_1TM_TIR__Rst_TIR_tm,0,V-plddts_67.05466.pdb
----
-::
-
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.02.018
+dataUrls:
+ - /rst_2tm_1tm_tir/Rst_2TM_1TM_TIR.Rst_2TM_1TM_TIR__Rst_2TM_TIR.0.V.pdb
+ - /rst_2tm_1tm_tir/Rst_2TM_1TM_TIR.Rst_2TM_1TM_TIR__Rst_1TM_TIR.0.V.pdb
+ - /rst_2tm_1tm_tir/Rst_2TM_1TM_TIR.Rst_2TM_1TM_TIR__Rst_TIR_tm.0.V.pdb
---
::
-
diff --git a/content/3.defense-systems/rst_3hp.md b/content/3.defense-systems/rst_3hp.md
index f4316f5aa293512d54d2915112ee3a2b8005f936..795e2eeae6befb457d9d865206ea48729a1c4e69 100644
--- a/content/3.defense-systems/rst_3hp.md
+++ b/content/3.defense-systems/rst_3hp.md
@@ -47,32 +47,24 @@ The system was detected in 89 different species.
Proportion of genome encoding the Rst_3HP system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Rst_3HP
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /rst_3hp/Rst_3HP,Rst_3HP__Hp1,0,V-plddts_92.97739.pdb
----
-::
+dataUrls:
+ - /rst_3hp/Rst_3HP.Rst_3HP__Hp1.0.V.pdb
+ - /rst_3hp/Rst_3HP.Rst_3HP__Hp3.0.V.pdb
+ - /rst_3hp/Rst_3HP.Rst_3HP__Hp2.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rst_3hp/Rst_3HP,Rst_3HP__Hp2,0,V-plddts_89.72402.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rst_3hp/Rst_3HP,Rst_3HP__Hp3,0,V-plddts_95.1843.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0
@@ -98,3 +90,4 @@ end
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/rst_duf4238.md b/content/3.defense-systems/rst_duf4238.md
index f84a78153f3a59d184498024acbbcf0eb3302cdc..c96e888d4fb0f2622470c06f775f21d403ce61cd 100644
--- a/content/3.defense-systems/rst_duf4238.md
+++ b/content/3.defense-systems/rst_duf4238.md
@@ -34,18 +34,22 @@ The system was detected in 37 different species.
Proportion of genome encoding the Rst_DUF4238 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Rst_DUF4238
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /rst_duf4238/Rst_DUF4238__DUF4238_Pers-plddts_94.11236.pdb
+dataUrls:
+ - /rst_duf4238/Rst_DUF4238__DUF4238_Pers.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0
@@ -69,13 +73,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.02.018
-
----
-::
diff --git a/content/3.defense-systems/rst_gop_beta_cll.md b/content/3.defense-systems/rst_gop_beta_cll.md
index e146cb8d102dbf5e533d69fd64c83fb00de4320b..44af6c64667cc43f08e771d6fe3f6fd9e457319f 100644
--- a/content/3.defense-systems/rst_gop_beta_cll.md
+++ b/content/3.defense-systems/rst_gop_beta_cll.md
@@ -34,32 +34,24 @@ The system was detected in 15 different species.
Proportion of genome encoding the Rst_gop_beta_cll system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Rst_gop_beta_cll
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /rst_gop_beta_cll/Rst_gop_beta_cll,Rst_gop_beta_cll__beta,0,V-plddts_93.90323.pdb
----
-::
+dataUrls:
+ - /rst_gop_beta_cll/Rst_gop_beta_cll.Rst_gop_beta_cll__cll.0.V.pdb
+ - /rst_gop_beta_cll/Rst_gop_beta_cll.Rst_gop_beta_cll__gop.0.V.pdb
+ - /rst_gop_beta_cll/Rst_gop_beta_cll.Rst_gop_beta_cll__beta.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rst_gop_beta_cll/Rst_gop_beta_cll,Rst_gop_beta_cll__cll,0,V-plddts_87.60729.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rst_gop_beta_cll/Rst_gop_beta_cll,Rst_gop_beta_cll__gop,0,V-plddts_74.94876.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0
@@ -85,13 +77,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.02.018
-
----
-::
diff --git a/content/3.defense-systems/rst_helicaseduf2290.md b/content/3.defense-systems/rst_helicaseduf2290.md
index cfed7c438fcdae199424c6e2887288737df22606..647094f8feef1ff79f4859a4f33e60e5dca3b313 100644
--- a/content/3.defense-systems/rst_helicaseduf2290.md
+++ b/content/3.defense-systems/rst_helicaseduf2290.md
@@ -49,25 +49,23 @@ The system was detected in 123 different species.
Proportion of genome encoding the Rst_HelicaseDUF2290 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Rst_HelicaseDUF2290
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /rst_helicaseduf2290/Rst_HelicaseDUF2290,Rst_HelicaseDUF2290__DUF2290,0,V-plddts_90.99466.pdb
----
-::
+dataUrls:
+ - /rst_helicaseduf2290/Rst_HelicaseDUF2290.Rst_HelicaseDUF2290__DUF2290.0.V.pdb
+ - /rst_helicaseduf2290/Rst_HelicaseDUF2290.Rst_HelicaseDUF2290__Helicase.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rst_helicaseduf2290/Rst_HelicaseDUF2290,Rst_HelicaseDUF2290__Helicase,0,V-plddts_87.6023.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0
@@ -92,3 +90,4 @@ end
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/rst_hydrolase-3tm.md b/content/3.defense-systems/rst_hydrolase-3tm.md
index 18fe66fe1b3269e17e37e2702e1d0d45422df51e..3f777d180a81802521a91a047ddef7a5ca2728b8 100644
--- a/content/3.defense-systems/rst_hydrolase-3tm.md
+++ b/content/3.defense-systems/rst_hydrolase-3tm.md
@@ -34,25 +34,23 @@ The system was detected in 34 different species.
Proportion of genome encoding the Rst_Hydrolase-3Tm system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Rst_Hydrolase-Tm
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /rst_hydrolase-3tm/Rst_Hydrolase-Tm,Rst_Hydrolase-Tm__Hydrolase,0,V-plddts_94.5717.pdb
----
-::
+dataUrls:
+ - /rst_hydrolase-3tm/Rst_Hydrolase-Tm.Rst_Hydrolase-Tm__Hydrolase.0.V.pdb
+ - /rst_hydrolase-3tm/Rst_Hydrolase-Tm.Rst_Hydrolase-Tm__Hydrolase-Tm.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rst_hydrolase-3tm/Rst_Hydrolase-Tm,Rst_Hydrolase-Tm__Hydrolase-Tm,0,V-plddts_87.29824.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0
@@ -76,13 +74,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.02.018
-
----
-::
diff --git a/content/3.defense-systems/rst_rt-nitrilase-tm.md b/content/3.defense-systems/rst_rt-nitrilase-tm.md
index 9e2d2085eed33e1b4916bdd59dcea843b64c9a61..286a6be9f17cf70accc1664ee1b22b1948f77590 100644
--- a/content/3.defense-systems/rst_rt-nitrilase-tm.md
+++ b/content/3.defense-systems/rst_rt-nitrilase-tm.md
@@ -34,25 +34,23 @@ The system was detected in 5 different species.
Proportion of genome encoding the Rst_RT-nitrilase-Tm system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Rst_RT-Tm
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /rst_rt-nitrilase-tm/Rst_RT-Tm,Rst_RT-Tm__RT,0,V-plddts_91.31746.pdb
----
-::
+dataUrls:
+ - /rst_rt-nitrilase-tm/Rst_RT-Tm.Rst_RT-Tm__RT-Tm.0.V.pdb
+ - /rst_rt-nitrilase-tm/Rst_RT-Tm.Rst_RT-Tm__RT.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rst_rt-nitrilase-tm/Rst_RT-Tm,Rst_RT-Tm__RT-Tm,0,V-plddts_89.04275.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0
@@ -76,13 +74,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.02.018
-
----
-::
diff --git a/content/3.defense-systems/rst_tir-nlr.md b/content/3.defense-systems/rst_tir-nlr.md
index b2ec23e6cce209e74e9af6437b6792d2b69700d5..1fb00c19d746745acf6066972f530f109dd9e8f3 100644
--- a/content/3.defense-systems/rst_tir-nlr.md
+++ b/content/3.defense-systems/rst_tir-nlr.md
@@ -34,18 +34,22 @@ The system was detected in 42 different species.
Proportion of genome encoding the Rst_TIR-NLR system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Rst_TIR-NLR
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /rst_tir-nlr/Rst_TIR-NLR__TIR-plddts_88.48123.pdb
+dataUrls:
+ - /rst_tir-nlr/Rst_TIR-NLR__TIR.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0
@@ -74,13 +78,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.02.018
-
----
-::
diff --git a/content/3.defense-systems/sanata.md b/content/3.defense-systems/sanata.md
index 82d1fe9fd8cf028e6b1478d66f85e3ce3f0d3056..f43723ec6ea99fd65de5e5308754710263d2d68a 100644
--- a/content/3.defense-systems/sanata.md
+++ b/content/3.defense-systems/sanata.md
@@ -48,25 +48,23 @@ The system was detected in 519 different species.
Proportion of genome encoding the SanaTA system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### SanaTA
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /sanata/SanaTA,SanaTA_SanaA,0,V-plddts_86.02229.pdb
----
-::
+dataUrls:
+ - /sanata/SanaTA.SanaTA_SanaA.0.V.pdb
+ - /sanata/SanaTA.SanaTA_SanaT.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /sanata/SanaTA,SanaTA_SanaT,0,V-plddts_94.5954.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Sberro_2013[<a href='https://doi.org/10.1016/j.molcel.2013.02.002'>Sberro et al., 2013</a>] --> Origin_0
@@ -92,3 +90,4 @@ end
</mermaid>
+
diff --git a/content/3.defense-systems/sefir.md b/content/3.defense-systems/sefir.md
index 11e0d0b995c30d85d4f7ddcdc907409b0caf6ec9..2a75ce4ab25874de6fdbc3f2375a94f7334baadb 100644
--- a/content/3.defense-systems/sefir.md
+++ b/content/3.defense-systems/sefir.md
@@ -52,18 +52,22 @@ The system was detected in 218 different species.
Proportion of genome encoding the SEFIR system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### SEFIR
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /sefir/SEFIR__bSEFIR-plddts_89.61831.pdb
+dataUrls:
+ - /sefir/SEFIR__bSEFIR.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -89,3 +93,4 @@ end
</mermaid>
+
diff --git a/content/3.defense-systems/septu.md b/content/3.defense-systems/septu.md
index 7277766d3231704c71062b47ae5cf9e91c2b973c..232f9b3ccc2a4baefdcd00f2feaaa0c0fa2045b7 100644
--- a/content/3.defense-systems/septu.md
+++ b/content/3.defense-systems/septu.md
@@ -34,41 +34,34 @@ The system was detected in 1112 different species.
Proportion of genome encoding the Septu system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Septu
+##### Example 1
-Example 1:
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /septu/Septu,Septu__PtuA,0,V-plddts_89.78955.pdb
----
-::
+dataUrls:
+ - /septu/Septu.Septu__PtuA.1.V.pdb
+ - /septu/Septu.Septu__PtuB.1.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /septu/Septu,Septu__PtuB,0,V-plddts_95.05244.pdb
---
::
+##### Example 2
-Example 2:
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /septu/Septu,Septu__PtuA,0,V-plddts_89.78955.pdb
----
-::
+dataUrls:
+ - /septu/Septu.Septu__PtuB.1.V.pdb
+ - /septu/Septu.Septu__PtuA.1.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /septu/Septu,Septu__PtuB,0,V-plddts_95.05244.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
@@ -101,15 +94,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.cell.2020.09.065
- - doi: 10.1093/nar/gkab883
- - doi: 10.1126/science.aar4120
-
----
-::
diff --git a/content/3.defense-systems/shango.md b/content/3.defense-systems/shango.md
index a964d599afc149db8ef24d39c4b2912c6b53144c..b174aaf8dfefe09c3aad6bb4657cc8906aea4226 100644
--- a/content/3.defense-systems/shango.md
+++ b/content/3.defense-systems/shango.md
@@ -49,34 +49,24 @@ The system was detected in 446 different species.
Proportion of genome encoding the Shango system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Shango
+##### Example 1
-Example 1:
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /shango/Shango.Shango__SngC.0.V-plddts_90.0493.pdb
----
-::
+dataUrls:
+ - /shango/Shango.Shango__SngA.0.V.pdb
+ - /shango/Shango.Shango__SngB.0.V.pdb
+ - /shango/Shango.Shango__SngC.0.V.pdb
-Example 2:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /shango/Shango.Shango__SngC.0.V-plddts_90.0493.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /shango/Shango,Shango__SngA,0,V-plddts_78.29927.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -103,3 +93,4 @@ end
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/shedu.md b/content/3.defense-systems/shedu.md
index 12651abebc71fea0b019b326e82ed5f350af97bc..5835ad1e65df71d3dcf9e5a7169cf519d426c022 100644
--- a/content/3.defense-systems/shedu.md
+++ b/content/3.defense-systems/shedu.md
@@ -53,18 +53,22 @@ The system was detected in 552 different species.
Proportion of genome encoding the Shedu system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Shedu
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /shedu/Shedu__SduA-plddts_87.27097.pdb
+dataUrls:
+ - /shedu/Shedu__SduA.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
@@ -92,3 +96,4 @@ end
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/shosta.md b/content/3.defense-systems/shosta.md
index 934c4230cbcdece5057a080b56fc7642bb6acbde..90f1cdd3cb261dca98bdfecb7f8c165693cdf616 100644
--- a/content/3.defense-systems/shosta.md
+++ b/content/3.defense-systems/shosta.md
@@ -48,25 +48,23 @@ The system was detected in 240 different species.
Proportion of genome encoding the ShosTA system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### ShosTA
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /shosta/ShosTA,ShosTA__ShosA,0,V-plddts_93.0196.pdb
----
-::
+dataUrls:
+ - /shosta/ShosTA.ShosTA__ShosA.0.V.pdb
+ - /shosta/ShosTA.ShosTA__ShosT.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /shosta/ShosTA,ShosTA__ShosT,0,V-plddts_91.38081.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -104,3 +102,4 @@ end
</mermaid>
+
diff --git a/content/3.defense-systems/sofic.md b/content/3.defense-systems/sofic.md
index 94390623306350174ea59b12a307a7c24aa88a14..3988f556d94b6e7588b802a54d51d30e3d96ef2f 100644
--- a/content/3.defense-systems/sofic.md
+++ b/content/3.defense-systems/sofic.md
@@ -34,18 +34,22 @@ The system was detected in 1160 different species.
Proportion of genome encoding the SoFIC system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### SoFic
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /sofic/SoFic__SoFic-plddts_95.70819.pdb
+dataUrls:
+ - /sofic/SoFic__SoFic.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -69,13 +73,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
diff --git a/content/3.defense-systems/spbk.md b/content/3.defense-systems/spbk.md
index 4f4f20b821dfc9b09ff9844b7181d7e859c1a218..6377138a815ff08ca4248fb556d501f4d449b70d 100644
--- a/content/3.defense-systems/spbk.md
+++ b/content/3.defense-systems/spbk.md
@@ -34,18 +34,22 @@ The system was detected in 90 different species.
Proportion of genome encoding the SpbK system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### SpbK
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /spbk/SpbK__SpbK-plddts_78.5012.pdb
+dataUrls:
+ - /spbk/SpbK__SpbK.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Johnson_2022[<a href='https://doi.org/10.1371/journal.pgen.1010065'>Johnson et al., 2022</a>] --> Origin_0
@@ -69,13 +73,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1371/journal.pgen.1010065
-
----
-::
diff --git a/content/3.defense-systems/sspbcde.md b/content/3.defense-systems/sspbcde.md
index fb3fac3e1844a2eea7ee5f6013169e6567c7b926..fabced18a8dbb1a3f566615919694a3817c47923 100644
--- a/content/3.defense-systems/sspbcde.md
+++ b/content/3.defense-systems/sspbcde.md
@@ -34,83 +34,40 @@ The system was detected in 299 different species.
Proportion of genome encoding the SspBCDE system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### SspBCDE
-
-Example 1:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /sspbcde/SspBCDE,SspBCDE__SspB,0,V-plddts_92.59451.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /sspbcde/SspBCDE,SspBCDE__SspC,0,V-plddts_85.51697.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /sspbcde/SspBCDE,SspBCDE__SspD,0,V-plddts_87.41069.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /sspbcde/SspBCDE,SspBCDE__SspE,0,V-plddts_88.74902.pdb
----
-::
-
-Example 2:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /sspbcde/SspBCDE,SspBCDE__SspB,0,V-plddts_92.59451.pdb
----
-::
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /sspbcde/SspBCDE,SspBCDE__SspC,0,V-plddts_85.51697.pdb
----
-::
+dataUrls:
+ - /sspbcde/SspBCDE.SspBCDE__SspC.1.V.pdb
+ - /sspbcde/SspBCDE.SspBCDE__SspD.0.V.pdb
+ - /sspbcde/SspBCDE.SspBCDE__SspE.0.V.pdb
+ - /sspbcde/SspBCDE.SspBCDE__SspB.1.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /sspbcde/SspBCDE,SspBCDE__SspD,0,V-plddts_87.41069.pdb
---
::
+##### Example 2
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /sspbcde/SspBCDE,SspBCDE__SspE,0,V-plddts_88.74902.pdb
----
-::
+dataUrls:
+ - /sspbcde/SspBCDE.SspBCDE__SspH.1.V.pdb
+ - /sspbcde/SspBCDE.SspBCDE__SspG.1.V.pdb
+ - /sspbcde/SspBCDE.SspBCDE__SspF.1.V.pdb
+ - /sspbcde/SspBCDE.SspBCDE__SspD.0.V.pdb
+ - /sspbcde/SspBCDE.SspBCDE__SspC.1.V.pdb
+ - /sspbcde/SspBCDE.SspBCDE__SspB.1.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /sspbcde/SspBCDE,SspBCDE__SspB,1,V-plddts_92.38727.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /sspbcde/SspBCDE,SspBCDE__SspC,1,V-plddts_84.03334.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Xiong_2020[<a href='https://doi.org/10.1038/s41564-020-0700-6'>Xiong et al., 2020</a>] --> Origin_0
@@ -183,14 +140,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1128/mBio.00613-21
- - doi: 10.1128/mBio.00613-21
-
----
-::
diff --git a/content/3.defense-systems/stk2.md b/content/3.defense-systems/stk2.md
index 6a0050272c85eeac4488385b861f037b716e7066..ce9a908eee7bbf2a1c247f95d55a1cda0ccca820 100644
--- a/content/3.defense-systems/stk2.md
+++ b/content/3.defense-systems/stk2.md
@@ -43,18 +43,22 @@ The system was detected in 29 different species.
Proportion of genome encoding the Stk2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Stk2
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /stk2/Stk2__Stk2-plddts_91.79541.pdb
+dataUrls:
+ - /stk2/Stk2__Stk2.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Depardieu_2016[<a href='https://doi.org/10.1016/j.chom.2016.08.010'>Depardieu et al., 2016</a>] --> Origin_0
@@ -89,13 +93,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2016.08.010
-
----
-::
diff --git a/content/3.defense-systems/thoeris.md b/content/3.defense-systems/thoeris.md
index 3fa07ce185f39bf236784bd1e1a6317017800167..3f8baaf0db0be52af94d65a816652fe5291fbcb5 100644
--- a/content/3.defense-systems/thoeris.md
+++ b/content/3.defense-systems/thoeris.md
@@ -34,41 +34,35 @@ The system was detected in 298 different species.
Proportion of genome encoding the Thoeris system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Thoeris_I
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /thoeris/Thoeris_I,Thoeris_I__ThsA_new_grand,0,V-plddts_93.92302.pdb
----
-::
+dataUrls:
+ - /thoeris/Thoeris_I.Thoeris_I__ThsA_new_grand.0.V.pdb
+ - /thoeris/Thoeris_I.Thoeris__ThsB_Global.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /thoeris/Thoeris_I,Thoeris__ThsB_Global,0,V-plddts_90.12702.pdb
---
::
-
### Thoeris_II
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /thoeris/Thoeris_II,Thoeris_II__ThsA_new_petit,0,V-plddts_88.7532.pdb
----
-::
+dataUrls:
+ - /thoeris/Thoeris_I.Thoeris__ThsB_Global.0.V.pdb
+ - /thoeris/Thoeris_II.Thoeris_II__ThsA_new_petit.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /thoeris/Thoeris_II,Thoeris__ThsB_Global,0,V-plddts_93.32159.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
@@ -127,14 +121,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41586-021-04098-7
- - doi: 10.1126/science.aar4120
-
----
-::
diff --git a/content/3.defense-systems/tiamat.md b/content/3.defense-systems/tiamat.md
index a7b31dcdb492b5dbf68e845e54bc5d84d1952efe..ac0dc63e7ac2ed8b5feb0561900946036232fbab 100644
--- a/content/3.defense-systems/tiamat.md
+++ b/content/3.defense-systems/tiamat.md
@@ -48,18 +48,22 @@ The system was detected in 251 different species.
Proportion of genome encoding the Tiamat system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Tiamat
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /tiamat/Tiamat__TmtA-plddts_86.46392.pdb
+dataUrls:
+ - /tiamat/Tiamat__TmtA.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -87,3 +91,4 @@ end
---
+
diff --git a/content/3.defense-systems/uzume.md b/content/3.defense-systems/uzume.md
index 29a9f1cc94750221e3449c9fdafdfdef22c63c71..4bdf5245ed9f5c1038c309f21ad01bf1148d802b 100644
--- a/content/3.defense-systems/uzume.md
+++ b/content/3.defense-systems/uzume.md
@@ -33,18 +33,22 @@ The system was detected in 87 different species.
Proportion of genome encoding the Uzume system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Uzume
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /uzume/Uzume__UzmA-plddts_94.2491.pdb
+dataUrls:
+ - /uzume/Uzume__UzmA.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -70,12 +74,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
diff --git a/content/3.defense-systems/viperin.md b/content/3.defense-systems/viperin.md
index 547bef777716f2349728c16dbe1baa52ba58f2ad..9248671fdffe58f45fc9759e80e90fbe279b1b7f 100644
--- a/content/3.defense-systems/viperin.md
+++ b/content/3.defense-systems/viperin.md
@@ -55,18 +55,22 @@ The system was detected in 95 different species.
Proportion of genome encoding the Viperin system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Viperin
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /viperin/Viperin__pVip-plddts_95.08271.pdb
+dataUrls:
+ - /viperin/Viperin__pVip.pdb
+
---
::
## Experimental validation
+
<mermaid>
graph LR;
Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_0
@@ -228,3 +232,4 @@ end
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
+
diff --git a/content/3.defense-systems/wadjet.md b/content/3.defense-systems/wadjet.md
index 5fe9639caaf036c2a3266edfed060d066f979e4e..8d55567adb3dcf645579a5b08d3d781509343061 100644
--- a/content/3.defense-systems/wadjet.md
+++ b/content/3.defense-systems/wadjet.md
@@ -42,105 +42,47 @@ The system was detected in 1467 different species.
Proportion of genome encoding the Wadjet system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Wadjet_I
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /wadjet/Wadjet_I,Wadjet__JetA_I,0,V-plddts_85.26647.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /wadjet/Wadjet_I,Wadjet__JetB_I,0,V-plddts_87.82736.pdb
----
-::
+dataUrls:
+ - /wadjet/Wadjet_I.Wadjet__JetA_I.0.V.pdb
+ - /wadjet/Wadjet_I.Wadjet__JetB_I.0.V.pdb
+ - /wadjet/Wadjet_I.Wadjet__JetC_I.0.V.pdb
+ - /wadjet/Wadjet_I.Wadjet__JetD_I.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /wadjet/Wadjet_I,Wadjet__JetC_I,0,V-plddts_84.15592.pdb
---
::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /wadjet/Wadjet_I,Wadjet__JetD_I,0,V-plddts_93.08112.pdb
----
-::
-
### Wadjet_II
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /wadjet/Wadjet_II,Wadjet__JetA_II,0,V-plddts_85.37749.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /wadjet/Wadjet_II,Wadjet__JetB_II,0,V-plddts_94.08089.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /wadjet/Wadjet_II,Wadjet__JetC_II,0,V-plddts_84.09293.pdb
----
-::
+dataUrls:
+ - /wadjet/Wadjet_II.Wadjet__JetD_II.0.V.pdb
+ - /wadjet/Wadjet_II.Wadjet__JetC_II.0.V.pdb
+ - /wadjet/Wadjet_II.Wadjet__JetB_II.0.V.pdb
+ - /wadjet/Wadjet_II.Wadjet__JetA_II.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /wadjet/Wadjet_II,Wadjet__JetD_II,0,V-plddts_92.28569.pdb
---
::
-
### Wadjet_III
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /wadjet/Wadjet_III,Wadjet__JetA_III,0,V-plddts_80.48148.pdb
----
-::
+dataUrls:
+ - /wadjet/Wadjet_III.Wadjet__JetD_III.0.V.pdb
+ - /wadjet/Wadjet_III.Wadjet__JetA_III.0.V.pdb
+ - /wadjet/Wadjet_III.Wadjet__JetB_III.0.V.pdb
+ - /wadjet/Wadjet_III.Wadjet__JetC_III.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /wadjet/Wadjet_III,Wadjet__JetB_III,0,V-plddts_80.7136.pdb
---
::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /wadjet/Wadjet_III,Wadjet__JetC_III,0,V-plddts_83.96933.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /wadjet/Wadjet_III,Wadjet__JetD_III,0,V-plddts_91.07357.pdb
----
-::
-
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aar4120
-
----
-::
-
diff --git a/content/3.defense-systems/zorya.md b/content/3.defense-systems/zorya.md
index c1cb4ae4ea5b2b6b25ee00da43f4b52c223fe522..ae950966a2bbc371fd96916b614fed8f6b8a5d1c 100644
--- a/content/3.defense-systems/zorya.md
+++ b/content/3.defense-systems/zorya.md
@@ -38,62 +38,38 @@ The system was detected in 310 different species.
Proportion of genome encoding the Zorya system for the 14 phyla with more than 50 genomes in the RefSeq database.
-## Structure
+## Structure
### Zorya_TypeI
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /zorya/Zorya_TypeI,Zorya_TypeI__ZorC,0,V-plddts_85.7807.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /zorya/Zorya_TypeI,Zorya_TypeI__ZorD,0,V-plddts_80.74261.pdb
----
-::
+dataUrls:
+ - /zorya/Zorya_TypeI.Zorya_TypeI__ZorC.0.V.pdb
+ - /zorya/Zorya_TypeI.Zorya_TypeI__ZorD.0.V.pdb
+ - /zorya/Zorya_TypeII.Zorya__ZorA.0.V.pdb
+ - /zorya/Zorya_TypeI.Zorya__ZorB.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /zorya/Zorya_TypeI,Zorya__ZorA,0,V-plddts_72.58295.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /zorya/Zorya_TypeI,Zorya__ZorB,0,V-plddts_88.9782.pdb
---
::
-
### Zorya_TypeII
+##### Example 1
::molstar-pdbe-plugin
---
height: 700
-dataUrl: /zorya/Zorya_TypeII,Zorya_TypeII__ZorE,0,V-plddts_88.59937.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /zorya/Zorya_TypeII,Zorya__ZorA,0,V-plddts_77.19519.pdb
----
-::
+dataUrls:
+ - /zorya/Zorya_TypeII.Zorya__ZorA.0.V.pdb
+ - /zorya/Zorya_TypeI.Zorya__ZorB.0.V.pdb
+ - /zorya/Zorya_TypeII.Zorya_TypeII__ZorE.0.V.pdb
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /zorya/Zorya_TypeII,Zorya__ZorB,0,V-plddts_91.39341.pdb
---
::
## Experimental validation
+
<mermaid>
graph LR;
Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
@@ -145,14 +121,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1093/nar/gkab883
- - doi: 10.1126/science.aar4120
-
----
-::