From 106ff90c0dddd23e15eb4443eb3ea4603b4255a7 Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Fri, 12 Apr 2024 14:56:45 +0200
Subject: [PATCH] update articles
---
content/3.defense-systems/abi2.md | 25 +---
content/3.defense-systems/abia.md | 10 +-
content/3.defense-systems/abib.md | 24 +--
content/3.defense-systems/abic.md | 24 +--
content/3.defense-systems/abid.md | 24 +--
content/3.defense-systems/abie.md | 25 +---
content/3.defense-systems/abig.md | 25 +---
content/3.defense-systems/abih.md | 24 +--
content/3.defense-systems/abii.md | 24 +--
content/3.defense-systems/abij.md | 24 +--
content/3.defense-systems/abik.md | 24 +--
content/3.defense-systems/abil.md | 25 +---
content/3.defense-systems/abin.md | 24 +--
content/3.defense-systems/abio.md | 24 +--
content/3.defense-systems/abip2.md | 24 +--
content/3.defense-systems/abiq.md | 32 +---
content/3.defense-systems/abir.md | 26 +---
content/3.defense-systems/abit.md | 25 +---
content/3.defense-systems/abiu.md | 24 +--
content/3.defense-systems/abiv.md | 23 +--
content/3.defense-systems/abiz.md | 24 +--
content/3.defense-systems/aditi.md | 24 +--
content/3.defense-systems/avs.md | 15 +-
content/3.defense-systems/azaca.md | 26 +---
content/3.defense-systems/borvo.md | 24 +--
content/3.defense-systems/brex.md | 82 +---------
content/3.defense-systems/bsta.md | 26 +---
content/3.defense-systems/bunzi.md | 25 +---
.../3.defense-systems/butters_gp30_gp31.md | 25 +---
content/3.defense-systems/butters_gp57r.md | 24 +--
content/3.defense-systems/caprel.md | 24 +--
content/3.defense-systems/card_nlr.md | 15 +-
content/3.defense-systems/cas.md | 15 +-
content/3.defense-systems/cbass.md | 65 +-------
content/3.defense-systems/charlie_gp32.md | 24 +--
content/3.defense-systems/dartg.md | 25 +---
content/3.defense-systems/dazbog.md | 33 +---
content/3.defense-systems/dctpdeaminase.md | 24 +--
content/3.defense-systems/ddmde.md | 26 +---
content/3.defense-systems/detocs.md | 35 +----
content/3.defense-systems/dgtpase.md | 24 +--
content/3.defense-systems/disarm.md | 49 +-----
content/3.defense-systems/dnd.md | 43 +-----
content/3.defense-systems/dodola.md | 25 +---
content/3.defense-systems/dpd.md | 35 +----
content/3.defense-systems/drt.md | 110 +-------------
content/3.defense-systems/druantia.md | 50 +------
content/3.defense-systems/dsr.md | 31 +---
content/3.defense-systems/eleos.md | 35 +----
content/3.defense-systems/fs_giy_yig.md | 24 +--
content/3.defense-systems/fs_hepn_tm.md | 20 +--
content/3.defense-systems/fs_hp.md | 24 +--
content/3.defense-systems/fs_hp_sdh_sah.md | 25 +---
content/3.defense-systems/fs_hsdr_like.md | 31 +---
content/3.defense-systems/fs_sma.md | 24 +--
content/3.defense-systems/gabija.md | 34 +----
content/3.defense-systems/gao_ape.md | 24 +--
content/3.defense-systems/gao_her.md | 58 +------
content/3.defense-systems/gao_hhe.md | 24 +--
content/3.defense-systems/gao_iet.md | 25 +---
content/3.defense-systems/gao_mza.md | 28 +---
content/3.defense-systems/gao_ppl.md | 24 +--
content/3.defense-systems/gao_qat.md | 27 +---
content/3.defense-systems/gao_rl.md | 27 +---
content/3.defense-systems/gao_tery.md | 26 +---
content/3.defense-systems/gao_tmn.md | 24 +--
content/3.defense-systems/gao_upx.md | 24 +--
content/3.defense-systems/gaps1.md | 24 +--
content/3.defense-systems/gaps2.md | 24 +--
content/3.defense-systems/gaps4.md | 26 +---
content/3.defense-systems/gaps6.md | 25 +---
content/3.defense-systems/gasdermin.md | 29 +---
content/3.defense-systems/hachiman.md | 25 +---
content/3.defense-systems/hna.md | 24 +--
content/3.defense-systems/isg15-like.md | 27 +---
content/3.defense-systems/jukab.md | 25 +---
content/3.defense-systems/kiwa.md | 25 +---
content/3.defense-systems/lamassu-fam.md | 141 +-----------------
content/3.defense-systems/lit.md | 24 +--
content/3.defense-systems/mads.md | 30 +---
content/3.defense-systems/mazef.md | 15 +-
content/3.defense-systems/menshen.md | 26 +---
content/3.defense-systems/mmb_gp29_gp30.md | 25 +---
content/3.defense-systems/mok_hok_sok.md | 24 +--
content/3.defense-systems/mokosh.md | 41 +----
content/3.defense-systems/mqsrac.md | 14 +-
content/3.defense-systems/nhi.md | 24 +--
content/3.defense-systems/nixi.md | 24 +--
content/3.defense-systems/nlr.md | 31 +---
content/3.defense-systems/old_exonuclease.md | 24 +--
content/3.defense-systems/olokun.md | 25 +---
content/3.defense-systems/pago.md | 32 +---
content/3.defense-systems/panchino_gp28.md | 24 +--
content/3.defense-systems/paris.md | 55 +------
content/3.defense-systems/pd-lambda-1.md | 24 +--
content/3.defense-systems/pd-lambda-2.md | 26 +---
content/3.defense-systems/pd-lambda-3.md | 26 +---
content/3.defense-systems/pd-lambda-4.md | 25 +---
content/3.defense-systems/pd-lambda-5.md | 25 +---
content/3.defense-systems/pd-lambda-6.md | 24 +--
content/3.defense-systems/pd-t4-1.md | 24 +--
content/3.defense-systems/pd-t4-10.md | 25 +---
content/3.defense-systems/pd-t4-2.md | 25 +---
content/3.defense-systems/pd-t4-3.md | 24 +--
content/3.defense-systems/pd-t4-4.md | 25 +---
content/3.defense-systems/pd-t4-5.md | 24 +--
content/3.defense-systems/pd-t4-6.md | 24 +--
content/3.defense-systems/pd-t4-7.md | 24 +--
content/3.defense-systems/pd-t4-8.md | 24 +--
content/3.defense-systems/pd-t4-9.md | 26 +---
content/3.defense-systems/pd-t7-1.md | 24 +--
content/3.defense-systems/pd-t7-2.md | 25 +---
content/3.defense-systems/pd-t7-3.md | 24 +--
content/3.defense-systems/pd-t7-4.md | 24 +--
content/3.defense-systems/pd-t7-5.md | 24 +--
content/3.defense-systems/pfiat.md | 30 +---
content/3.defense-systems/phrann_gp29_gp30.md | 15 +-
content/3.defense-systems/pif.md | 25 +---
content/3.defense-systems/prrc.md | 33 +---
content/3.defense-systems/psyrta.md | 25 +---
content/3.defense-systems/pycsar.md | 45 +-----
content/3.defense-systems/radar.md | 75 +---------
content/3.defense-systems/retron.md | 141 +-----------------
content/3.defense-systems/rexab.md | 25 +---
content/3.defense-systems/rloc.md | 24 +--
content/3.defense-systems/rm.md | 26 +---
content/3.defense-systems/rnlab.md | 25 +---
content/3.defense-systems/rosmerta.md | 25 +---
content/3.defense-systems/rst_2tm_1tm_tir.md | 26 ++--
content/3.defense-systems/rst_3hp.md | 26 +---
content/3.defense-systems/rst_duf4238.md | 24 +--
content/3.defense-systems/rst_gop_beta_cll.md | 26 +---
.../3.defense-systems/rst_helicaseduf2290.md | 25 +---
.../3.defense-systems/rst_hydrolase-3tm.md | 25 +---
.../3.defense-systems/rst_rt-nitrilase-tm.md | 25 +---
content/3.defense-systems/rst_tir-nlr.md | 24 +--
content/3.defense-systems/sanata.md | 25 +---
content/3.defense-systems/sefir.md | 24 +--
content/3.defense-systems/septu.md | 48 +-----
content/3.defense-systems/shango.md | 26 +---
content/3.defense-systems/shedu.md | 24 +--
content/3.defense-systems/shosta.md | 25 +---
content/3.defense-systems/sofic.md | 24 +--
content/3.defense-systems/spbk.md | 24 +--
content/3.defense-systems/sspbcde.md | 38 +----
content/3.defense-systems/stk2.md | 24 +--
content/3.defense-systems/thoeris.md | 48 +-----
content/3.defense-systems/tiamat.md | 24 +--
content/3.defense-systems/uzume.md | 24 +--
content/3.defense-systems/viperin.md | 24 +--
content/3.defense-systems/wadjet.md | 67 +--------
content/3.defense-systems/zorya.md | 36 +----
152 files changed, 1151 insertions(+), 3374 deletions(-)
diff --git a/content/3.defense-systems/abi2.md b/content/3.defense-systems/abi2.md
index 0c2570d4..669f3944 100644
--- a/content/3.defense-systems/abi2.md
+++ b/content/3.defense-systems/abi2.md
@@ -44,30 +44,21 @@ As far as we are aware, the molecular mechanisms remain unclear.
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Abi2 is detected in 1231 genomes (5.4 %).
-
-The system was detected in 202 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Abi2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
-## Structure
+## Structure
-### Abi2/AbiD
+### List predicted structures
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /abid/AbiD__AbiD.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
-
## Experimental validation
As Abi2 is a group of different Abortive infection systems, here is the experimental validation of AbiD:
diff --git a/content/3.defense-systems/abia.md b/content/3.defense-systems/abia.md
index e1c75307..62541bd3 100644
--- a/content/3.defense-systems/abia.md
+++ b/content/3.defense-systems/abia.md
@@ -54,11 +54,11 @@ The AbiA_small system in *Alicyclobacillus sp. SO9* (GCF_016406125.1, NZ_CP06633
::article-system-distribution-plot
::
-
## Structure
+### List predicted structures
-::system-operon-structure
+::article-structure
::
### pDockQ matrix
@@ -66,12 +66,6 @@ The AbiA_small system in *Alicyclobacillus sp. SO9* (GCF_016406125.1, NZ_CP06633
::pdockq-matrix
::
-### List predicted structures
-
-::article-structure
-::
-
-
## Experimental validation
diff --git a/content/3.defense-systems/abib.md b/content/3.defense-systems/abib.md
index 47765f3e..75d232dc 100644
--- a/content/3.defense-systems/abib.md
+++ b/content/3.defense-systems/abib.md
@@ -38,27 +38,19 @@ The AbiB system in *Lactococcus cremoris* (GCF_000312685.1, NC_019430) is compos
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the AbiB is detected in 11 genomes (0.05 %).
-
-The system was detected in 5 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the AbiB system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### AbiB
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /abib/AbiB__AbiB.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/abic.md b/content/3.defense-systems/abic.md
index df23651d..dd2e6e73 100644
--- a/content/3.defense-systems/abic.md
+++ b/content/3.defense-systems/abic.md
@@ -45,27 +45,19 @@ The AbiC system in *Cupriavidus pauculus* (GCF_008693385.1, NZ_CP044066) is comp
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the AbiC is detected in 91 genomes (0.4 %).
-
-The system was detected in 57 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the AbiC system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### AbiC
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /abic/AbiC__AbiC.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/abid.md b/content/3.defense-systems/abid.md
index 6520eff8..a8337d0e 100644
--- a/content/3.defense-systems/abid.md
+++ b/content/3.defense-systems/abid.md
@@ -45,27 +45,19 @@ The AbiD system in *Idiomarina sp. OT37-5b* (GCF_002968395.1, NZ_CP027188) is co
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the AbiD is detected in 2713 genomes (11.9 %).
-
-The system was detected in 964 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the AbiD system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### AbiD
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /abid/AbiD__AbiD.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/abie.md b/content/3.defense-systems/abie.md
index 10ca234e..d27e6ef9 100644
--- a/content/3.defense-systems/abie.md
+++ b/content/3.defense-systems/abie.md
@@ -48,28 +48,19 @@ The AbiE system in *Halomonas piezotolerans* (GCF_012427705.1, NZ_CP048602) is c
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the AbiE is detected in 3708 genomes (16.26 %).
-
-The system was detected in 1107 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the AbiE system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### AbiE
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /abie/AbiE.AbiE__AbiEi.0.V.cif
- - /abie/AbiE.AbiE__AbiEii.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/abig.md b/content/3.defense-systems/abig.md
index 9801bd37..49370bcb 100644
--- a/content/3.defense-systems/abig.md
+++ b/content/3.defense-systems/abig.md
@@ -45,28 +45,19 @@ The AbiG system in *Staphylococcus simulans* (GCF_900474685.1, NZ_LS483313) is c
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the AbiG is detected in 32 genomes (0.14 %).
-
-The system was detected in 22 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the AbiG system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### AbiG
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /abig/AbiG.AbiG__AbiGi.0.V.cif
- - /abig/AbiG.AbiG__AbiGii.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/abih.md b/content/3.defense-systems/abih.md
index 3c5afac5..d7c2ce68 100644
--- a/content/3.defense-systems/abih.md
+++ b/content/3.defense-systems/abih.md
@@ -43,27 +43,19 @@ The AbiH system in *Bacteroides faecium* (GCF_012113595.1, NZ_CP050831) is compo
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the AbiH is detected in 1225 genomes (5.37 %).
-
-The system was detected in 439 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the AbiH system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### AbiH
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /abih/AbiH__AbiH.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/abii.md b/content/3.defense-systems/abii.md
index dee72be7..24b87d64 100644
--- a/content/3.defense-systems/abii.md
+++ b/content/3.defense-systems/abii.md
@@ -39,27 +39,19 @@ The AbiI system in *Macrococcus brunensis* (GCF_022343725.1, NZ_CP092179) is com
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the AbiI is detected in 6 genomes (0.03 %).
-
-The system was detected in 6 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the AbiI system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### AbiI
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /abii/AbiI__AbiI.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/abij.md b/content/3.defense-systems/abij.md
index e5ca455a..b164e2df 100644
--- a/content/3.defense-systems/abij.md
+++ b/content/3.defense-systems/abij.md
@@ -44,27 +44,19 @@ The AbiJ system in *Marinobacter sp. LQ44* (GCF_001447155.2, NZ_CP014754) is com
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the AbiJ is detected in 686 genomes (3.01 %).
-
-The system was detected in 261 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the AbiJ system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### AbiJ
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /abij/AbiJ__AbiJ.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/abik.md b/content/3.defense-systems/abik.md
index 8d64fed9..44274543 100644
--- a/content/3.defense-systems/abik.md
+++ b/content/3.defense-systems/abik.md
@@ -48,27 +48,19 @@ The AbiK system in *Lactobacillus ultunensis* (GCF_016647595.1, NZ_CP059829) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the AbiK is detected in 107 genomes (0.47 %).
-
-The system was detected in 32 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the AbiK system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### AbiK
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /abik/AbiK__AbiK.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/abil.md b/content/3.defense-systems/abil.md
index f8034e56..4b521a70 100644
--- a/content/3.defense-systems/abil.md
+++ b/content/3.defense-systems/abil.md
@@ -40,28 +40,19 @@ The AbiL system in *Sulfurimonas sp. SWIR-19* (GCF_020410885.1, NZ_CP084578) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the AbiL is detected in 188 genomes (0.82 %).
-
-The system was detected in 126 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the AbiL system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### AbiL
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /abil/AbiL.AbiL__AbiLi.0.V.cif
- - /abil/AbiL.AbiL__AbiLii.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/abin.md b/content/3.defense-systems/abin.md
index 4198f089..3de1357d 100644
--- a/content/3.defense-systems/abin.md
+++ b/content/3.defense-systems/abin.md
@@ -42,27 +42,19 @@ The AbiN system in *Listeria innocua* (GCF_023078395.1, NZ_CP095723) is composed
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the AbiN is detected in 165 genomes (0.72 %).
-
-The system was detected in 52 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the AbiN system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### AbiN
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /abin/AbiN__AbiN.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/abio.md b/content/3.defense-systems/abio.md
index efce870b..2f01cf3e 100644
--- a/content/3.defense-systems/abio.md
+++ b/content/3.defense-systems/abio.md
@@ -45,27 +45,19 @@ The AbiO system in *Pantoea agglomerans* (GCF_004117135.1, NZ_CP034477) is compo
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the AbiO is detected in 100 genomes (0.44 %).
-
-The system was detected in 61 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the AbiO system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### AbiO
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /abio/AbiO__AbiO.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/abip2.md b/content/3.defense-systems/abip2.md
index 320dd470..d2656ac0 100644
--- a/content/3.defense-systems/abip2.md
+++ b/content/3.defense-systems/abip2.md
@@ -50,27 +50,19 @@ The AbiP2 system in *Halomonas alkaliphila* (GCF_003612795.1, NZ_CP024811) is co
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the AbiP2 is detected in 299 genomes (1.31 %).
-
-The system was detected in 96 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the AbiP2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### AbiP2
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /abip2/AbiP2__AbiP2.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/abiq.md b/content/3.defense-systems/abiq.md
index 0772b389..8c5697c3 100644
--- a/content/3.defense-systems/abiq.md
+++ b/content/3.defense-systems/abiq.md
@@ -49,39 +49,19 @@ The AbiQ system in *Planococcus faecalis* (GCF_002009235.1, NZ_CP019401) is comp
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the AbiQ is detected in 258 genomes (1.13 %).
-
-The system was detected in 111 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the AbiQ system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
+::article-system-distribution-plot
+::
## Structure
-### Experimentally determined structure
-From :ref{doi=10.1111/mmi.12129} in *Lactococcus lactis*:
+### List predicted structures
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /abiq/4glk_LlAbiQ_1mer.cif
----
+::article-structure
::
+### pDockQ matrix
-## Structure
-### AbiQ
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /abiq/AbiQ__AbiQ.cif
-
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/abir.md b/content/3.defense-systems/abir.md
index ac281bc6..a48e2424 100644
--- a/content/3.defense-systems/abir.md
+++ b/content/3.defense-systems/abir.md
@@ -45,29 +45,19 @@ The AbiR system in *Clostridium perfringens* (GCF_016027155.1, NZ_CP065677) is c
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the AbiR is detected in 51 genomes (0.22 %).
-
-The system was detected in 28 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the AbiR system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### AbiR
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /abir/AbiR.AbiR__AbiRc.0.V.cif
- - /abir/AbiR.AbiR__AbiRb.0.V.cif
- - /abir/AbiR.AbiR__AbiRa.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/abit.md b/content/3.defense-systems/abit.md
index 17acc1a4..49bd9228 100644
--- a/content/3.defense-systems/abit.md
+++ b/content/3.defense-systems/abit.md
@@ -44,28 +44,19 @@ The AbiT system in *Bdellovibrio bacteriovorus* (GCF_000317895.1, NC_019567) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the AbiT is detected in 8 genomes (0.04 %).
-
-The system was detected in 6 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the AbiT system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### AbiT
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /abit/AbiT.AbiT__AbiTi.0.V.cif
- - /abit/AbiT.AbiT__AbiTii.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/abiu.md b/content/3.defense-systems/abiu.md
index 152653e0..69ed85f0 100644
--- a/content/3.defense-systems/abiu.md
+++ b/content/3.defense-systems/abiu.md
@@ -38,27 +38,19 @@ The AbiU system in *Bacillus subtilis* (GCF_001889385.1, NZ_CP018295) is compose
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the AbiU is detected in 950 genomes (4.17 %).
-
-The system was detected in 389 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the AbiU system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### AbiU
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /abiu/AbiU__AbiU.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/abiv.md b/content/3.defense-systems/abiv.md
index fc5be91c..df5c181a 100644
--- a/content/3.defense-systems/abiv.md
+++ b/content/3.defense-systems/abiv.md
@@ -41,26 +41,19 @@ The AbiV system in *Bacillus mycoides* (GCF_018739365.1, NZ_CP035984) is compose
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the AbiV is detected in 97 genomes (0.43 %).
-
-The system was detected in 61 different species.
-
-{max-width=750px}
+::article-system-distribution-plot
+::
-Proportion of genome encoding the AbiV system for the 14 phyla with more than 50 genomes in the RefSeq database.
+## Structure
+### List predicted structures
+::article-structure
+::
-## Structure
-### AbiV
-##### Example 1
+### pDockQ matrix
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /abiv/AbiV__AbiV.cif
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/abiz.md b/content/3.defense-systems/abiz.md
index aa6ef19f..5aa742b4 100644
--- a/content/3.defense-systems/abiz.md
+++ b/content/3.defense-systems/abiz.md
@@ -41,27 +41,19 @@ The AbiZ system in *Fusobacterium pseudoperiodonticum* (GCF_002763695.1, NZ_CP02
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the AbiZ is detected in 118 genomes (0.52 %).
-
-The system was detected in 97 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the AbiZ system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### AbiZ
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /abiz/AbiZ__AbiZ.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/aditi.md b/content/3.defense-systems/aditi.md
index 41c7cdf6..f795d173 100644
--- a/content/3.defense-systems/aditi.md
+++ b/content/3.defense-systems/aditi.md
@@ -38,27 +38,19 @@ The Aditi system in *Streptococcus suis* (GCF_003288175.1, NZ_CP025419) is compo
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Aditi is detected in 40 genomes (0.18 %).
-
-The system was detected in 19 different species.
-
-{max-width=750px}
+::article-system-distribution-plot
+::
-Proportion of genome encoding the Aditi system for the 14 phyla with more than 50 genomes in the RefSeq database.
+## Structure
+### List predicted structures
+::article-structure
+::
-## Structure
-### Aditi
-##### Example 1
+### pDockQ matrix
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /aditi/Aditi.Aditi__DitB.0.V.cif
- - /aditi/Aditi.Aditi__DitA.0.V.cif
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/avs.md b/content/3.defense-systems/avs.md
index dfc62f59..6c5fe28e 100644
--- a/content/3.defense-systems/avs.md
+++ b/content/3.defense-systems/avs.md
@@ -66,23 +66,20 @@ The Avs_V system in *Klebsiella variicola* (GCF_015287155.1, NZ_CP063912) is com
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Avs is detected in 978 genomes (4.29 %).
-
-The system was detected in 366 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Avs system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
::article-system-distribution-plot
::
## Structure
+### List predicted structures
+
::article-structure
::
+### pDockQ matrix
+
+::pdockq-matrix
+::
## Experimental validation
diff --git a/content/3.defense-systems/azaca.md b/content/3.defense-systems/azaca.md
index 4d7b1da5..d12ca1c1 100644
--- a/content/3.defense-systems/azaca.md
+++ b/content/3.defense-systems/azaca.md
@@ -27,29 +27,19 @@ The Azaca system in *Gordonia polyisoprenivorans* (GCF_018135605.1, NZ_CP073075)
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Azaca is detected in 203 genomes (0.89 %).
-
-The system was detected in 166 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Azaca system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Azaca
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /azaca/Azaca.Azaca__ZacA.0.V.cif
- - /azaca/Azaca.Azaca__ZacB.0.V.cif
- - /azaca/Azaca.Azaca__ZacC.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/borvo.md b/content/3.defense-systems/borvo.md
index ef634f1c..63f6fa85 100644
--- a/content/3.defense-systems/borvo.md
+++ b/content/3.defense-systems/borvo.md
@@ -39,27 +39,19 @@ The Borvo system in *Enterobacter cloacae complex sp. ECL78* (GCF_019056615.1, N
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Borvo is detected in 177 genomes (0.78 %).
-
-The system was detected in 79 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Borvo system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Borvo
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /borvo/Borvo__BovA.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/brex.md b/content/3.defense-systems/brex.md
index 015028c9..0138b3af 100644
--- a/content/3.defense-systems/brex.md
+++ b/content/3.defense-systems/brex.md
@@ -75,91 +75,19 @@ The BREX_VI system in *Virgibacillus halodenitrificans* (GCF_001878675.1, NZ_CP0
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the BREX is detected in 1658 genomes (7.27 %).
-
-The system was detected in 888 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the BREX system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
+::article-system-distribution-plot
+::
## Structure
+### List predicted structures
::article-structure
::
+### pDockQ matrix
-### BREX_II
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /brex/BREX_VI.BREX__brxHI.0.DF.cif
- - /brex/BREX_VI.BREX__brxD.0.DF.cif
- - /brex/BREX_II.BREX__pglY.0.DF.cif
- - /brex/BREX_II.BREX__pglX2.0.DF.cif
- - /brex/BREX_II.BREX__pglW.0.DF.cif
-
----
-::
-### BREX_III
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /brex/BREX_III.BREX__brxF.0.DF.cif
- - /brex/BREX_III.BREX__pglXI.0.DF.cif
- - /brex/BREX_V.BREX__brxHII.0.DF.cif
- - /brex/BREX_III.BREX__pglZ3.0.DF.cif
- - /brex/BREX_III.BREX__brxA.0.DF.cif
-
----
-::
-### BREX_IV
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /brex/BREX_IV.BREX__brxP.0.DF.cif
- - /brex/BREX_IV.BREX__PglZ.0.DF.cif
-
----
-::
-### BREX_V
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /brex/BREX_V.BREX__brxHII.0.DF.cif
- - /brex/BREX_VI.BREX__pglZA.0.DF.cif
-
----
-::
-### BREX_VI
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /brex/BREX_VI.BREX__brxHI.0.DF.cif
- - /brex/BREX_VI.BREX__brxD.0.DF.cif
- - /brex/BREX_VI.BREX__pglZA.0.DF.cif
- - /brex/BREX_VI.BREX_brxA.0.DF.cif
- - /brex/BREX_VI.BREX__brxE.0.DF.cif
-
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/bsta.md b/content/3.defense-systems/bsta.md
index dd03995d..c3b156df 100644
--- a/content/3.defense-systems/bsta.md
+++ b/content/3.defense-systems/bsta.md
@@ -41,29 +41,19 @@ The BstA system in *Vibrio harveyi* (GCF_021397735.1, NZ_CP090179) is composed o
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the BstA is detected in 236 genomes (1.03 %).
-
-The system was detected in 88 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the BstA system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### BstA
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /bsta/BstA__BstA.cif
- - /bsta/BstA__BstA1.cif
- - /bsta/BstA__BstA2.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/bunzi.md b/content/3.defense-systems/bunzi.md
index 8b63b2ed..48fc105c 100644
--- a/content/3.defense-systems/bunzi.md
+++ b/content/3.defense-systems/bunzi.md
@@ -36,28 +36,19 @@ The Bunzi system in *Shewanella loihica* (GCF_000016065.1, NC_009092) is compose
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Bunzi is detected in 103 genomes (0.45 %).
-
-The system was detected in 58 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Bunzi system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Bunzi
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /bunzi/Bunzi.Bunzi__BnzB.0.V.cif
- - /bunzi/Bunzi.Bunzi__BnzA.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/butters_gp30_gp31.md b/content/3.defense-systems/butters_gp30_gp31.md
index 371b37a7..32f7e6fa 100644
--- a/content/3.defense-systems/butters_gp30_gp31.md
+++ b/content/3.defense-systems/butters_gp30_gp31.md
@@ -40,28 +40,19 @@ The Butters_gp30_gp31 system in *Snodgrassella alvi* (GCF_022870965.1, NZ_CP0915
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Butters_gp30_gp31 is detected in 38 genomes (0.17 %).
-
-The system was detected in 34 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Butters_gp30_gp31 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Butters_gp30_gp31
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /butters_gp30_gp31/Butters_gp30_gp31__Butters_gp30.cif
- - /butters_gp30_gp31/Butters_gp30_gp31__Butters_gp31.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/butters_gp57r.md b/content/3.defense-systems/butters_gp57r.md
index 55c95246..7102ea93 100644
--- a/content/3.defense-systems/butters_gp57r.md
+++ b/content/3.defense-systems/butters_gp57r.md
@@ -26,27 +26,19 @@ The Butters_gp57r system in *Mycobacteroides immunogenum* (GCF_001605725.1, NZ_C
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Butters_gp57r is detected in 10 genomes (0.04 %).
-
-The system was detected in 7 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Butters_gp57r system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Butters_gp57r
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /butters_gp57r/Butters_gp57r__gp57r.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/caprel.md b/content/3.defense-systems/caprel.md
index 0570be53..d0b88319 100644
--- a/content/3.defense-systems/caprel.md
+++ b/content/3.defense-systems/caprel.md
@@ -42,27 +42,19 @@ The CapRel system in *Campylobacter sp. RM12175* (GCF_002139875.1, NZ_CP018793)
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the CapRel is detected in 398 genomes (1.75 %).
-
-The system was detected in 217 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the CapRel system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### CapRel
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /caprel/CapRel__CapRel.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/card_nlr.md b/content/3.defense-systems/card_nlr.md
index e6b6fe9b..e1e2e0d9 100644
--- a/content/3.defense-systems/card_nlr.md
+++ b/content/3.defense-systems/card_nlr.md
@@ -51,18 +51,19 @@ The CARD_NLR_like system in *Sphingomonas sanguinis* (GCF_019297835.1, NZ_CP0792
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the CARD_NLR is detected in 80 genomes (0.35 %).
+::article-system-distribution-plot
+::
-The system was detected in 57 different species.
+## Structure
-{max-width=750px}
+### List predicted structures
-Proportion of genome encoding the CARD_NLR system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-structure
+::
-## Structure
+### pDockQ matrix
-::info
-This section is empty
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/cas.md b/content/3.defense-systems/cas.md
index 67a297f2..fb2d14fa 100644
--- a/content/3.defense-systems/cas.md
+++ b/content/3.defense-systems/cas.md
@@ -46,18 +46,19 @@ The CAS_Class2-Subtype-VI-A system in *Leptotrichia shahii* (GCF_008327825.1, NZ
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the AbiC is detected in 8581 genomes (37.63 %).
+::article-system-distribution-plot
+::
-The system was detected in 2905 different species.
+## Structure
-{max-width=750px}
+### List predicted structures
-Proportion of genome encoding the AbiC system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-structure
+::
-## Structure
+### pDockQ matrix
-::info
-This section is empty
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/cbass.md b/content/3.defense-systems/cbass.md
index c38627e0..30a11efa 100644
--- a/content/3.defense-systems/cbass.md
+++ b/content/3.defense-systems/cbass.md
@@ -44,72 +44,19 @@ The CBASS_IV system in *Flavobacterium alkalisoli* (GCF_008000935.1, NZ_CP042831
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the CBASS is detected in 2914 genomes (12.78 %).
-
-The system was detected in 1290 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the CBASS system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
-
-## Structure
-### CBASS_I
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /cbass/CBASS_I.CBASS__Cyclase_II.0.V.cif
- - /cbass/CBASS_I.CBASS__TM.0.V.cif
-
----
+::article-system-distribution-plot
::
-### CBASS_II
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /cbass/CBASS_II.CBASS__Phospholipase.0.V.cif
- - /cbass/CBASS_II.CBASS__AG_E2_Prok-E2.0.V.cif
- - /cbass/CBASS_I.CBASS__Cyclase_II.0.V.cif
- - /cbass/CBASS_II.CBASS__Jab.0.V.cif
----
-::
-### CBASS_III
-##### Example 1
+## Structure
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /cbass/CBASS_III.CBASS__Endonuc_small.0.V.cif
- - /cbass/CBASS_I.CBASS__Cyclase_II.0.V.cif
- - /cbass/CBASS_III.CBASS__bacHORMA_2.0.V.cif
- - /cbass/CBASS_III.CBASS__HORMA.0.V.cif
- - /cbass/CBASS_III.CBASS__TRIP13.0.V.cif
+### List predicted structures
----
+::article-structure
::
-### CBASS_IV
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /cbass/CBASS_IV.CBASS__QueC.0.DF.cif
- - /cbass/CBASS_IV.CBASS__TGT.0.DF.cif
- - /cbass/CBASS_IV.CBASS__Cyclase_SMODS.0.DF.cif
- - /cbass/CBASS_IV.CBASS__2TM_type_IV.0.DF.cif
- - /cbass/CBASS_IV.CBASS__OGG.0.DF.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/charlie_gp32.md b/content/3.defense-systems/charlie_gp32.md
index 345f56cc..7c7d5150 100644
--- a/content/3.defense-systems/charlie_gp32.md
+++ b/content/3.defense-systems/charlie_gp32.md
@@ -26,27 +26,19 @@ The Charlie_gp32 system in *Mycobacterium liflandii* (GCF_000026445.2, NC_020133
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Charlie_gp32 is detected in 343 genomes (1.5 %).
-
-The system was detected in 47 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Charlie_gp32 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Charlie_gp32
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /charlie_gp32/Charlie_gp32__gp32.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/dartg.md b/content/3.defense-systems/dartg.md
index 35c3cfb9..451d5b7b 100644
--- a/content/3.defense-systems/dartg.md
+++ b/content/3.defense-systems/dartg.md
@@ -41,28 +41,19 @@ The DarTG system in *Leptodesmis sichuanensis* (GCF_021379005.1, NZ_CP075171) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the DarTG is detected in 952 genomes (4.17 %).
-
-The system was detected in 386 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the DarTG system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### DarTG
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /dartg/DarTG.DarTG_DarT.0.DF.cif
- - /dartg/DarTG.DarTG_DarG.0.DF.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/dazbog.md b/content/3.defense-systems/dazbog.md
index b8b0edd3..bf2b202e 100644
--- a/content/3.defense-systems/dazbog.md
+++ b/content/3.defense-systems/dazbog.md
@@ -36,40 +36,19 @@ The Dazbog system in *Cyanobium gracile* (GCF_000316515.1, NC_019675) is compose
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Dazbog is detected in 55 genomes (0.24 %).
-
-The system was detected in 50 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Dazbog system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
+::article-system-distribution-plot
+::
## Structure
-### Dazbog
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /dazbog/Dazbog.Dazbog__DzbA.1.V.cif
- - /dazbog/Dazbog.Dazbog__DzbB.1.V.cif
+### List predicted structures
----
+::article-structure
::
-##### Example 2
+### pDockQ matrix
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /dazbog/Dazbog.Dazbog__DzbA.1.V.cif
- - /dazbog/Dazbog.Dazbog__DzbB.1.V.cif
-
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/dctpdeaminase.md b/content/3.defense-systems/dctpdeaminase.md
index b09fc6a9..fc05d4b3 100644
--- a/content/3.defense-systems/dctpdeaminase.md
+++ b/content/3.defense-systems/dctpdeaminase.md
@@ -41,27 +41,19 @@ The dCTPdeaminase system in *Pseudomonas entomophila* (GCF_023277925.1, NZ_CP063
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the dCTPdeaminase is detected in 501 genomes (2.2 %).
-
-The system was detected in 294 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the dCTPdeaminase system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### dCTPdeaminase
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /dctpdeaminase/dCTPdeaminase__dCTPdeaminase.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/ddmde.md b/content/3.defense-systems/ddmde.md
index b0eab052..d9fa40cd 100644
--- a/content/3.defense-systems/ddmde.md
+++ b/content/3.defense-systems/ddmde.md
@@ -23,30 +23,20 @@ The DdmDE system in *Vibrio coralliilyticus* (GCF_000772065.1, NZ_CP009617) is c
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the DdmDE is detected in 135 genomes (0.59 %).
-
-The system was detected in 50 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the DdmDE system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
+::article-system-distribution-plot
+::
## Structure
-### DdmDE
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /ddmde/DdmDE.DdmDE__DdmD.0.V.cif
- - /ddmde/DdmDE.DdmDE__DdmE.0.V.cif
+### List predicted structures
----
+::article-structure
::
+### pDockQ matrix
+
+::pdockq-matrix
+::
## Experimental validation
diff --git a/content/3.defense-systems/detocs.md b/content/3.defense-systems/detocs.md
index 70b563b2..45bca73c 100644
--- a/content/3.defense-systems/detocs.md
+++ b/content/3.defense-systems/detocs.md
@@ -56,42 +56,19 @@ The Detocs_hydrolase system in *Yersinia canariae* (GCF_009831415.1, NZ_CP043727
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Detocs is detected in 215 genomes (0.94 %).
-
-The system was detected in 128 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Detocs system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
+::article-system-distribution-plot
+::
## Structure
-### Detocs
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /detocs/Detocs__dtcC.cif
- - /detocs/Detocs__dtcB.cif
- - /detocs/Detocs__dtcA.cif
+### List predicted structures
----
+::article-structure
::
-### Detocs_hydrolase
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /detocs/Detocs_hydrolase__dtcC.cif
- - /detocs/Detocs_hydrolase__dtcB.cif
- - /detocs/Detocs_hydrolase__dtcA.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/dgtpase.md b/content/3.defense-systems/dgtpase.md
index f98bca97..ff96476a 100644
--- a/content/3.defense-systems/dgtpase.md
+++ b/content/3.defense-systems/dgtpase.md
@@ -36,27 +36,19 @@ The dGTPase system in *Citrobacter sp. RHBSTW-00986* (GCF_013783065.1, NZ_CP0562
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the dGTPase is detected in 1531 genomes (6.71 %).
-
-The system was detected in 449 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the dGTPase system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### dGTPase
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /dgtpase/dGTPase__Sp_dGTPase.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/disarm.md b/content/3.defense-systems/disarm.md
index 8dfbc5b7..923a9fc7 100644
--- a/content/3.defense-systems/disarm.md
+++ b/content/3.defense-systems/disarm.md
@@ -55,56 +55,19 @@ The DISARM_2 system in *Bacillus halotolerans* (GCF_018417515.1, NZ_CP070976) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the DISARM is detected in 298 genomes (1.31 %).
-
-The system was detected in 201 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the DISARM system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-## Structure
-### Experimentally determined structure
-From :ref{doi=10.1038/s41586-023-06855-2} in *Serratia sp*:
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /disarm/7s9v_DrmAB_1_1mer.cif
- - /disarm/7s9w_DrmAB_1_1mer_dna.cif
----
+::article-system-distribution-plot
::
-### DISARM_1
-##### Example 1
+## Structure
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /disarm/DISARM_2.DISARM__drmC.0.V.cif
- - /disarm/DISARM_2.DISARM__drmB.0.V.cif
- - /disarm/DISARM_1.DISARM__drmA.0.DF.cif
- - /disarm/DISARM_1.DISARM_1__drmMI.0.DF.cif
- - /disarm/DISARM_1.DISARM_1__drmD.0.DF.cif
+### List predicted structures
----
+::article-structure
::
-### DISARM_2
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /disarm/DISARM_1.DISARM__drmA.0.DF.cif
- - /disarm/DISARM_2.DISARM__drmC.0.V.cif
- - /disarm/DISARM_2.DISARM_2__drmMII.0.V.cif
- - /disarm/DISARM_2.DISARM__drmB.0.V.cif
- - /disarm/DISARM_2.DISARM_2__drmE.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/dnd.md b/content/3.defense-systems/dnd.md
index 29901798..0a2769df 100644
--- a/content/3.defense-systems/dnd.md
+++ b/content/3.defense-systems/dnd.md
@@ -32,50 +32,19 @@ The Dnd_ABCDEFGH system in *Shewanella acanthi* (GCF_019457475.1, NZ_CP080413) i
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Dnd is detected in 376 genomes (1.65 %).
-
-The system was detected in 237 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Dnd system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
+::article-system-distribution-plot
+::
## Structure
-### Dnd_ABCDE
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /dnd/Dnd_ABCDE.Dnd__DndD.0.DF.cif
- - /dnd/Dnd_ABCDE.Dnd__DndE.0.DF.cif
- - /dnd/Dnd_ABCDE.Dnd__DndD.0.DF.cif
- - /dnd/Dnd_ABCDE.Dnd__DndC.0.DF.cif
- - /dnd/Dnd_ABCDEFGH.Dnd__DndB.0.DF.cif
- - /dnd/Dnd_ABCDE.Dnd__DndA.0.DF.cif
+### List predicted structures
----
+::article-structure
::
-### Dnd_ABCDEFGH
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /dnd/Dnd_ABCDE.Dnd__DndA.0.DF.cif
- - /dnd/Dnd_ABCDEFGH.Dnd__DndB.0.DF.cif
- - /dnd/Dnd_ABCDE.Dnd__DndC.0.DF.cif
- - /dnd/Dnd_ABCDE.Dnd__DndD.0.DF.cif
- - /dnd/Dnd_ABCDE.Dnd__DndE.0.DF.cif
- - /dnd/Dnd_ABCDEFGH.Dnd_ABCDEFGH__DptH.0.DF.cif
- - /dnd/Dnd_ABCDEFGH.Dnd_ABCDEFGH__DptG.0.DF.cif
- - /dnd/Dnd_ABCDEFGH.Dnd_ABCDEFGH__DptF.0.DF.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/dodola.md b/content/3.defense-systems/dodola.md
index 06726599..addf6f8d 100644
--- a/content/3.defense-systems/dodola.md
+++ b/content/3.defense-systems/dodola.md
@@ -39,28 +39,19 @@ The Dodola system in *Lacrimispora saccharolytica* (GCF_000144625.1, NC_014376)
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Dodola is detected in 312 genomes (1.37 %).
-
-The system was detected in 91 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Dodola system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Dodola
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /dodola/Dodola.Dodola__DolB.0.V.cif
- - /dodola/Dodola.Dodola__DolA.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/dpd.md b/content/3.defense-systems/dpd.md
index 272ef4b4..25ac81e6 100644
--- a/content/3.defense-systems/dpd.md
+++ b/content/3.defense-systems/dpd.md
@@ -24,38 +24,19 @@ The Dpd system in *Colwellia sp. PAMC 20917* (GCF_001767295.1, NZ_CP014944) is c
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Dpd is detected in 225 genomes (0.99 %).
-
-The system was detected in 103 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Dpd system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Dpd
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /dpd/Dpd.Dpd__QueD.0.DF.cif
- - /dpd/Dpd.Dpd__DpdD.0.DF.cif
- - /dpd/Dpd.Dpd__DpdK.0.DF.cif
- - /dpd/Dpd.Dpd__DpdJ.0.DF.cif
- - /dpd/Dpd.Dpd__DpdI.0.DF.cif
- - /dpd/Dpd.Dpd__DpdH.0.DF.cif
- - /dpd/Dpd.Dpd__DpdG.0.DF.cif
- - /dpd/Dpd.Dpd__DpdF.0.DF.cif
- - /dpd/Dpd.Dpd__DpdE.0.DF.cif
- - /dpd/Dpd.Dpd__DpdB.0.DF.cif
- - /dpd/Dpd.Dpd__DpdA.0.DF.cif
- - /dpd/Dpd.Dpd__DpdC.0.DF.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/drt.md b/content/3.defense-systems/drt.md
index dc38258d..5eeceffb 100644
--- a/content/3.defense-systems/drt.md
+++ b/content/3.defense-systems/drt.md
@@ -85,117 +85,19 @@ The DRT_5 system in *Klebsiella pasteurii* (GCF_018139045.1, NZ_CP073236) is com
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the DRT is detected in 1195 genomes (5.24 %).
-
-The system was detected in 577 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the DRT system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
-
-## Structure
-### DRT6
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /drt/DRT6__DRT6.cif
-
----
+::article-system-distribution-plot
::
-### DRT7
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /drt/DRT7__DRT7.cif
-
----
-::
-### DRT8
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /drt/DRT8__DRT8.cif
-
----
-::
-### DRT9
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /drt/DRT9__DRT9.cif
----
-::
-### DRT_1
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /drt/DRT_1.DRT_1__drt1b.0.V.cif
- - /drt/DRT_1.DRT_1__drt1a.0.V.cif
-
----
-::
-### DRT_2
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /drt/DRT_2__drt2.cif
-
----
-::
-### DRT_3
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /drt/DRT_3.DRT_3__drt3b.0.V.cif
- - /drt/DRT_3.DRT_3__drt3a.0.V.cif
-
----
-::
-### DRT_4
-##### Example 1
+## Structure
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /drt/DRT_4__drt4.cif
+### List predicted structures
----
+::article-structure
::
-### DRT_5
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /drt/DRT_5__drt5.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/druantia.md b/content/3.defense-systems/druantia.md
index 64a4057a..36200b51 100644
--- a/content/3.defense-systems/druantia.md
+++ b/content/3.defense-systems/druantia.md
@@ -46,57 +46,19 @@ The Druantia_III system in *Citrobacter werkmanii* (GCF_002025225.1, NZ_CP019986
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Druantia is detected in 807 genomes (3.54 %).
-
-The system was detected in 303 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Druantia system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
+::article-system-distribution-plot
+::
## Structure
-### Druantia_I
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /druantia/Druantia_I.Druantia_I__DruA.0.V.cif
- - /druantia/Druantia_I.Druantia_I__DruB.0.V.cif
- - /druantia/Druantia_I.Druantia_I__DruC.0.V.cif
- - /druantia/Druantia_I.Druantia_I__DruD.0.V.cif
- - /druantia/Druantia_I.Druantia__DruE.0.V.cif
+### List predicted structures
----
+::article-structure
::
-### Druantia_II
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /druantia/Druantia_II.Druantia_II__DruM.0.DF.cif
- - /druantia/Druantia_II.Druantia_II__DruF.0.DF.cif
- - /druantia/Druantia_II.Druantia_II__DruG.0.DF.cif
- - /druantia/Druantia_II.Druantia__DruE_2.0.DF.cif
-
----
-::
-### Druantia_III
-##### Example 1
+### pDockQ matrix
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /druantia/Druantia_III.Druantia_III__DruH.0.DF.cif
- - /druantia/Druantia_III.Druantia__DruE_3.0.DF.cif
-
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/dsr.md b/content/3.defense-systems/dsr.md
index b8e0d950..49f678a3 100644
--- a/content/3.defense-systems/dsr.md
+++ b/content/3.defense-systems/dsr.md
@@ -32,38 +32,19 @@ The Dsr_II system in *Deinococcus deserti* (GCF_000020685.1, NC_012526) is compo
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Dsr is detected in 246 genomes (1.08 %).
-
-The system was detected in 162 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Dsr system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
+::article-system-distribution-plot
+::
## Structure
-### Dsr_I
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /dsr/Dsr_I__Dsr1.cif
+### List predicted structures
----
+::article-structure
::
-### Dsr_II
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /dsr/Dsr_II__Dsr2.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/eleos.md b/content/3.defense-systems/eleos.md
index 11b7288d..6565e9c6 100644
--- a/content/3.defense-systems/eleos.md
+++ b/content/3.defense-systems/eleos.md
@@ -39,40 +39,19 @@ The Eleos system in *Synechococcus sp. CBW1002* (GCF_015840915.1, NZ_CP060398) i
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Eleos is detected in 414 genomes (1.82 %).
-
-The system was detected in 223 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Eleos system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
-
-## Structure
-### Experimentaly determined structure
-From :ref{doi=10.1371/journal.pone.0107211} in *Escherichia coli* (ETEC) strain H10407:
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /eleos/4aur_LeoA_1mer.pdb
----
+::article-system-distribution-plot
::
+## Structure
+### List predicted structures
-### Eleos
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /eleos/Eleos.Eleos__LeoBC.0.V.cif
- - /eleos/Eleos.Eleos__LeoA.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/fs_giy_yig.md b/content/3.defense-systems/fs_giy_yig.md
index 618bd181..146a696a 100644
--- a/content/3.defense-systems/fs_giy_yig.md
+++ b/content/3.defense-systems/fs_giy_yig.md
@@ -37,27 +37,19 @@ The FS_GIY_YIG system in *Klebsiella pneumoniae* (GCF_021389995.1, NZ_CP089989)
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the FS_GIY_YIG is detected in 159 genomes (0.7 %).
-
-The system was detected in 87 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the FS_GIY_YIG system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### FS_GIY_YIG
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /fs_giy_yig/FS_GIY_YIG__GIY_YIG.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/fs_hepn_tm.md b/content/3.defense-systems/fs_hepn_tm.md
index 2f22ea48..98e20185 100644
--- a/content/3.defense-systems/fs_hepn_tm.md
+++ b/content/3.defense-systems/fs_hepn_tm.md
@@ -14,23 +14,19 @@ relevantAbstracts:
## Distribution of the system among prokaryotes
-::info
-This section is empty
+::article-system-distribution-plot
::
-
## Structure
-### FS_HEPN_TM
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /fs_hepn_tm/FS_HEPN_TM__TM.cif
- - /fs_hepn_tm/FS_HEPN_TM__HEPN.cif
+### List predicted structures
----
+::article-structure
+::
+
+### pDockQ matrix
+
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/fs_hp.md b/content/3.defense-systems/fs_hp.md
index 14b81801..cbd856b3 100644
--- a/content/3.defense-systems/fs_hp.md
+++ b/content/3.defense-systems/fs_hp.md
@@ -37,27 +37,19 @@ The FS_HP system in *Escherichia coli* (GCF_016944735.1, NZ_CP063511) is compose
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the FS_HP is detected in 93 genomes (0.41 %).
-
-The system was detected in 29 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the FS_HP system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### FS_HP
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /fs_hp/FS_HP__HP.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/fs_hp_sdh_sah.md b/content/3.defense-systems/fs_hp_sdh_sah.md
index 7eb720c5..1afc1f87 100644
--- a/content/3.defense-systems/fs_hp_sdh_sah.md
+++ b/content/3.defense-systems/fs_hp_sdh_sah.md
@@ -27,28 +27,19 @@ The FS_HP_SDH_sah system in *Escherichia coli* (GCF_904831805.1, NZ_LR882990) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the FS_HP_SDH_sah is detected in 6 genomes (0.03 %).
-
-The system was detected in 3 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the FS_HP_SDH_sah system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### FS_HP_SDH_sah
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /fs_hp_sdh_sah/FS_HP_SDH_sah__SDH_sah.cif
- - /fs_hp_sdh_sah/FS_HP_SDH_sah__HP.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/fs_hsdr_like.md b/content/3.defense-systems/fs_hsdr_like.md
index ef1367d9..51e83187 100644
--- a/content/3.defense-systems/fs_hsdr_like.md
+++ b/content/3.defense-systems/fs_hsdr_like.md
@@ -38,38 +38,19 @@ The FS_HsdR_like system in *Klebsiella pneumoniae* (GCF_009661415.2, NZ_CP062997
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the FS_HsdR_like is detected in 39 genomes (0.17 %).
-
-The system was detected in 15 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the FS_HsdR_like system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
+::article-system-distribution-plot
+::
## Structure
-### FS_HsdR_like_HP-plddts_74.75219.html
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /fs_hsdr_like/FS_HsdR_like_HP.cif
+### List predicted structures
----
+::article-structure
::
-### FS_HsdR_like_HdrR-plddts_88.7069.html
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /fs_hsdr_like/FS_HsdR_like_HdrR.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/fs_sma.md b/content/3.defense-systems/fs_sma.md
index 3f3f87bb..78d02dfa 100644
--- a/content/3.defense-systems/fs_sma.md
+++ b/content/3.defense-systems/fs_sma.md
@@ -34,27 +34,19 @@ The Sma system in *Staphylococcus aureus* (GCF_022869625.1, NZ_CP064365) is comp
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Sma is detected in 578 genomes (2.53 %).
-
-The system was detected in 20 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the FS_Sma system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### FS_Sma
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /fs_sma/FS_Sma__Sma.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/gabija.md b/content/3.defense-systems/gabija.md
index 32edba4e..a2823935 100644
--- a/content/3.defense-systems/gabija.md
+++ b/content/3.defense-systems/gabija.md
@@ -45,41 +45,19 @@ The Gabija system in *Roseomonas fluvialis* (GCF_022846615.1, NZ_AP025637) is co
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Gabija is detected in 2999 genomes (13.15 %).
-
-The system was detected in 1375 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Gabija system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
+::article-system-distribution-plot
+::
## Structure
-### Experimentaly determined structure
-From :ref{doi=10.1038/s41586-023-06855-2} in *Bacillus cereus* VD045:
+### List predicted structures
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /gabija/8sm3-assembly1_BcGajAB_4_4mer.cif
- - /gabija/8u7i-assembly1_BcGajAB_4_4mer_gad1.cif
----
+::article-structure
::
-### Gabija
-##### Example 1
+### pDockQ matrix
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /gabija/Gabija.Gabija__GajA.0.V.cif
- - /gabija/Gabija.Gabija_GajB.0.V.cif
-
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/gao_ape.md b/content/3.defense-systems/gao_ape.md
index ac95b51b..c913056f 100644
--- a/content/3.defense-systems/gao_ape.md
+++ b/content/3.defense-systems/gao_ape.md
@@ -38,27 +38,19 @@ The Gao_Ape system in *Enterobacter mori* (GCF_018638795.1, NZ_CP071064) is comp
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Gao_Ape is detected in 76 genomes (0.33 %).
-
-The system was detected in 45 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Gao_Ape system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Gao_Ape
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /gao_ape/Gao_Ape__ApeA.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/gao_her.md b/content/3.defense-systems/gao_her.md
index 4d8cf20b..1a28df60 100644
--- a/content/3.defense-systems/gao_her.md
+++ b/content/3.defense-systems/gao_her.md
@@ -35,65 +35,19 @@ The Gao_Her_SIR system in *Xanthomonas citri* (GCF_018831325.1, NZ_CP029270) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Gao_Her is detected in 231 genomes (1.01 %).
-
-The system was detected in 134 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Gao_Her system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
-
-## Structure
-
-### Experimentaly determined structure
-
-From :ref{doi=10.1016/j.molcel.2023.11.010} in *Escherichia coli*:
-
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /gao_her/8j4u_EcHerA_SIR2_6_12mer.cif
----
-::
-
-From :ref{doi=10.1016/j.molcel.2023.11.007} in *Escherichia coli*:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /gao_her/8sxx_EcSIR2_12mer.pdb
- - /gao_her/8sxx_EcHerA_SIR2_5_12mer.cif
- - /gao_her/8uae_EcHerA_SIR2_6_12mer_atpgamas.cif
- - /gao_her/8uaf_EcHerA_SIR2_6_12mer_nad.cif
----
+::article-system-distribution-plot
::
-### Gao_Her_DUF
-##### Example 1
+## Structure
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /gao_her/Gao_Her_DUF.Gao_Her_DUF__DUF4297.0.V.cif
- - /gao_her/Gao_Her_DUF.Gao_Her_DUF__HerA_DUF.0.V.cif
+### List predicted structures
----
+::article-structure
::
-### Gao_Her_SIR
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /gao_her/Gao_Her_SIR.Gao_Her_SIR__HerA_SIR2.0.V.cif
- - /gao_her/Gao_Her_SIR.Gao_Her_SIR__SIR2.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/gao_hhe.md b/content/3.defense-systems/gao_hhe.md
index 14eeda07..def0be67 100644
--- a/content/3.defense-systems/gao_hhe.md
+++ b/content/3.defense-systems/gao_hhe.md
@@ -36,27 +36,19 @@ The Gao_Hhe system in *Thioalkalivibrio paradoxus* (GCF_000227685.2, NZ_CP007029
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Gao_Hhe is detected in 276 genomes (1.21 %).
-
-The system was detected in 56 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Gao_Hhe system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Gao_Hhe
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /gao_hhe/Gao_Hhe__HheA.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/gao_iet.md b/content/3.defense-systems/gao_iet.md
index 7b059d99..445195a8 100644
--- a/content/3.defense-systems/gao_iet.md
+++ b/content/3.defense-systems/gao_iet.md
@@ -38,28 +38,19 @@ The Gao_Iet system in *Salmonella sp. SJTUF14076* (GCF_015534835.1, NZ_CP064674)
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Gao_Iet is detected in 389 genomes (1.71 %).
-
-The system was detected in 185 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Gao_Iet system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Gao_Iet
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /gao_iet/Gao_Iet.Gao_Iet__IetA.0.V.cif
- - /gao_iet/Gao_Iet.Gao_Iet__IetS.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/gao_mza.md b/content/3.defense-systems/gao_mza.md
index 7465559a..a8ec68d0 100644
--- a/content/3.defense-systems/gao_mza.md
+++ b/content/3.defense-systems/gao_mza.md
@@ -36,31 +36,19 @@ The Gao_Mza system in *Massilia sp. Se16.2.3* (GCF_014171595.1, NZ_CP050451) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Gao_Mza is detected in 68 genomes (0.3 %).
-
-The system was detected in 32 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Gao_Mza system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Gao_Mza
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /gao_mza/Gao_Mza.Gao_Mza__MzaE.0.V.cif
- - /gao_mza/Gao_Mza.Gao_Mza__MzaD.0.V.cif
- - /gao_mza/Gao_Mza.Gao_Mza__MzaC.0.V.cif
- - /gao_mza/Gao_Mza.Gao_Mza__MzaB.0.V.cif
- - /gao_mza/Gao_Mza.Gao_Mza__MzaA.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/gao_ppl.md b/content/3.defense-systems/gao_ppl.md
index 5eb5f79a..3bc45fb5 100644
--- a/content/3.defense-systems/gao_ppl.md
+++ b/content/3.defense-systems/gao_ppl.md
@@ -37,27 +37,19 @@ The Gao_Ppl system in *Enterobacter sp. E76* (GCF_008931465.1, NZ_CP042499) is c
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Gao_Ppl is detected in 276 genomes (1.21 %).
-
-The system was detected in 104 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Gao_Ppl system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Gao_Ppl
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /gao_ppl/Gao_Ppl__PplA.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/gao_qat.md b/content/3.defense-systems/gao_qat.md
index 51c8c19f..284ba815 100644
--- a/content/3.defense-systems/gao_qat.md
+++ b/content/3.defense-systems/gao_qat.md
@@ -27,30 +27,19 @@ The Gao_Qat system in *Ralstonia wenshanensis* (GCF_021173085.1, NZ_CP076413) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Gao_Qat is detected in 621 genomes (2.72 %).
-
-The system was detected in 267 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Gao_Qat system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Gao_Qat
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /gao_qat/Gao_Qat.Gao_Qat__QatA.0.V.cif
- - /gao_qat/Gao_Qat.Gao_Qat__QatB.0.V.cif
- - /gao_qat/Gao_Qat.Gao_Qat__QatC.0.V.cif
- - /gao_qat/Gao_Qat.Gao_Qat__QatD.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/gao_rl.md b/content/3.defense-systems/gao_rl.md
index 3e9c6fc7..92cc2f0b 100644
--- a/content/3.defense-systems/gao_rl.md
+++ b/content/3.defense-systems/gao_rl.md
@@ -38,30 +38,19 @@ The Gao_RL system in *Methylocystis heyeri* (GCF_004802635.2, NZ_CP046053) is co
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Gao_RL is detected in 131 genomes (0.57 %).
-
-The system was detected in 74 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Gao_RL system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Gao_RL
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /gao_rl/Gao_RL.Gao_RL__RL_A.0.V.cif
- - /gao_rl/Gao_RL.Gao_RL__RL_D.0.V.cif
- - /gao_rl/Gao_RL.Gao_RL__RL_B.0.V.cif
- - /gao_rl/Gao_RL.Gao_RL__RL_C.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/gao_tery.md b/content/3.defense-systems/gao_tery.md
index 315610c6..5bceeea4 100644
--- a/content/3.defense-systems/gao_tery.md
+++ b/content/3.defense-systems/gao_tery.md
@@ -26,29 +26,19 @@ The Gao_TerY system in *Arachidicoccus terrestris* (GCF_020042345.1, NZ_CP083387
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Gao_TerY is detected in 126 genomes (0.55 %).
-
-The system was detected in 74 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Gao_TerY system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Gao_TerY
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /gao_tery/Gao_TerY.Gao_TerY__TerYA.0.V.cif
- - /gao_tery/Gao_TerY.Gao_TerY__TerYB.0.V.cif
- - /gao_tery/Gao_TerY.Gao_TerY__TerYC.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/gao_tmn.md b/content/3.defense-systems/gao_tmn.md
index 75f1ad68..66959396 100644
--- a/content/3.defense-systems/gao_tmn.md
+++ b/content/3.defense-systems/gao_tmn.md
@@ -37,27 +37,19 @@ The Gao_Tmn system in *Pectobacterium carotovorum* (GCF_009931215.1, NZ_CP034237
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Gao_Tmn is detected in 394 genomes (1.73 %).
-
-The system was detected in 84 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Gao_Tmn system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Gao_Tmn
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /gao_tmn/Gao_Tmn__TmnA.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/gao_upx.md b/content/3.defense-systems/gao_upx.md
index 5a1c9124..b5d09991 100644
--- a/content/3.defense-systems/gao_upx.md
+++ b/content/3.defense-systems/gao_upx.md
@@ -36,27 +36,19 @@ The Gao_Upx system in *Serratia sp. JSRIV001* (GCF_019968745.1, NZ_CP074147) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Gao_Upx is detected in 39 genomes (0.17 %).
-
-The system was detected in 33 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Gao_Upx system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Gao_Upx
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /gao_upx/Gao_Upx__UpxA.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/gaps1.md b/content/3.defense-systems/gaps1.md
index 15b49aa0..a4db6c6f 100644
--- a/content/3.defense-systems/gaps1.md
+++ b/content/3.defense-systems/gaps1.md
@@ -37,27 +37,19 @@ The GAPS1 system in *Hydrogenophaga sp. BPS33* (GCF_009859475.1, NZ_CP044549) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the GAPS1 is detected in 434 genomes (1.9 %).
-
-The system was detected in 56 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the GAPS1 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### GAPS1
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /gaps1/GAPS1__GAPS1.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/gaps2.md b/content/3.defense-systems/gaps2.md
index 83bb496f..eabc3489 100644
--- a/content/3.defense-systems/gaps2.md
+++ b/content/3.defense-systems/gaps2.md
@@ -35,27 +35,19 @@ The GAPS2 system in *Mannheimia sp. USDA-ARS-USMARC-1261* (GCF_000521605.1, NZ_C
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the GAPS2 is detected in 725 genomes (3.18 %).
-
-The system was detected in 208 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the GAPS2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### GAPS2
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /gaps2/GAPS2__GAPS2.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/gaps4.md b/content/3.defense-systems/gaps4.md
index 065ccb14..9040bf81 100644
--- a/content/3.defense-systems/gaps4.md
+++ b/content/3.defense-systems/gaps4.md
@@ -36,29 +36,19 @@ The GAPS4 system in *Hafnia alvei* (GCF_902387815.1, NZ_LR699008) is composed of
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the GAPS4 is detected in 118 genomes (0.52 %).
-
-The system was detected in 74 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the GAPS4 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
+::article-system-distribution-plot
+::
## Structure
-### GAPS4
-##### Example 1
+### List predicted structures
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /gaps4/GAPS4__GAPS4a.cif
- - /gaps4/GAPS4__GAPS4b.cif
+::article-structure
+::
----
+### pDockQ matrix
+
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/gaps6.md b/content/3.defense-systems/gaps6.md
index 22188f4c..968bc7f8 100644
--- a/content/3.defense-systems/gaps6.md
+++ b/content/3.defense-systems/gaps6.md
@@ -38,30 +38,19 @@ The GAPS6 system in *Escherichia coli* (GCF_013372365.1, NZ_CP054227) is compose
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the GAPS6 is detected in 50 genomes (0.22 %).
-
-The system was detected in 33 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the GAPS6 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
+::article-system-distribution-plot
+::
## Structure
-### GAPS6
+### List predicted structures
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /gaps6/GAPS6__GAPS6a.cif
- - /gaps6/GAPS6__GAPS6b.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/gasdermin.md b/content/3.defense-systems/gasdermin.md
index 277462ff..82296b66 100644
--- a/content/3.defense-systems/gasdermin.md
+++ b/content/3.defense-systems/gasdermin.md
@@ -39,32 +39,19 @@ The GasderMIN system in *Flavobacterium johnsoniae* (GCF_000016645.1, NC_009441)
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the GasderMIN is detected in 27 genomes (0.12 %).
-
-The system was detected in 26 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the GasderMIN system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### GasderMIN
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /gasdermin/GasderMIN__bGSDM.cif
- - /gasdermin/GasderMIN__Protease1.cif
- - /gasdermin/GasderMIN__Protease2.cif
- - /gasdermin/GasderMIN__ATPase.cif
- - /gasdermin/GasderMIN__Protease.cif
- - /gasdermin/GasderMIN__bGSDM1.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/hachiman.md b/content/3.defense-systems/hachiman.md
index 275b7110..00d8159c 100644
--- a/content/3.defense-systems/hachiman.md
+++ b/content/3.defense-systems/hachiman.md
@@ -38,28 +38,19 @@ The Hachiman system in *Vibrio metschnikovii* (GCF_009763925.1, NZ_CP046822) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Hachiman is detected in 1256 genomes (5.51 %).
-
-The system was detected in 541 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Hachiman system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Hachiman
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /hachiman/Hachiman.Hachiman__HamB.0.V.cif
- - /hachiman/Hachiman.Hachiman__HamA.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/hna.md b/content/3.defense-systems/hna.md
index d45fc91e..1d9750dd 100644
--- a/content/3.defense-systems/hna.md
+++ b/content/3.defense-systems/hna.md
@@ -27,27 +27,19 @@ The Hna system in *Aggregatimonas sangjinii* (GCF_005943945.1, NZ_CP040710) is c
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Hna is detected in 493 genomes (2.16 %).
-
-The system was detected in 305 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Hna system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Hna
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /hna/Hna__Hna.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/isg15-like.md b/content/3.defense-systems/isg15-like.md
index 083a59c0..e0e5b94c 100644
--- a/content/3.defense-systems/isg15-like.md
+++ b/content/3.defense-systems/isg15-like.md
@@ -39,30 +39,19 @@ The ISG15-like system in *Caulobacter segnis* (GCF_023935105.1, NZ_CP096040) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the ISG15-like is detected in 43 genomes (0.19 %).
-
-The system was detected in 39 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the ISG15-like system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### ISG15-like
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.cif
- - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.cif
- - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.cif
- - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/jukab.md b/content/3.defense-systems/jukab.md
index 95d1c407..b45a1f84 100644
--- a/content/3.defense-systems/jukab.md
+++ b/content/3.defense-systems/jukab.md
@@ -40,28 +40,19 @@ The JukAB system in *Kosakonia oryzae* (GCF_020544365.1, NZ_CP065358) is compose
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the JukAB is detected in 133 genomes (0.58 %).
-
-The system was detected in 50 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the JukAB system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### JukAB
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /jukab/JukAB__JukB.cif
- - /jukab/JukAB__JukA.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/kiwa.md b/content/3.defense-systems/kiwa.md
index 21d26d74..03dc0886 100644
--- a/content/3.defense-systems/kiwa.md
+++ b/content/3.defense-systems/kiwa.md
@@ -38,28 +38,19 @@ The Kiwa system in *Dickeya zeae* (GCF_019464635.1, NZ_CP040817) is composed of
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Kiwa is detected in 1095 genomes (4.8 %).
-
-The system was detected in 382 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Kiwa system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Kiwa
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /kiwa/Kiwa.Kiwa__KwaB.0.V.cif
- - /kiwa/Kiwa.Kiwa__KwaA.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/lamassu-fam.md b/content/3.defense-systems/lamassu-fam.md
index e1820da0..d0a893c8 100644
--- a/content/3.defense-systems/lamassu-fam.md
+++ b/content/3.defense-systems/lamassu-fam.md
@@ -87,148 +87,19 @@ The Lamassu-Sir2 system in *Enterococcus faecalis* (GCF_023375525.1, NZ_CP091235
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Lamassu-Fam is detected in 2867 genomes (12.57 %).
-
-The system was detected in 1220 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Lamassu-Fam system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
-
-## Structure
-### Lamassu-Amidase
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /lamassu-fam/Lamassu-Amidase.Lamassu-Fam__LmuA_effector_Amidase.0.DF.cif
- - /lamassu-fam/Lamassu-Amidase.Lamassu-Fam__LmuB_SMC_Amidase.0.DF.cif
-
----
-::
-### Lamassu-Cap4_nuclease
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuA_effector_Cap4_nuclease_II.0.DF.cif
- - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuC_acc_Cap4_nuclease.0.DF.cif
- - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II.0.DF.cif
-
----
-::
-##### Example 2
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuA_effector_Cap4_nuclease.1.DF.cif
- - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam_undetected_LmuC.1.DF.cif
- - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuB_SMC_Cap4_nuclease.1.DF.cif
-
----
-::
-### Lamassu-FMO
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /lamassu-fam/Lamassu-FMO.Lamassu-Fam__LmuB_SMC_FMO.0.DF.cif
- - /lamassu-fam/Lamassu-FMO.Lamassu-Fam__LmuC_acc_FMO.0.DF.cif
- - /lamassu-fam/Lamassu-FMO.Lamassu-Fam__LmuA_effector_FMO.0.DF.cif
-
----
+::article-system-distribution-plot
::
-### Lamassu-Fam_Hydrolase_Protease
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /lamassu-fam/Lamassu-Fam_Hydrolase_Protease.Lamassu-Fam__LmuA_effector_Hydrolase.0.V.cif
- - /lamassu-fam/Lamassu-Fam_Hydrolase_Protease.Lamassu-Fam__LmuA_effector_Protease.0.V.cif
- - /lamassu-fam/Lamassu-Fam_Hydrolase_Protease.Lamassu-Fam__LmuC_acc_hydrolase_protease.0.V.cif
- - /lamassu-fam/Lamassu-Fam_Hydrolase_Protease.Lamassu-Fam__LmuB_SMC_Hydrolase_protease.0.V.cif
-
----
-::
-### Lamassu-Fam_Mrr
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /lamassu-fam/Lamassu-Fam_Mrr.Lamassu-Fam__LmuA_effector_Mrr.0.V.cif
- - /lamassu-fam/Lamassu-Fam_Mrr.Lamassu-Fam__LmuC_acc_Mrr.0.V.cif
- - /lamassu-fam/Lamassu-Fam_Mrr.Lamassu-Fam__LmuB_SMC_Mrr.0.V.cif
-
----
-::
-### Lamassu-Fam_PDDEXK
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuA_effector_PDDEXK.0.V.cif
- - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuB_SMC_PDDEXK.0.V.cif
- - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuC_acc_PDDEXK.0.V.cif
- - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuC_acc_PDDEXK.0.V.cif
- - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuB_SMC_PDDEXK.0.V.cif
- - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuA_effector_PDDEXK.0.V.cif
----
-::
-### Lamassu-Hypothetical
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /lamassu-fam/Lamassu-Hypothetical.Lamassu-Fam__LmuB_SMC_hypothetical.0.DF.cif
- - /lamassu-fam/Lamassu-Hypothetical.Lamassu-Fam__LmuC_acc_hypothetical.0.DF.cif
- - /lamassu-fam/Lamassu-Hypothetical.Lamassu-Fam__LmuA_effector_hypothetical.0.DF.cif
-
----
-::
-### Lamassu-Lipase
-##### Example 1
+## Structure
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /lamassu-fam/Lamassu-Lipase.Lamassu-Fam__LmuB_SMC_Lipase.0.DF.cif
- - /lamassu-fam/Lamassu-Lipase.Lamassu-Fam__LmuC_acc_Lipase.0.DF.cif
- - /lamassu-fam/Lamassu-Lipase.Lamassu-Fam__LmuA_effector_Lipase.0.DF.cif
+### List predicted structures
----
+::article-structure
::
-### Lamassu-Sir2
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /lamassu-fam/Lamassu-Sir2.Lamassu-Fam__LmuB_SMC_Sir2.0.DF.cif
- - /lamassu-fam/Lamassu-Sir2.Lamassu-Fam__LmuC_acc_Sir2.0.DF.cif
- - /lamassu-fam/Lamassu-Sir2.Lamassu-Fam__LmuA_effector_Sir2.0.DF.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/lit.md b/content/3.defense-systems/lit.md
index f1acccaa..1c476011 100644
--- a/content/3.defense-systems/lit.md
+++ b/content/3.defense-systems/lit.md
@@ -42,27 +42,19 @@ The Lit system in *Klebsiella pneumoniae* (GCF_002180175.1, NZ_CP021686) is comp
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Lit is detected in 222 genomes (0.97 %).
-
-The system was detected in 78 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Lit system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Lit
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /lit/Lit__Lit.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/mads.md b/content/3.defense-systems/mads.md
index 601be4c1..19dd0c7b 100644
--- a/content/3.defense-systems/mads.md
+++ b/content/3.defense-systems/mads.md
@@ -27,33 +27,19 @@ The MADS system in *Pseudomonas otitidis* (GCF_019879085.1, NZ_CP082244) is comp
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the MADS is detected in 72 genomes (0.32 %).
-
-The system was detected in 63 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the MADS system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### MADS
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /mads/MADS__mad8.cif
- - /mads/MADS__mad7.cif
- - /mads/MADS__mad4.cif
- - /mads/MADS__mad3.cif
- - /mads/MADS__mad1.cif
- - /mads/MADS__mad5.cif
- - /mads/MADS__mad2.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/mazef.md b/content/3.defense-systems/mazef.md
index fd693320..8d770bbc 100644
--- a/content/3.defense-systems/mazef.md
+++ b/content/3.defense-systems/mazef.md
@@ -27,18 +27,19 @@ The MazEF system in *Pantoea vagans* (GCF_004792415.1, NZ_CP038853) is composed
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the MazEF is detected in 4457 genomes (19.55 %).
+::article-system-distribution-plot
+::
-The system was detected in 993 different species.
+## Structure
-{max-width=750px}
+### List predicted structures
-Proportion of genome encoding the MazEF system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-structure
+::
-## Structure
+### pDockQ matrix
-::info
-This section is empty
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/menshen.md b/content/3.defense-systems/menshen.md
index 32158af1..800defc4 100644
--- a/content/3.defense-systems/menshen.md
+++ b/content/3.defense-systems/menshen.md
@@ -38,29 +38,19 @@ The Menshen system in *Streptomyces marincola* (GCF_020410765.1, NZ_CP084541) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Menshen is detected in 430 genomes (1.89 %).
-
-The system was detected in 263 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Menshen system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Menshen
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /menshen/Menshen.Menshen__NsnA.0.V.cif
- - /menshen/Menshen.Menshen__NsnB.0.V.cif
- - /menshen/Menshen.Menshen__NsnC.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/mmb_gp29_gp30.md b/content/3.defense-systems/mmb_gp29_gp30.md
index edef2f74..ec67c707 100644
--- a/content/3.defense-systems/mmb_gp29_gp30.md
+++ b/content/3.defense-systems/mmb_gp29_gp30.md
@@ -32,28 +32,19 @@ The MMB_gp29_gp30 system in *Mycolicibacterium insubricum* (GCF_010731615.1, NZ_
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the MMB_gp29_gp30 is detected in 5 genomes (0.02 %).
-
-The system was detected in 4 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the MMB_gp29_gp30 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### MMB_gp29_gp30
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /mmb_gp29_gp30/MMB_gp29_gp30__gp29.cif
- - /mmb_gp29_gp30/MMB_gp29_gp30__gp30.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/mok_hok_sok.md b/content/3.defense-systems/mok_hok_sok.md
index 4dbdd5f4..3aba6271 100644
--- a/content/3.defense-systems/mok_hok_sok.md
+++ b/content/3.defense-systems/mok_hok_sok.md
@@ -42,27 +42,19 @@ The Mok_Hok_Sok system in *Escherichia fergusonii* (GCF_013819565.1, NZ_CP057221
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Mok_Hok_Sok is detected in 1656 genomes (7.26 %).
-
-The system was detected in 83 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Mok_Hok_Sok system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Mok_Hok_Sok
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /mok_hok_sok/Mok_Hok_Sok__Hok.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/mokosh.md b/content/3.defense-systems/mokosh.md
index 57e54f97..10c35dc9 100644
--- a/content/3.defense-systems/mokosh.md
+++ b/content/3.defense-systems/mokosh.md
@@ -57,48 +57,19 @@ The Mokosh_Type_I_E system in *Planococcus faecalis* (GCF_002009235.1, NZ_CP0194
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Mokosh is detected in 1607 genomes (7.05 %).
-
-The system was detected in 577 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Mokosh system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
+::article-system-distribution-plot
+::
## Structure
-### Mokosh_TypeI
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /mokosh/Mokosh_TypeI.Mokosh_TypeI__MkoB.0.V.cif
+### List predicted structures
----
+::article-structure
::
-##### Example 2
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /mokosh/Mokosh_TypeI.Mokosh_TypeI__MkoB.0.V.cif
-
----
-::
-### Mokosh_TypeII
-##### Example 1
+### pDockQ matrix
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /mokosh/Mokosh_TypeII__MkoC.cif
-
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/mqsrac.md b/content/3.defense-systems/mqsrac.md
index 7342d996..718a2290 100644
--- a/content/3.defense-systems/mqsrac.md
+++ b/content/3.defense-systems/mqsrac.md
@@ -35,16 +35,20 @@ The MqsRAC system in *Shigella dysenteriae* (GCF_002949935.1, NZ_CP026827) is co
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the MqsRAC is detected in 26 genomes (0.11 %).
+::article-system-distribution-plot
+::
-The system was detected in 20 different species.
+## Structure
-{max-width=750px}
+### List predicted structures
-Proportion of genome encoding the MqsRAC system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-structure
+::
+### pDockQ matrix
-## Structure
+::pdockq-matrix
+::
## Experimental validation
<mermaid>
diff --git a/content/3.defense-systems/nhi.md b/content/3.defense-systems/nhi.md
index cc0f4a95..0d121aa8 100644
--- a/content/3.defense-systems/nhi.md
+++ b/content/3.defense-systems/nhi.md
@@ -39,27 +39,19 @@ The Nhi system in *Staphylococcus sp. MZ9* (GCF_018622975.1, NZ_CP076029) is com
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Nhi is detected in 199 genomes (0.87 %).
-
-The system was detected in 61 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Nhi system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Nhi
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /nhi/Nhi__Nhi.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/nixi.md b/content/3.defense-systems/nixi.md
index 697c4e6c..e019f2e8 100644
--- a/content/3.defense-systems/nixi.md
+++ b/content/3.defense-systems/nixi.md
@@ -34,27 +34,19 @@ The NixI system in *Apilactobacillus kunkeei* (GCF_001314945.1, NZ_CP012920) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the NixI is detected in 8 genomes (0.04 %).
-
-The system was detected in 5 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the NixI system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### NixI
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /nixi/NixI__NixI.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/nlr.md b/content/3.defense-systems/nlr.md
index fbe157b7..54679b58 100644
--- a/content/3.defense-systems/nlr.md
+++ b/content/3.defense-systems/nlr.md
@@ -46,38 +46,19 @@ The NLR_like_bNACHT09 system in *Parabacteroides johnsonii* (GCF_020735865.1, NZ
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the NLR is detected in 453 genomes (1.99 %).
-
-The system was detected in 205 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the NLR system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
+::article-system-distribution-plot
+::
## Structure
-### NLR_like_bNACHT01
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /nlr/NLR_like_bNACHT01__NLR_like_bNACHT01.cif
+### List predicted structures
----
+::article-structure
::
-### NLR_like_bNACHT09
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /nlr/NLR_like_bNACHT09__NLR_like_bNACHT09.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/old_exonuclease.md b/content/3.defense-systems/old_exonuclease.md
index 23beca38..b4721d9d 100644
--- a/content/3.defense-systems/old_exonuclease.md
+++ b/content/3.defense-systems/old_exonuclease.md
@@ -37,27 +37,19 @@ The Old_exonuclease system in *Shewanella xiamenensis* (GCF_022453805.1, NZ_CP09
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Old_exonuclease is detected in 102 genomes (0.45 %).
-
-The system was detected in 56 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Old_exonuclease system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Old_exonuclease
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /old_exonuclease/Old_exonuclease__Old_exonuclease.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/olokun.md b/content/3.defense-systems/olokun.md
index 2ddd2092..1bdf04ff 100644
--- a/content/3.defense-systems/olokun.md
+++ b/content/3.defense-systems/olokun.md
@@ -43,28 +43,19 @@ The Olokun system in *Klebsiella quasipneumoniae* (GCF_015286025.1, NZ_CP063902)
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Olokun is detected in 242 genomes (1.06 %).
-
-The system was detected in 137 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Olokun system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Olokun
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /olokun/Olokun.Olokun__OloA.0.V.cif
- - /olokun/Olokun.Olokun__OloB.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pago.md b/content/3.defense-systems/pago.md
index 5f012c98..d965ddb2 100644
--- a/content/3.defense-systems/pago.md
+++ b/content/3.defense-systems/pago.md
@@ -89,37 +89,19 @@ The pAgo_SPARTA system in *Roseivivax sp. THAF30* (GCF_009363575.1, NZ_CP045389)
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the pAgo is detected in 575 genomes (2.52 %).
-
-The system was detected in 464 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the pAgo system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
+::article-system-distribution-plot
+::
## Structure
-### pAgo
+### List predicted structures
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pago/pAgo__pAgo_LongA.cif
- - /pago/pAgo__pAgo_LongB.cif
- - /pago/pAgo__pAgo_S1A.cif
- - /pago/pAgo__SIR2APAZ.cif
- - /pago/pAgo__pAgo_S1B.cif
- - /pago/pAgo__XAPAZ.cif
- - /pago/pAgo__pAgo_S2B.cif
- - /pago/pAgo__TIRAPAZ.cif
- - /pago/pAgo__pAgo_SPARTA.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/panchino_gp28.md b/content/3.defense-systems/panchino_gp28.md
index 5600bdc4..a42ec3d1 100644
--- a/content/3.defense-systems/panchino_gp28.md
+++ b/content/3.defense-systems/panchino_gp28.md
@@ -35,27 +35,19 @@ The Panchino_gp28 system in *Burkholderia pseudomallei* (GCF_018228585.1, NZ_CP0
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Panchino_gp28 is detected in 16 genomes (0.07 %).
-
-The system was detected in 5 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Panchino_gp28 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Panchino_gp28
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /panchino_gp28/Panchino_gp28__gp28.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/paris.md b/content/3.defense-systems/paris.md
index a09b72fc..b9647f28 100644
--- a/content/3.defense-systems/paris.md
+++ b/content/3.defense-systems/paris.md
@@ -42,62 +42,19 @@ The PARIS_I_merge system in *Rhizobium sp. SL42* (GCF_021729845.1, NZ_CP063397)
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Paris is detected in 1128 genomes (4.95 %).
-
-The system was detected in 518 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Paris system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
-
-## Structure
-### PARIS_I
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /paris/PARIS_I.PARIS_I__AAA_15.0.V.cif
- - /paris/PARIS_I.Rst_PARIS__DUF4435.0.V.cif
-
----
+::article-system-distribution-plot
::
-### PARIS_II
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /paris/PARIS_I.Rst_PARIS__DUF4435.0.V.cif
- - /paris/PARIS_II.PARIS_II__AAA_21.0.V.cif
----
-::
-### PARIS_II_merge
-##### Example 1
+## Structure
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /paris/PARIS_II_merge__AAA_21_DUF4435.cif
+### List predicted structures
----
+::article-structure
::
-### PARIS_I_merge
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /paris/PARIS_I_merge__AAA_15_DUF4435.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-lambda-1.md b/content/3.defense-systems/pd-lambda-1.md
index 15d14dfd..28d33bdc 100644
--- a/content/3.defense-systems/pd-lambda-1.md
+++ b/content/3.defense-systems/pd-lambda-1.md
@@ -39,27 +39,19 @@ The PD-Lambda-1 system in *Gemmata massiliana* (GCF_901538265.1, NZ_LR593886) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-Lambda-1 is detected in 1301 genomes (5.71 %).
-
-The system was detected in 483 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-Lambda-1 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-Lambda-1
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-lambda-1/PD-Lambda-1__PD-Lambda-1.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-lambda-2.md b/content/3.defense-systems/pd-lambda-2.md
index 7889243f..2eb3ff77 100644
--- a/content/3.defense-systems/pd-lambda-2.md
+++ b/content/3.defense-systems/pd-lambda-2.md
@@ -27,29 +27,19 @@ The PD-Lambda-2 system in *Vibrio parahaemolyticus* (GCF_013393845.1, NZ_CP04010
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-Lambda-2 is detected in 122 genomes (0.54 %).
-
-The system was detected in 59 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-Lambda-2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-Lambda-2
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-lambda-2/PD-Lambda-2.PD-Lambda-2__PD-Lambda-2_C.0.V.cif
- - /pd-lambda-2/PD-Lambda-2.PD-Lambda-2__PD-Lambda-2_B.0.V.cif
- - /pd-lambda-2/PD-Lambda-2.PD-Lambda-2__PD-Lambda-2_A.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-lambda-3.md b/content/3.defense-systems/pd-lambda-3.md
index 2b8b0dc3..c0ae6bb7 100644
--- a/content/3.defense-systems/pd-lambda-3.md
+++ b/content/3.defense-systems/pd-lambda-3.md
@@ -36,29 +36,19 @@ The PD-Lambda-3 system in *Enterobacter sp. CRENT-193* (GCF_002787395.1, NZ_CP02
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-Lambda-3 is detected in 72 genomes (0.32 %).
-
-The system was detected in 28 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-Lambda-3 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-Lambda-3
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-lambda-3/PD-Lambda-3.PD-Lambda-3__PD-Lambda-3_A.0.V.cif
- - /pd-lambda-3/PD-Lambda-3.PD-Lambda-3__PD-Lambda-3_B.0.V.cif
- - /pd-lambda-3/PD-Lambda-3.PD-Lambda-3__PD-Lambda-3_C.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-lambda-4.md b/content/3.defense-systems/pd-lambda-4.md
index 0759b3d9..bb6f3a2a 100644
--- a/content/3.defense-systems/pd-lambda-4.md
+++ b/content/3.defense-systems/pd-lambda-4.md
@@ -26,28 +26,19 @@ The PD-Lambda-4 system in *Serratia sp. LS-1* (GCF_003719595.1, NZ_CP033504) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-Lambda-4 is detected in 69 genomes (0.3 %).
-
-The system was detected in 14 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-Lambda-4 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-Lambda-4
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-lambda-4/PD-Lambda-4.PD-Lambda-4__PD-Lambda-4_B.0.V.cif
- - /pd-lambda-4/PD-Lambda-4.PD-Lambda-4__PD-Lambda-4_A.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-lambda-5.md b/content/3.defense-systems/pd-lambda-5.md
index c8c35d1a..32b04043 100644
--- a/content/3.defense-systems/pd-lambda-5.md
+++ b/content/3.defense-systems/pd-lambda-5.md
@@ -35,28 +35,19 @@ The PD-Lambda-5 system in *Plantactinospora sp. BB1* (GCF_003030385.1, NZ_CP0281
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-Lambda-5 is detected in 286 genomes (1.25 %).
-
-The system was detected in 186 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-Lambda-5 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-Lambda-5
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-lambda-5/PD-Lambda-5.PD-Lambda-5__PD-Lambda-5_A.0.V.cif
- - /pd-lambda-5/PD-Lambda-5.PD-Lambda-5__PD-Lambda-5_B.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-lambda-6.md b/content/3.defense-systems/pd-lambda-6.md
index bcd1ab87..8c7b0722 100644
--- a/content/3.defense-systems/pd-lambda-6.md
+++ b/content/3.defense-systems/pd-lambda-6.md
@@ -26,27 +26,19 @@ The PD-Lambda-6 system in *Enterobacter asburiae* (GCF_013782005.1, NZ_CP056126)
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-Lambda-6 is detected in 20 genomes (0.09 %).
-
-The system was detected in 11 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-Lambda-6 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-Lambda-6
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-lambda-6/PD-Lambda-6__PD-Lambda-6.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-t4-1.md b/content/3.defense-systems/pd-t4-1.md
index b720c788..1a42a604 100644
--- a/content/3.defense-systems/pd-t4-1.md
+++ b/content/3.defense-systems/pd-t4-1.md
@@ -27,27 +27,19 @@ The PD-T4-1 system in *Macrococcus armenti* (GCF_020097055.1, NZ_CP083595) is co
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-T4-1 is detected in 209 genomes (0.92 %).
-
-The system was detected in 38 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-T4-1 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-T4-1
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-t4-1/PD-T4-1__PD-T4-1.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-t4-10.md b/content/3.defense-systems/pd-t4-10.md
index 2eaa1f3c..5a8a14da 100644
--- a/content/3.defense-systems/pd-t4-10.md
+++ b/content/3.defense-systems/pd-t4-10.md
@@ -36,28 +36,19 @@ The PD-T4-10 system in *Escherichia fergusonii* (GCF_019047545.1, NZ_CP077242) i
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-T4-10 is detected in 33 genomes (0.14 %).
-
-The system was detected in 23 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-T4-10 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-T4-10
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-t4-10/PD-T4-10.PD-T4-10__PD-T4-10_B.0.V.cif
- - /pd-t4-10/PD-T4-10.PD-T4-10__PD-T4-10_A.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-t4-2.md b/content/3.defense-systems/pd-t4-2.md
index c4abdd50..ed34ca63 100644
--- a/content/3.defense-systems/pd-t4-2.md
+++ b/content/3.defense-systems/pd-t4-2.md
@@ -27,28 +27,19 @@ The PD-T4-2 system in *Jeotgalibaca sp. PTS2502* (GCF_001975685.1, NZ_CP019433)
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-T4-2 is detected in 33 genomes (0.14 %).
-
-The system was detected in 28 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-T4-2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-T4-2
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-t4-2/PD-T4-2.PD-T4-2__PD-T4-2_A.0.DF.cif
- - /pd-t4-2/PD-T4-2.PD-T4-2__PD-T4-2_B.0.DF.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-t4-3.md b/content/3.defense-systems/pd-t4-3.md
index d4b6592a..259f4bf3 100644
--- a/content/3.defense-systems/pd-t4-3.md
+++ b/content/3.defense-systems/pd-t4-3.md
@@ -37,27 +37,19 @@ The PD-T4-3 system in *Morganella morganii* (GCF_018802485.1, NZ_CP064826) is co
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-T4-3 is detected in 1314 genomes (5.76 %).
-
-The system was detected in 172 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-T4-3 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-T4-3
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-t4-3/PD-T4-3__PD-T4-3.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-t4-4.md b/content/3.defense-systems/pd-t4-4.md
index 3fe34c40..c9b9a5bd 100644
--- a/content/3.defense-systems/pd-t4-4.md
+++ b/content/3.defense-systems/pd-t4-4.md
@@ -35,28 +35,19 @@ The PD-T4-4 system in *Thiothrix subterranea* (GCF_016772315.1, NZ_CP053482) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-T4-4 is detected in 50 genomes (0.22 %).
-
-The system was detected in 37 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-T4-4 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-T4-4
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-t4-4/PD-T4-4.PD-T4-4__PD-T4-4_B.0.V.cif
- - /pd-t4-4/PD-T4-4.PD-T4-4__PD-T4-4_A.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-t4-5.md b/content/3.defense-systems/pd-t4-5.md
index 920b09c2..65f9ebae 100644
--- a/content/3.defense-systems/pd-t4-5.md
+++ b/content/3.defense-systems/pd-t4-5.md
@@ -27,27 +27,19 @@ The PD-T4-5 system in *Grimontia hollisae* (GCF_009665295.1, NZ_CP035690) is com
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-T4-5 is detected in 587 genomes (2.57 %).
-
-The system was detected in 128 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-T4-5 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-T4-5
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-t4-5/PD-T4-5__PD-T4-5.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-t4-6.md b/content/3.defense-systems/pd-t4-6.md
index da6dc01a..0b44e211 100644
--- a/content/3.defense-systems/pd-t4-6.md
+++ b/content/3.defense-systems/pd-t4-6.md
@@ -36,27 +36,19 @@ The PD-T4-6 system in *Streptococcus ruminantium* (GCF_021654555.1, NZ_AP025333)
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-T4-6 is detected in 88 genomes (0.39 %).
-
-The system was detected in 18 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-T4-6 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-T4-6
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-t4-6/PD-T4-6__PD-T4-6.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-t4-7.md b/content/3.defense-systems/pd-t4-7.md
index 8c174abd..76c792ed 100644
--- a/content/3.defense-systems/pd-t4-7.md
+++ b/content/3.defense-systems/pd-t4-7.md
@@ -38,27 +38,19 @@ The PD-T4-7 system in *Thalassospira sp. B30-1* (GCF_015767575.1, NZ_CP065232) i
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-T4-7 is detected in 155 genomes (0.68 %).
-
-The system was detected in 100 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-T4-7 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-T4-7
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-t4-7/PD-T4-7__PD-T4-7.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-t4-8.md b/content/3.defense-systems/pd-t4-8.md
index cfdf7c6c..e92aee6e 100644
--- a/content/3.defense-systems/pd-t4-8.md
+++ b/content/3.defense-systems/pd-t4-8.md
@@ -36,27 +36,19 @@ The PD-T4-8 system in *Algoriphagus sp. Y33* (GCF_014838715.1, NZ_CP061947) is c
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-T4-8 is detected in 89 genomes (0.39 %).
-
-The system was detected in 50 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-T4-8 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-T4-8
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-t4-8/PD-T4-8__PD-T4-8.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-t4-9.md b/content/3.defense-systems/pd-t4-9.md
index 5ed10b96..4d3f0226 100644
--- a/content/3.defense-systems/pd-t4-9.md
+++ b/content/3.defense-systems/pd-t4-9.md
@@ -27,29 +27,19 @@ The PD-T4-9 system in *Vibrio parahaemolyticus* (GCF_001700835.1, NZ_CP010883) i
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-T4-9 is detected in 141 genomes (0.62 %).
-
-The system was detected in 88 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-T4-9 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-T4-9
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-t4-9/PD-T4-9.PD-T4-9__PD-T4-9_A.0.V.cif
- - /pd-t4-9/PD-T4-9.PD-T4-9__PD-T4-9_B.0.V.cif
- - /pd-t4-9/PD-T4-9.PD-T4-9__PD-T4-9_C.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-t7-1.md b/content/3.defense-systems/pd-t7-1.md
index 00c61220..5ab3285a 100644
--- a/content/3.defense-systems/pd-t7-1.md
+++ b/content/3.defense-systems/pd-t7-1.md
@@ -35,27 +35,19 @@ The PD-T7-1 system in *Klebsiella sp. P1927* (GCF_018204675.1, NZ_CP073377) is c
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-T7-1 is detected in 748 genomes (3.28 %).
-
-The system was detected in 146 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-T7-1 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-T7-1
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-t7-1/PD-T7-1__PD-T7-1.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-t7-2.md b/content/3.defense-systems/pd-t7-2.md
index 614e7123..de2c86dc 100644
--- a/content/3.defense-systems/pd-t7-2.md
+++ b/content/3.defense-systems/pd-t7-2.md
@@ -27,28 +27,19 @@ The PD-T7-2 system in *Lederbergia lenta* (GCF_900478165.1, NZ_LS483476) is comp
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-T7-2 is detected in 1483 genomes (6.5 %).
-
-The system was detected in 667 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-T7-2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-T7-2
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-t7-2/PD-T7-2.PD-T7-2__PD-T7-2_B.0.V.cif
- - /pd-t7-2/PD-T7-2.PD-T7-2__PD-T7-2_A.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-t7-3.md b/content/3.defense-systems/pd-t7-3.md
index 7ab9e526..6ff2ecf8 100644
--- a/content/3.defense-systems/pd-t7-3.md
+++ b/content/3.defense-systems/pd-t7-3.md
@@ -36,27 +36,19 @@ The PD-T7-3 system in *Paraglaciecola psychrophila* (GCF_000347635.1, NC_020514)
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-T7-3 is detected in 209 genomes (0.92 %).
-
-The system was detected in 130 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-T7-3 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-T7-3
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-t7-3/PD-T7-3__PD-T7-3.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-t7-4.md b/content/3.defense-systems/pd-t7-4.md
index 06321a93..80d6831e 100644
--- a/content/3.defense-systems/pd-t7-4.md
+++ b/content/3.defense-systems/pd-t7-4.md
@@ -27,27 +27,19 @@ The PD-T7-4 system in *Salinibacterium hongtaonis* (GCF_003065485.1, NZ_CP026951
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-T7-4 is detected in 492 genomes (2.16 %).
-
-The system was detected in 218 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-T7-4 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-T7-4
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-t7-4/PD-T7-4__PD-T7-4.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pd-t7-5.md b/content/3.defense-systems/pd-t7-5.md
index 7fd1bf8f..cc9f5c14 100644
--- a/content/3.defense-systems/pd-t7-5.md
+++ b/content/3.defense-systems/pd-t7-5.md
@@ -34,27 +34,19 @@ The PD-T7-5 system in *Shewanella putrefaciens* (GCF_019599085.1, NZ_CP080633) i
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PD-T7-5 is detected in 336 genomes (1.47 %).
-
-The system was detected in 129 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PD-T7-5 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PD-T7-5
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pd-t7-5/PD-T7-5__PD-T7-5.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pfiat.md b/content/3.defense-systems/pfiat.md
index 7cd97f60..59524ff2 100644
--- a/content/3.defense-systems/pfiat.md
+++ b/content/3.defense-systems/pfiat.md
@@ -50,33 +50,19 @@ The PfiAT system in *Desulfoscipio gibsoniae* (GCF_000233715.2, NC_021184) is co
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PfiAT is detected in 819 genomes (3.59 %).
-Among the 22,803 complete genomes of RefSeq, the PfiAT is detected in 819 genomes (3.59 %).
-
-The system was detected in 308 different species.
-The system was detected in 308 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PfiAT system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
+::article-system-distribution-plot
+::
-Proportion of genome encoding the PfiAT system for the 14 phyla with more than 50 genomes in the RefSeq database.
+## Structure
+### List predicted structures
+::article-structure
+::
-## Structure
-### PfiAT
-##### Example 1
-##### Example 1
+### pDockQ matrix
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pfiat/PfiAT.PfiAT__PfiA.0.V.cif
- - /pfiat/PfiAT.PfiAT__PfiT.0.V.cif
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/phrann_gp29_gp30.md b/content/3.defense-systems/phrann_gp29_gp30.md
index d604dfb0..89616df4 100644
--- a/content/3.defense-systems/phrann_gp29_gp30.md
+++ b/content/3.defense-systems/phrann_gp29_gp30.md
@@ -23,18 +23,19 @@ The Phrann_gp29_gp30 system in *Demequina sp. TMPB413* (GCF_020447105.2, NZ_CP09
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Phrann_gp29_gp30 is detected in 312 genomes (1.37 %).
+::article-system-distribution-plot
+::
-The system was detected in 35 different species.
+## Structure
-{max-width=750px}
+### List predicted structures
-Proportion of genome encoding the Phrann_gp29_gp30 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-structure
+::
-## Structure
+### pDockQ matrix
-::info
-This section is empty
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pif.md b/content/3.defense-systems/pif.md
index c7486c9b..e51a4ed3 100644
--- a/content/3.defense-systems/pif.md
+++ b/content/3.defense-systems/pif.md
@@ -41,28 +41,19 @@ The Pif system in *Shigella flexneri* (GCF_022353545.1, NZ_CP055168) is composed
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Pif is detected in 140 genomes (0.61 %).
-
-The system was detected in 25 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Pif system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Pif
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pif/Pif.Pif__PifA.0.V.cif
- - /pif/Pif.Pif__PifC.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/prrc.md b/content/3.defense-systems/prrc.md
index 7fe3c826..1abfcdc9 100644
--- a/content/3.defense-systems/prrc.md
+++ b/content/3.defense-systems/prrc.md
@@ -41,40 +41,19 @@ The PrrC system in *Parazoarcus communis* (GCF_003111645.1, NZ_CP022187) is comp
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PrrC is detected in 705 genomes (3.09 %).
-
-The system was detected in 309 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PrrC system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
+::article-system-distribution-plot
+::
## Structure
-### PrrC
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /prrc/PrrC__EcoprrI.cif
- - /prrc/PrrC__PrrC.cif
+### List predicted structures
----
+::article-structure
::
-### RM
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /prrc/RM__Type_I_S.cif
- - /prrc/RM__Type_I_REases.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/psyrta.md b/content/3.defense-systems/psyrta.md
index b0bdf27c..4fd035a8 100644
--- a/content/3.defense-systems/psyrta.md
+++ b/content/3.defense-systems/psyrta.md
@@ -57,28 +57,19 @@ The PsyrTA system in *Providencia rettgeri* (GCF_013702265.1, NZ_CP059348) is co
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the PsyrTA is detected in 629 genomes (2.76 %).
-
-The system was detected in 132 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the PsyrTA system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### PsyrTA
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /psyrta/PsyrTA.PsyrTA__PsyrT.0.V.cif
- - /psyrta/PsyrTA.PsyrTA__PsyrA.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/pycsar.md b/content/3.defense-systems/pycsar.md
index 1cd9084b..ade7f2f6 100644
--- a/content/3.defense-systems/pycsar.md
+++ b/content/3.defense-systems/pycsar.md
@@ -46,52 +46,19 @@ The Pycsar system in *Nocardioides sambongensis* (GCF_006494815.1, NZ_CP041091)
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Pycsar is detected in 552 genomes (2.42 %).
-
-The system was detected in 295 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Pycsar system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
-
-## Structure
-
-### Experimentaly determined structure
-From :ref{doi=10.1016/j.cell.2021.09.031} in *Burkholderia cepacia* LK29:
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pycsar/7r65-assembly1_Cyclase_2mer.cif
----
+::article-system-distribution-plot
::
+## Structure
-### Pycsar
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pycsar/Pycsar.Pycsar__AG_cyclase.1.V.cif
- - /pycsar/Pycsar.CBASS__TIR.0.V.cif
+### List predicted structures
----
+::article-structure
::
-##### Example 2
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /pycsar/Pycsar.CBASS_TM.1.V.cif
- - /pycsar/Pycsar.Pycsar__AG_cyclase.1.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/radar.md b/content/3.defense-systems/radar.md
index 02677495..11d75e8d 100644
--- a/content/3.defense-systems/radar.md
+++ b/content/3.defense-systems/radar.md
@@ -44,82 +44,19 @@ The radar_II system in *Enterobacter sp. JH25* (GCF_021725435.1, NZ_CP091319) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the RADAR is detected in 135 genomes (0.59 %).
-
-The system was detected in 44 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the RADAR system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
-
-## Structure
-
-### Experimentally determined structure
-
-From :ref{doi=10.1016/j.cell.2023.01.012} in *Escherichia coli*:
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /radar/8fnt_EcRdrA_7mer.pdb
- - /radar/8fnv_EcRdrB_12mer.pdb
- - /radar/8fnw_EcRdrAB_7_12mer.cif
----
-::
-
-
-From :ref{doi=10.1016/j.cell.2023.01.012} in *Streptococcus suis*:
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /radar/8fnu_SsRdrA_7mer.pdb
----
-::
-
-From :ref{doi=10.1016/j.cell.2023.01.026} in *Escherichia coli*:
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /radar/8hr8_EcRdrA_7mer.pdb
- - /radar/8hr9_EcRdrA_14mer.pdb
- - /radar/8hrc_EcRdrB_12mer.pdb
- - /radar/8hr7_EcRdrAB_7_12mer.cif
- - /radar/8hra_EcRdrA_7mer_rna.pdb
- - /radar/8hrb_EcRdrA_14mer_rna.pdb
----
+::article-system-distribution-plot
::
-### radar_I
-##### Example 1
+## Structure
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /radar/radar_I.radar_I__rdrB_I.0.V.cif
- - /radar/radar_I.radar_I__rdrA_I.0.V.cif
+### List predicted structures
----
+::article-structure
::
-### radar_II
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /radar/radar_II.radar_II__rdrC_II.0.V.cif
- - /radar/radar_II.radar_II__rdrB_II.0.V.cif
- - /radar/radar_II.radar_II__rdrA_II.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/retron.md b/content/3.defense-systems/retron.md
index 7bc29cfe..f3e2d29b 100644
--- a/content/3.defense-systems/retron.md
+++ b/content/3.defense-systems/retron.md
@@ -114,148 +114,19 @@ The Retron_XIII system in *Clostridium saccharobutylicum* (GCF_002003365.1, NZ_C
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Retron is detected in 2537 genomes (11.13 %).
-
-The system was detected in 840 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Retron system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
-
-## Structure
-### RT_Ec67_SLATT
-##### Example Ec57
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /retron/RT_Ec67_SLATT.AbiA__AbiA_small_SLATT.Ec57.V.cif
-
----
-::
-##### Example Ec67
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /retron/DRT_3.DRT_3__drt3a.0.V.cif
-
----
-::
-### Retron_II
-##### Example Ec73
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /retron/Retron_II.Retron_II__NDT.Ec73.V.cif
-
----
-::
-##### Example Ec86
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /retron/Retron_II.Retron_II__NDT.Ec73.V.cif
-
----
-::
-### Retron_III
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /retron/Retron_III.Retron_III__PRTase.0.DF.cif
- - /retron/Retron_III.Retron_III__WH.0.DF.cif
-
----
-::
-##### Example 2
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /retron/Retron_III.Retron_III__PRTase_WH.1.DF.cif
-
----
-::
-### Retron_IV
-##### Example Ec48
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /retron/Retron_IV.Retron_IV__2TM.Ec48.V.cif
-
----
-::
-### Retron_I_A
-##### Example Ec83
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /retron/Retron_I_A.Retron__RT_Tot.Ec83.V.cif
- - /retron/Retron_I_A.Retron_I_A__ATPase_TypeIA.Vc95.V.cif
-
----
-::
-##### Example Vc95
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /retron/Retron_I_A.Retron_I_A__ATPase_TypeIA.Vc95.V.cif
- - /retron/Retron_I_A.Retron__RT_Tot.Ec83.V.cif
-
----
+::article-system-distribution-plot
::
-### Retron_I_B
-##### Example Eco8
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /retron/Retron_I_B.Retron_I_B__ATPase_TOPRIM_COG3593.Eco8.V.cif
----
-::
-### Retron_VI
-##### Example 1
+## Structure
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /retron/Retron_VI.Retron_VI__HTH.0.DF.cif
- - /retron/Retron_VI.Possible_Retron_VI__SP.0.DF.cif
+### List predicted structures
----
+::article-structure
::
-### Retron_VII_2
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /retron/Retron_VII_2.Retron_VII_2__DUF3800.0.DF.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/rexab.md b/content/3.defense-systems/rexab.md
index c2f0f8d3..f3567062 100644
--- a/content/3.defense-systems/rexab.md
+++ b/content/3.defense-systems/rexab.md
@@ -27,28 +27,19 @@ The RexAB system in *Klebsiella pneumoniae* (GCF_016780145.1, NZ_CP068798) is co
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the RexAB is detected in 73 genomes (0.32 %).
-
-The system was detected in 18 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the RexAB system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### RexAB
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /rexab/RexAB.RexAB_RexB.0.V.cif
- - /rexab/RexAB.RexAB_RexA.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/rloc.md b/content/3.defense-systems/rloc.md
index 446ca90b..d478c859 100644
--- a/content/3.defense-systems/rloc.md
+++ b/content/3.defense-systems/rloc.md
@@ -41,27 +41,19 @@ The RloC system in *Pseudomonas aeruginosa* (GCF_000981825.1, NZ_CP011317) is co
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the RloC is detected in 1944 genomes (8.53 %).
-
-The system was detected in 919 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the RloC system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### RloC
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /rloc/RloC__RloC.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/rm.md b/content/3.defense-systems/rm.md
index 2cb561dc..443b7ef9 100644
--- a/content/3.defense-systems/rm.md
+++ b/content/3.defense-systems/rm.md
@@ -61,35 +61,19 @@ The RM_Type_IV system in *Halobaculum rubrum* (GCF_019880225.1, NZ_CP082284) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the RM is detected in 18264 genomes (80.09 %).
-
-The system was detected in 6137 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the RM system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
::article-system-distribution-plot
::
## Structure
-### Experimentaly determined structure
+### List predicted structures
-Many structure for the different types of restriction-modification system are available on the [Protein Data Bank](https://www.rcsb.org).
+::article-structure
+::
-### RM
-#### Restriction modification Type I Prr
+### pDockQ matrix
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /rm/RM__Type_I_REases-plddts_86.33796.pdb
- - /rm/RM__Type_I_S-plddts_91.98582.pdb
- - /prrc/PrrC__EcoprrI-plddts_91.30003.pdb
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/rnlab.md b/content/3.defense-systems/rnlab.md
index 27394c82..9d2a6325 100644
--- a/content/3.defense-systems/rnlab.md
+++ b/content/3.defense-systems/rnlab.md
@@ -38,28 +38,19 @@ The RnlAB system in *Bacteroides caecimuris* (GCF_001688725.2, NZ_CP015401) is c
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the RnlAB is detected in 279 genomes (1.22 %).
-
-The system was detected in 68 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the RnlAB system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### RnlAB
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /rnlab/RnlAB.RnlAB__RnlA.0.DF.cif
- - /rnlab/RnlAB.RnlAB__RnlB.0.DF.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/rosmerta.md b/content/3.defense-systems/rosmerta.md
index 6d2af2a5..8b0b0744 100644
--- a/content/3.defense-systems/rosmerta.md
+++ b/content/3.defense-systems/rosmerta.md
@@ -39,28 +39,19 @@ The RosmerTA system in *Paucibacter sp. KCTC 42545* (GCF_001477625.1, NZ_CP01369
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the RosmerTA is detected in 2080 genomes (9.12 %).
-
-The system was detected in 613 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the RosmerTA system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### RosmerTA
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /rosmerta/RosmerTA.RosmerTA__RmrA.0.V.cif
- - /rosmerta/RosmerTA.RosmerTA__RmrT.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/rst_2tm_1tm_tir.md b/content/3.defense-systems/rst_2tm_1tm_tir.md
index 7346d9f4..3d105202 100644
--- a/content/3.defense-systems/rst_2tm_1tm_tir.md
+++ b/content/3.defense-systems/rst_2tm_1tm_tir.md
@@ -39,28 +39,20 @@ The Rst_2TM_1TM_TIR system in *Escherichia coli* (GCF_004006575.1, NZ_CP034787)
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Rst_2TM_1TM_TIR is detected in 2 genomes (0.01 %).
-
-The system was detected in 1 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Rst_2TM_1TM_TIR system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Rst_2TM_1TM_TIR
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /rst_2tm_1tm_tir/Rst_2TM_1TM_TIR.Rst_2TM_1TM_TIR__Rst_2TM_TIR.0.V.cif
- - /rst_2tm_1tm_tir/Rst_2TM_1TM_TIR.Rst_2TM_1TM_TIR__Rst_1TM_TIR.0.V.cif
- - /rst_2tm_1tm_tir/Rst_2TM_1TM_TIR.Rst_2TM_1TM_TIR__Rst_TIR_tm.0.V.cif
+### pDockQ matrix
+::pdockq-matrix
+::
## Experimental validation
diff --git a/content/3.defense-systems/rst_3hp.md b/content/3.defense-systems/rst_3hp.md
index b20735b5..b7863c45 100644
--- a/content/3.defense-systems/rst_3hp.md
+++ b/content/3.defense-systems/rst_3hp.md
@@ -38,29 +38,19 @@ The Rst_3HP system in *Aquitalea denitrificans* (GCF_009856625.1, NZ_CP047241) i
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Rst_3HP is detected in 417 genomes (1.83 %).
-
-The system was detected in 89 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Rst_3HP system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Rst_3HP
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /rst_3hp/Rst_3HP.Rst_3HP__Hp1.0.V.cif
- - /rst_3hp/Rst_3HP.Rst_3HP__Hp3.0.V.cif
- - /rst_3hp/Rst_3HP.Rst_3HP__Hp2.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/rst_duf4238.md b/content/3.defense-systems/rst_duf4238.md
index 4ba8aeb3..4bc1f290 100644
--- a/content/3.defense-systems/rst_duf4238.md
+++ b/content/3.defense-systems/rst_duf4238.md
@@ -38,27 +38,19 @@ The Rst_DUF4238 system in *Novosphingobium pentaromativorans* (GCF_000767465.1,
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Rst_DUF4238 is detected in 46 genomes (0.2 %).
-
-The system was detected in 37 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Rst_DUF4238 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Rst_DUF4238
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /rst_duf4238/Rst_DUF4238__DUF4238_Pers.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/rst_gop_beta_cll.md b/content/3.defense-systems/rst_gop_beta_cll.md
index 28bba674..cd108f37 100644
--- a/content/3.defense-systems/rst_gop_beta_cll.md
+++ b/content/3.defense-systems/rst_gop_beta_cll.md
@@ -45,29 +45,19 @@ The Rst_gop_beta_cll system in *Klebsiella grimontii* (GCF_019334465.1, NZ_CP079
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Rst_gop_beta_cll is detected in 37 genomes (0.16 %).
-
-The system was detected in 15 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Rst_gop_beta_cll system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Rst_gop_beta_cll
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /rst_gop_beta_cll/Rst_gop_beta_cll.Rst_gop_beta_cll__cll.0.V.cif
- - /rst_gop_beta_cll/Rst_gop_beta_cll.Rst_gop_beta_cll__gop.0.V.cif
- - /rst_gop_beta_cll/Rst_gop_beta_cll.Rst_gop_beta_cll__beta.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/rst_helicaseduf2290.md b/content/3.defense-systems/rst_helicaseduf2290.md
index 43b3872e..8b586bf1 100644
--- a/content/3.defense-systems/rst_helicaseduf2290.md
+++ b/content/3.defense-systems/rst_helicaseduf2290.md
@@ -40,28 +40,19 @@ The Rst_HelicaseDUF2290 system in *Klebsiella quasipneumoniae* (GCF_003020825.1,
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Rst_HelicaseDUF2290 is detected in 207 genomes (0.91 %).
-
-The system was detected in 123 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Rst_HelicaseDUF2290 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Rst_HelicaseDUF2290
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /rst_helicaseduf2290/Rst_HelicaseDUF2290.Rst_HelicaseDUF2290__DUF2290.0.V.cif
- - /rst_helicaseduf2290/Rst_HelicaseDUF2290.Rst_HelicaseDUF2290__Helicase.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/rst_hydrolase-3tm.md b/content/3.defense-systems/rst_hydrolase-3tm.md
index b5ada2fa..635f04ea 100644
--- a/content/3.defense-systems/rst_hydrolase-3tm.md
+++ b/content/3.defense-systems/rst_hydrolase-3tm.md
@@ -27,28 +27,19 @@ The Rst_Hydrolase-Tm system in *Pectobacterium versatile* (GCF_003031305.1, NZ_C
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Rst_Hydrolase-3Tm is detected in 42 genomes (0.18 %).
-
-The system was detected in 34 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Rst_Hydrolase-3Tm system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Rst_Hydrolase-Tm
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /rst_hydrolase-3tm/Rst_Hydrolase-Tm.Rst_Hydrolase-Tm__Hydrolase.0.V.cif
- - /rst_hydrolase-3tm/Rst_Hydrolase-Tm.Rst_Hydrolase-Tm__Hydrolase-Tm.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/rst_rt-nitrilase-tm.md b/content/3.defense-systems/rst_rt-nitrilase-tm.md
index 18566046..9adbf48d 100644
--- a/content/3.defense-systems/rst_rt-nitrilase-tm.md
+++ b/content/3.defense-systems/rst_rt-nitrilase-tm.md
@@ -42,28 +42,19 @@ The Rst_RT-Tm system in *Morganella morganii* (GCF_900478755.1, NZ_LS483498) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Rst_RT-nitrilase-Tm is detected in 25 genomes (0.11 %).
-
-The system was detected in 5 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Rst_RT-nitrilase-Tm system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Rst_RT-Tm
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /rst_rt-nitrilase-tm/Rst_RT-Tm.Rst_RT-Tm__RT-Tm.0.V.cif
- - /rst_rt-nitrilase-tm/Rst_RT-Tm.Rst_RT-Tm__RT.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/rst_tir-nlr.md b/content/3.defense-systems/rst_tir-nlr.md
index 3b7a456d..2ceba637 100644
--- a/content/3.defense-systems/rst_tir-nlr.md
+++ b/content/3.defense-systems/rst_tir-nlr.md
@@ -40,27 +40,19 @@ The Rst_TIR-NLR system in *Methylosinus sp. C49* (GCF_009936375.1, NZ_AP022332)
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Rst_TIR-NLR is detected in 233 genomes (1.02 %).
-
-The system was detected in 42 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Rst_TIR-NLR system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Rst_TIR-NLR
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /rst_tir-nlr/Rst_TIR-NLR__TIR.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/sanata.md b/content/3.defense-systems/sanata.md
index 19ce4926..6636e47c 100644
--- a/content/3.defense-systems/sanata.md
+++ b/content/3.defense-systems/sanata.md
@@ -39,28 +39,19 @@ The SanaTA system in *Euzebyella marina* (GCF_003687485.1, NZ_CP032050) is compo
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the SanaTA is detected in 992 genomes (4.35 %).
-
-The system was detected in 519 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the SanaTA system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### SanaTA
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /sanata/SanaTA.SanaTA_SanaA.0.V.cif
- - /sanata/SanaTA.SanaTA_SanaT.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/sefir.md b/content/3.defense-systems/sefir.md
index 992d587f..18d6c785 100644
--- a/content/3.defense-systems/sefir.md
+++ b/content/3.defense-systems/sefir.md
@@ -43,27 +43,19 @@ The SEFIR system in *Haliangium ochraceum* (GCF_000024805.1, NC_013440) is compo
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the SEFIR is detected in 358 genomes (1.57 %).
-
-The system was detected in 218 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the SEFIR system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### SEFIR
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /sefir/SEFIR__bSEFIR.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/septu.md b/content/3.defense-systems/septu.md
index f31c2b2b..48315906 100644
--- a/content/3.defense-systems/septu.md
+++ b/content/3.defense-systems/septu.md
@@ -52,55 +52,19 @@ The Septu system in *Burkholderia pyrrocinia* (GCF_001028665.1, NZ_CP011503) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Septu is detected in 2130 genomes (9.34 %).
-
-The system was detected in 1112 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Septu system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
-
-## Structure
-
-### Experimentaly determined structure
-
-From :ref{doi=10.1038/s41594-023-01172-8} in *Escherichia coli*:
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /septu/8ee4_EcPtuA_6mer.pdb
- - /septu/8ee7_EcPtuAB_2_1mer.pdb
- - /septu/8eea_EcPtuAB_6_3mer.pdb
----
+::article-system-distribution-plot
::
-### Septu
-##### Example 1
+## Structure
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /septu/Septu.Septu__PtuA.1.V.cif
- - /septu/Septu.Septu__PtuB.1.V.cif
+### List predicted structures
----
+::article-structure
::
-##### Example 2
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /septu/Septu.Septu__PtuB.1.V.cif
- - /septu/Septu.Septu__PtuA.1.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/shango.md b/content/3.defense-systems/shango.md
index bca0b500..cb8b8845 100644
--- a/content/3.defense-systems/shango.md
+++ b/content/3.defense-systems/shango.md
@@ -40,29 +40,19 @@ The Shango system in *Anoxybacillus sp. B2M1* (GCF_001634265.1, NZ_CP015435) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Shango is detected in 1095 genomes (4.8 %).
-
-The system was detected in 446 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Shango system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Shango
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /shango/Shango.Shango__SngA.0.V.cif
- - /shango/Shango.Shango__SngB.0.V.cif
- - /shango/Shango.Shango__SngC.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/shedu.md b/content/3.defense-systems/shedu.md
index df718488..e781729c 100644
--- a/content/3.defense-systems/shedu.md
+++ b/content/3.defense-systems/shedu.md
@@ -44,27 +44,19 @@ The Shedu system in *Bradyrhizobium ottawaense* (GCF_002278135.2, NZ_CP029425) i
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Shedu is detected in 876 genomes (3.84 %).
-
-The system was detected in 552 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Shedu system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Shedu
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /shedu/Shedu__SduA.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/shosta.md b/content/3.defense-systems/shosta.md
index 2228e895..7bee24cf 100644
--- a/content/3.defense-systems/shosta.md
+++ b/content/3.defense-systems/shosta.md
@@ -41,28 +41,19 @@ The ShosTA system in *Enterobacter cloacae* (GCF_009707405.1, NZ_CP046116) is co
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the ShosTA is detected in 535 genomes (2.35 %).
-
-The system was detected in 240 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the ShosTA system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### ShosTA
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /shosta/ShosTA.ShosTA__ShosA.0.V.cif
- - /shosta/ShosTA.ShosTA__ShosT.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/sofic.md b/content/3.defense-systems/sofic.md
index 0723dfdf..041f6681 100644
--- a/content/3.defense-systems/sofic.md
+++ b/content/3.defense-systems/sofic.md
@@ -27,27 +27,19 @@ The SoFic system in *Morococcus cerebrosus* (GCF_022749515.1, NZ_CP094242) is co
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the SoFIC is detected in 2266 genomes (9.94 %).
-
-The system was detected in 1160 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the SoFIC system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### SoFic
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /sofic/SoFic__SoFic.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/spbk.md b/content/3.defense-systems/spbk.md
index 9bc251c5..010b17fc 100644
--- a/content/3.defense-systems/spbk.md
+++ b/content/3.defense-systems/spbk.md
@@ -27,27 +27,19 @@ The SpbK system in *Hymenobacter busanensis* (GCF_009906935.1, NZ_CP047647) is c
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the SpbK is detected in 214 genomes (0.94 %).
-
-The system was detected in 90 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the SpbK system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### SpbK
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /spbk/SpbK__SpbK.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/sspbcde.md b/content/3.defense-systems/sspbcde.md
index 725dbd1f..1a690831 100644
--- a/content/3.defense-systems/sspbcde.md
+++ b/content/3.defense-systems/sspbcde.md
@@ -28,45 +28,19 @@ The SspBCDE system in *Vibrio fluvialis* (GCF_018140575.1, NZ_CP073273) is compo
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the SspBCDE is detected in 578 genomes (2.53 %).
-
-The system was detected in 299 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the SspBCDE system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
+::article-system-distribution-plot
+::
## Structure
-### SspBCDE
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /sspbcde/SspBCDE.SspBCDE__SspC.1.V.cif
- - /sspbcde/SspBCDE.SspBCDE__SspD.0.V.cif
- - /sspbcde/SspBCDE.SspBCDE__SspE.0.V.cif
- - /sspbcde/SspBCDE.SspBCDE__SspB.1.V.cif
+### List predicted structures
----
+::article-structure
::
-##### Example 2
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /sspbcde/SspBCDE.SspBCDE__SspH.1.V.cif
- - /sspbcde/SspBCDE.SspBCDE__SspG.1.V.cif
- - /sspbcde/SspBCDE.SspBCDE__SspF.1.V.cif
- - /sspbcde/SspBCDE.SspBCDE__SspD.0.V.cif
- - /sspbcde/SspBCDE.SspBCDE__SspC.1.V.cif
- - /sspbcde/SspBCDE.SspBCDE__SspB.1.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/stk2.md b/content/3.defense-systems/stk2.md
index ce301fae..ca8d9619 100644
--- a/content/3.defense-systems/stk2.md
+++ b/content/3.defense-systems/stk2.md
@@ -40,27 +40,19 @@ The Stk2 system in *Bacillus rugosus* (GCF_023238245.1, NZ_CP096590) is composed
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Stk2 is detected in 140 genomes (0.61 %).
-
-The system was detected in 29 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Stk2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Stk2
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /stk2/Stk2__Stk2.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/thoeris.md b/content/3.defense-systems/thoeris.md
index cbe4bcbc..e08b25bb 100644
--- a/content/3.defense-systems/thoeris.md
+++ b/content/3.defense-systems/thoeris.md
@@ -47,55 +47,19 @@ The Thoeris_I system in *Sneathia vaginalis* (GCF_000973085.1, NZ_CP011280) is c
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Thoeris is detected in 777 genomes (3.41 %).
-
-The system was detected in 298 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Thoeris system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
-
-## Structure
-
-### Experimentaly determined structure
-
-From :ref{doi=10.1038/s41467-020-16703-w} in *Bacillus cereus* MSX-D12:
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /thoeris/6lhx_BcThsA_4mer.pdb
- - /thoeris/6lhy_BcThsB_1mer.pdb
- - /thoeris/7uxs_BcThsA_2mer_cdpr.pdb
----
+::article-system-distribution-plot
::
-### Thoeris_I
-##### Example 1
+## Structure
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /thoeris/Thoeris_I.Thoeris_I__ThsA_new_grand.0.V.cif
- - /thoeris/Thoeris_I.Thoeris__ThsB_Global.0.V.cif
+### List predicted structures
----
+::article-structure
::
-### Thoeris_II
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /thoeris/Thoeris_I.Thoeris__ThsB_Global.0.V.cif
- - /thoeris/Thoeris_II.Thoeris_II__ThsA_new_petit.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/tiamat.md b/content/3.defense-systems/tiamat.md
index 27814054..5c93fe33 100644
--- a/content/3.defense-systems/tiamat.md
+++ b/content/3.defense-systems/tiamat.md
@@ -40,27 +40,19 @@ The Tiamat system in *Undibacterium parvum* (GCF_003955735.1, NZ_CP034464) is co
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Tiamat is detected in 326 genomes (1.43 %).
-
-The system was detected in 251 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Tiamat system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Tiamat
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /tiamat/Tiamat__TmtA.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/uzume.md b/content/3.defense-systems/uzume.md
index 1e80fc27..a83d028e 100644
--- a/content/3.defense-systems/uzume.md
+++ b/content/3.defense-systems/uzume.md
@@ -26,27 +26,19 @@ The Uzume system in *Priestia megaterium* (GCF_013146705.1, NZ_CP045273) is comp
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Uzume is detected in 125 genomes (0.55 %).
-
-The system was detected in 87 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Uzume system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Uzume
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /uzume/Uzume__UzmA.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/viperin.md b/content/3.defense-systems/viperin.md
index 55cfa34c..ffb6f126 100644
--- a/content/3.defense-systems/viperin.md
+++ b/content/3.defense-systems/viperin.md
@@ -47,27 +47,19 @@ The Viperin system in *Vibrio sp. SCSIO 43009* (GCF_023716525.1, NZ_CP071842) is
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Viperin is detected in 118 genomes (0.52 %).
-
-The system was detected in 95 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Viperin system for the 14 phyla with more than 50 genomes in the RefSeq database.
+::article-system-distribution-plot
+::
+## Structure
+### List predicted structures
-## Structure
-### Viperin
-##### Example 1
+::article-structure
+::
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /viperin/Viperin__pVip.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
diff --git a/content/3.defense-systems/wadjet.md b/content/3.defense-systems/wadjet.md
index b7cf6be6..893a109c 100644
--- a/content/3.defense-systems/wadjet.md
+++ b/content/3.defense-systems/wadjet.md
@@ -51,75 +51,20 @@ The Wadjet_III system in *Cytobacillus spongiae* (GCF_021390075.1, NZ_CP089997)
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Wadjet is detected in 2351 genomes (10.31 %).
-
-The system was detected in 1467 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Wadjet system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
-
-## Structure
-
-### Experimentally determined structure
-
-From :ref{doi=10.1098/rstb.2004.1606} in *Pseudomonas aeruginosa* PA14:
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /wadjet/7til_JetD_2mer.pdb
- - /wadjet/8dk1_JetABC_2_4_2mer_head.pdb
- - /wadjet/8dk2_JetABC_2_4_2mer_dna.cif
----
+::article-system-distribution-plot
::
-### Wadjet_I
-##### Example 1
+## Structure
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /wadjet/Wadjet_I.Wadjet__JetA_I.0.V.cif
- - /wadjet/Wadjet_I.Wadjet__JetB_I.0.V.cif
- - /wadjet/Wadjet_I.Wadjet__JetC_I.0.V.cif
- - /wadjet/Wadjet_I.Wadjet__JetD_I.0.V.cif
+### List predicted structures
----
+::article-structure
::
-### Wadjet_II
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /wadjet/Wadjet_II.Wadjet__JetD_II.0.V.cif
- - /wadjet/Wadjet_II.Wadjet__JetC_II.0.V.cif
- - /wadjet/Wadjet_II.Wadjet__JetB_II.0.V.cif
- - /wadjet/Wadjet_II.Wadjet__JetA_II.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
-### Wadjet_III
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /wadjet/Wadjet_III.Wadjet__JetD_III.0.V.cif
- - /wadjet/Wadjet_III.Wadjet__JetA_III.0.V.cif
- - /wadjet/Wadjet_III.Wadjet__JetB_III.0.V.cif
- - /wadjet/Wadjet_III.Wadjet__JetC_III.0.V.cif
-
----
-::
-
## Experimental validation
diff --git a/content/3.defense-systems/zorya.md b/content/3.defense-systems/zorya.md
index 0ec6e008..888c4da8 100644
--- a/content/3.defense-systems/zorya.md
+++ b/content/3.defense-systems/zorya.md
@@ -54,43 +54,19 @@ The Zorya_TypeII system in *Pectobacterium aroidearum* (GCF_015689195.1, NZ_CP06
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the Zorya is detected in 803 genomes (3.52 %).
-
-The system was detected in 310 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the Zorya system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
+::article-system-distribution-plot
+::
## Structure
-### Zorya_TypeI
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /zorya/Zorya_TypeI.Zorya_TypeI__ZorC.0.V.cif
- - /zorya/Zorya_TypeI.Zorya_TypeI__ZorD.0.V.cif
- - /zorya/Zorya_TypeII.Zorya__ZorA.0.V.cif
- - /zorya/Zorya_TypeI.Zorya__ZorB.0.V.cif
+### List predicted structures
----
+::article-structure
::
-### Zorya_TypeII
-##### Example 1
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
- - /zorya/Zorya_TypeII.Zorya__ZorA.0.V.cif
- - /zorya/Zorya_TypeI.Zorya__ZorB.0.V.cif
- - /zorya/Zorya_TypeII.Zorya_TypeII__ZorE.0.V.cif
+### pDockQ matrix
----
+::pdockq-matrix
::
## Experimental validation
--
GitLab