From c71470ce3fc740d81b019c839ad675f87eeb8818 Mon Sep 17 00:00:00 2001
From: jeanrjc <jean.cury@normalesup.org>
Date: Sat, 23 Dec 2023 18:44:31 +0100
Subject: [PATCH] update pdb path
---
content/3.defense-systems/abia.md | 21 +-
content/3.defense-systems/abib.md | 9 +-
content/3.defense-systems/abic.md | 18 +-
content/3.defense-systems/abid.md | 18 +-
content/3.defense-systems/abie.md | 25 +--
content/3.defense-systems/abig.md | 24 +-
content/3.defense-systems/abih.md | 9 +-
content/3.defense-systems/abii.md | 17 +-
content/3.defense-systems/abij.md | 18 +-
content/3.defense-systems/abik.md | 19 +-
content/3.defense-systems/abil.md | 15 +-
content/3.defense-systems/abin.md | 17 +-
content/3.defense-systems/abio.md | 18 +-
content/3.defense-systems/abip2.md | 19 +-
content/3.defense-systems/abiq.md | 19 +-
content/3.defense-systems/abir.md | 32 +--
content/3.defense-systems/abit.md | 24 +-
content/3.defense-systems/abiu.md | 9 +-
content/3.defense-systems/abiv.md | 18 +-
content/3.defense-systems/abiz.md | 17 +-
content/3.defense-systems/aditi.md | 23 +-
content/3.defense-systems/avs.md | 57 ++++-
content/3.defense-systems/azaca.md | 31 +--
content/3.defense-systems/borvo.md | 9 +-
content/3.defense-systems/brex.md | 205 +++--------------
content/3.defense-systems/bsta.md | 35 +--
content/3.defense-systems/bunzi.md | 15 +-
.../3.defense-systems/butters_gp30_gp31.md | 21 +-
content/3.defense-systems/butters_gp57r.md | 15 +-
content/3.defense-systems/caprel.md | 21 +-
content/3.defense-systems/cbass.md | 127 +++--------
content/3.defense-systems/charlie_gp32.md | 15 +-
content/3.defense-systems/dartg.md | 15 +-
content/3.defense-systems/dazbog.md | 28 +--
content/3.defense-systems/dctpdeaminase.md | 9 +-
content/3.defense-systems/ddmde.md | 23 +-
content/3.defense-systems/detocs.md | 43 ++--
content/3.defense-systems/dgtpase.md | 9 +-
content/3.defense-systems/disarm.md | 32 +++
content/3.defense-systems/dnd.md | 109 ++-------
content/3.defense-systems/dodola.md | 15 +-
content/3.defense-systems/dpd.md | 106 ++-------
content/3.defense-systems/drt.md | 69 +++---
content/3.defense-systems/druantia.md | 87 ++------
content/3.defense-systems/dsr.md | 24 +-
content/3.defense-systems/eleos.md | 23 +-
content/3.defense-systems/fs_giy_yig.md | 15 +-
content/3.defense-systems/fs_hepn_tm.md | 21 +-
content/3.defense-systems/fs_hp.md | 9 +-
content/3.defense-systems/fs_hp_sdh_sah.md | 22 +-
content/3.defense-systems/fs_hsdr_like.md | 23 +-
content/3.defense-systems/fs_sma.md | 16 +-
content/3.defense-systems/gabija.md | 15 +-
content/3.defense-systems/gao_ape.md | 9 +-
content/3.defense-systems/gao_her.md | 35 +--
content/3.defense-systems/gao_hhe.md | 9 +-
content/3.defense-systems/gao_iet.md | 23 +-
content/3.defense-systems/gao_mza.md | 39 +---
content/3.defense-systems/gao_ppl.md | 16 +-
content/3.defense-systems/gao_qat.md | 39 +---
content/3.defense-systems/gao_rl.md | 31 +--
content/3.defense-systems/gao_tery.md | 30 +--
content/3.defense-systems/gao_tmn.md | 9 +-
content/3.defense-systems/gao_upx.md | 9 +-
content/3.defense-systems/gaps1.md | 9 +-
content/3.defense-systems/gaps2.md | 16 +-
content/3.defense-systems/gaps4.md | 21 +-
content/3.defense-systems/gaps6.md | 21 +-
content/3.defense-systems/gasdermin.md | 47 +---
content/3.defense-systems/hachiman.md | 32 +--
content/3.defense-systems/hna.md | 16 +-
content/3.defense-systems/isg15-like.md | 151 +++----------
content/3.defense-systems/jukab.md | 22 +-
content/3.defense-systems/kiwa.md | 15 +-
content/3.defense-systems/lamassu-fam.md | 207 +++++-------------
content/3.defense-systems/lit.md | 9 +-
content/3.defense-systems/mads.md | 62 +-----
content/3.defense-systems/menshen.md | 23 +-
content/3.defense-systems/mmb_gp29_gp30.md | 15 +-
content/3.defense-systems/mok_hok_sok.md | 9 +-
content/3.defense-systems/mokosh.md | 32 ++-
content/3.defense-systems/nhi.md | 9 +-
content/3.defense-systems/nixi.md | 9 +-
content/3.defense-systems/nlr.md | 23 +-
content/3.defense-systems/old_exonuclease.md | 9 +-
content/3.defense-systems/olokun.md | 15 +-
content/3.defense-systems/pago.md | 77 ++-----
content/3.defense-systems/panchino_gp28.md | 16 +-
content/3.defense-systems/paris.md | 47 ++--
content/3.defense-systems/pd-lambda-1.md | 9 +-
content/3.defense-systems/pd-lambda-2.md | 31 +--
content/3.defense-systems/pd-lambda-3.md | 23 +-
content/3.defense-systems/pd-lambda-4.md | 22 +-
content/3.defense-systems/pd-lambda-5.md | 15 +-
content/3.defense-systems/pd-lambda-6.md | 16 +-
content/3.defense-systems/pd-t4-1.md | 17 +-
content/3.defense-systems/pd-t4-10.md | 15 +-
content/3.defense-systems/pd-t4-2.md | 23 +-
content/3.defense-systems/pd-t4-3.md | 9 +-
content/3.defense-systems/pd-t4-4.md | 15 +-
content/3.defense-systems/pd-t4-5.md | 17 +-
content/3.defense-systems/pd-t4-6.md | 9 +-
content/3.defense-systems/pd-t4-7.md | 9 +-
content/3.defense-systems/pd-t4-8.md | 9 +-
content/3.defense-systems/pd-t4-9.md | 31 +--
content/3.defense-systems/pd-t7-1.md | 16 +-
content/3.defense-systems/pd-t7-2.md | 23 +-
content/3.defense-systems/pd-t7-3.md | 9 +-
content/3.defense-systems/pd-t7-4.md | 17 +-
content/3.defense-systems/pd-t7-5.md | 16 +-
content/3.defense-systems/pfiat.md | 24 +-
content/3.defense-systems/pif.md | 15 +-
content/3.defense-systems/prrc.md | 17 +-
content/3.defense-systems/psyrta.md | 15 +-
content/3.defense-systems/pycsar.md | 36 +--
content/3.defense-systems/radar.md | 47 +---
content/3.defense-systems/retron.md | 157 ++++---------
content/3.defense-systems/rexab.md | 23 +-
content/3.defense-systems/rloc.md | 18 +-
content/3.defense-systems/rnlab.md | 23 +-
content/3.defense-systems/rosmerta.md | 23 +-
content/3.defense-systems/rst_2tm_1tm_tir.md | 32 +--
content/3.defense-systems/rst_3hp.md | 23 +-
content/3.defense-systems/rst_duf4238.md | 17 +-
content/3.defense-systems/rst_gop_beta_cll.md | 31 +--
.../3.defense-systems/rst_helicaseduf2290.md | 15 +-
.../3.defense-systems/rst_hydrolase-3tm.md | 23 +-
.../3.defense-systems/rst_rt-nitrilase-tm.md | 23 +-
content/3.defense-systems/rst_tir-nlr.md | 17 +-
content/3.defense-systems/sanata.md | 15 +-
content/3.defense-systems/sefir.md | 9 +-
content/3.defense-systems/septu.md | 38 +---
content/3.defense-systems/shango.md | 25 +--
content/3.defense-systems/shedu.md | 9 +-
content/3.defense-systems/shosta.md | 15 +-
content/3.defense-systems/sofic.md | 17 +-
content/3.defense-systems/spbk.md | 17 +-
content/3.defense-systems/sspbcde.md | 85 ++-----
content/3.defense-systems/stk2.md | 17 +-
content/3.defense-systems/thoeris.md | 36 +--
content/3.defense-systems/tiamat.md | 9 +-
content/3.defense-systems/uzume.md | 16 +-
content/3.defense-systems/viperin.md | 9 +-
content/3.defense-systems/wadjet.md | 96 ++------
content/3.defense-systems/zorya.md | 60 ++---
145 files changed, 1367 insertions(+), 2850 deletions(-)
diff --git a/content/3.defense-systems/abia.md b/content/3.defense-systems/abia.md
index 767f5802..e0fba523 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 63d2aafc..0b8fb135 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 aaa95780..6876763d 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 f41523d2..6cf817e3 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 e8f45950..706909d8 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 1d85b256..87b0b196 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 475a4ffd..7b937eff 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 6a004f1f..97b709b0 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 2a60a053..03b87ac9 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 284f5d9d..607fec7f 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 5f3fba64..c7bc8f34 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 2599e996..b8033079 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 88ef2590..483e179b 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 0b4bd616..83840172 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 b9bec1ad..2c65ede1 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 5336f7b1..7edcc5ad 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 943c0852..6e79b4a1 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 a94e3073..d8b3722b 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 05084642..db416918 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 5bfcd31d..aa18e65a 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 ff6c7c2c..452259dc 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 16d148c5..ceed5067 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 87bb9fd3..15ae31cb 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 9cd6a064..457341c1 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 15d782af..7b3a1e2b 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 3f005e10..58ea6fcc 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 1a28925d..95b0915b 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 6794f44d..87963a3b 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 2e6e5d61..7279df46 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 b5778536..63938fdd 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 06c6bcfc..3981e257 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 04aa34b1..397b2562 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 89bf5e39..7b8a0e29 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 83f019ea..6060fa8f 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 6cca2256..4f0235f7 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 d09c53d7..9f9fe28f 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 5a9a42d3..3ddb8843 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 6e19ae2a..55ce9aaf 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 99b73d5e..a1d2d802 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 d6f19002..2e06e4fa 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 15002c7c..a7c02de8 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 efa443fa..2301fb98 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 4297087b..20be54df 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 6179376f..835f6555 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 0c90ee00..03e3cf23 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 ebd6dde8..8220a15c 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 7a8084b6..210603c6 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 f6d2095e..c53fc9ff 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 b256ce11..e78e5658 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 335c2cdd..0334531a 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 0da466dd..90d07a4a 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 037cf211..9931ce08 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 5c18050c..d255ba39 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 a371e7c6..a5da96e7 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 e3f668fb..c942058d 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 e39c90a5..9d6f96e5 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 92f0e5cf..5c0f1dd3 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 837f5218..73877416 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 036156d0..a5aa0cc2 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 9c3da94f..c0129613 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 06631e1b..5f77504e 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 42bf18b1..21910352 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 c7511731..d4cc024c 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 9bdf3daa..f83ae2c2 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 c7eb1ed5..14b2de50 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 8eb3e73c..46a20217 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 a926ef52..4fe4db65 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 2a8e4241..3b218b60 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 13302581..64bd8d76 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 4d52aee3..5a8515cf 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 82d73c2d..56a84f17 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 7b71a70c..314be5d1 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 54409b21..b650585e 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 7e83855f..87a2bc70 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 3fcb7cea..8b5be319 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 701cbb90..55de9768 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 c9ba94ff..e13fcc40 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 536decd9..6678c81f 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 1669c5f9..1985314e 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 a7bc48e6..ddcf152d 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 15224c64..0c365bcb 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 3c1dc2e5..08d379f4 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 3f115bb7..ac4971e6 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 311bef41..c463d483 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 e438b40a..8359ab39 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 390ba0af..4b48a329 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 7028073c..86caf2b4 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 0535dd85..e197f1d8 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 5a2f7ab7..c9b25cc4 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 45179650..b09ecd28 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 c8f17049..a6d47cfc 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 00b4eea3..06508b69 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 2ec229f2..2890057b 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 b18ff6c2..e19d460d 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 19b5a462..70128d2a 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 9d41d4a2..5f5d9c36 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 4c479ab1..18d40210 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 2e094b66..289fd9cb 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 9d2ac092..ea87f4c9 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 6821b9a3..b7693c80 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 bb7b919e..dd2b3118 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 9ead59fa..6c419ca3 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 e60b1dd2..0cb3aa71 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 b1cd9b9c..dbc3b0c1 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 56c98f57..8a6b8a36 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 b7085c3e..c0953753 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 fcc69e05..bd62bba0 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 469689e5..7ff45688 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 9a17b142..6658dba5 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 22c4aff5..564c4bfe 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 a29dab03..c21eec60 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 8279c80f..0785faf0 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 09da95b9..8e7517d5 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 cd7deb73..6e1d4fa9 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 dde91165..f33d2091 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 3af879dc..11aae90b 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 be5a790d..a9daa09d 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 06ccbd3a..ee6c0c51 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 798e25f9..3bb39164 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 9bff2f85..7aec609f 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 cca150e7..c59f85c1 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 a616b177..7865f437 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 f4316f5a..795e2eea 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 f84a7815..c96e888d 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 e146cb8d..44af6c64 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 cfed7c43..647094f8 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 18fe66fe..3f777d18 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 9e2d2085..286a6be9 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 b2ec23e6..1fb00c19 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 82d1fe9f..f43723ec 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 11e0d0b9..2a75ce4a 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 7277766d..232f9b3c 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 a964d599..b174aaf8 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 12651abe..5835ad1e 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 934c4230..90f1cdd3 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 94390623..3988f556 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 4f4f20b8..6377138a 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 fb3fac3e..fabced18 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 6a005027..ce9a908e 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 3fa07ce1..3f8baaf0 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 a7b31dcd..ac0dc63e 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 29a9f1cc..4bdf5245 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 547bef77..9248671f 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 5fe9639c..8d55567a 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 c1cb4ae4..ae950966 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
-
----
-::
--
GitLab