Merge branch 'operon-struct-type-article' into operon-struct-type

.gitlab-ci.yml

@@ -518,7 +518,7 @@ build:prod:wiki:
 deploy:dev:
   extends: .deploy
   rules:
-    - if: $CI_COMMIT_BRANCH == "dev" || $CI_COMMIT_BRANCH == "operon-struct-type-article-update"
+    - if: $CI_COMMIT_BRANCH == "dev" || $CI_COMMIT_BRANCH == "operon-struct-type-article"
   needs:
     - "build:dev:wiki"
   when: manual

content/3.defense-systems/abi2.md

@@ -44,30 +44,14 @@ 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.
-
-![abi2](/abi2/Distribution_Abi2.svg){max-width=750px}
-
-Proportion of genome encoding the Abi2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-## Structure 
-
-### Abi2/AbiD
-
-##### Example 1
+::article-system-distribution-plot
+::
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
-   - /abid/AbiD__AbiD.cif
+## Structure
 
----
+::article-structure
 ::
 
-
 ## Experimental validation 
 
 As Abi2 is a group of different Abortive infection systems, here is the experimental validation of AbiD:

content/3.defense-systems/abia.md

@@ -54,24 +54,11 @@ The AbiA_small system in *Alicyclobacillus sp. SO9* (GCF_016406125.1, NZ_CP06633
 ::article-system-distribution-plot
 ::
 
-
 ## Structure
 
-
-::system-operon-structure
-::
-
-### pDockQ matrix
-
-::pdockq-matrix
-::
-
-### List predicted structures
-
 ::article-structure
 ::
 
-
 ## Experimental validation
 
 

content/3.defense-systems/abib.md

@@ -38,27 +38,12 @@ 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.
-
-![abib](/abib/Distribution_AbiB.svg){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
-### AbiB
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
-   - /abib/AbiB__AbiB.cif
 
----
+::article-structure
 ::
 
 ## Experimental validation

content/3.defense-systems/abic.md

@@ -45,27 +45,12 @@ 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.
-
-![abic](/abic/Distribution_AbiC.svg){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
-### AbiC
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
-   - /abic/AbiC__AbiC.cif
 
----
+::article-structure
 ::
 
 ## Experimental validation

content/3.defense-systems/abid.md

@@ -45,27 +45,12 @@ 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.
-
-![abid](/abid/Distribution_AbiD.svg){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
-### AbiD
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
-   - /abid/AbiD__AbiD.cif
 
----
+::article-structure
 ::
 
 ## Experimental validation

content/3.defense-systems/abie.md

@@ -48,28 +48,12 @@ 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.
-
-![abie](/abie/Distribution_AbiE.svg){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
-### AbiE
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
-   - /abie/AbiE.AbiE__AbiEi.0.V.cif
-   - /abie/AbiE.AbiE__AbiEii.0.V.cif
 
----
+::article-structure
 ::
 
 ## Experimental validation

content/3.defense-systems/abig.md

@@ -45,28 +45,12 @@ 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.
-
-![abig](/abig/Distribution_AbiG.svg){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
-### AbiG
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
-   - /abig/AbiG.AbiG__AbiGi.0.V.cif
-   - /abig/AbiG.AbiG__AbiGii.0.V.cif
 
----
+::article-structure
 ::
 
 ## Experimental validation

content/3.defense-systems/abih.md

@@ -43,27 +43,12 @@ 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.
-
-![abih](/abih/Distribution_AbiH.svg){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
-### AbiH
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
-   - /abih/AbiH__AbiH.cif
 
----
+::article-structure
 ::
 
 ## Experimental validation

content/3.defense-systems/abii.md

@@ -39,27 +39,12 @@ 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.
-
-![abii](/abii/Distribution_AbiI.svg){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
-### AbiI
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
-   - /abii/AbiI__AbiI.cif
 
----
+::article-structure
 ::
 
 ## Experimental validation

content/3.defense-systems/abij.md

@@ -44,27 +44,12 @@ 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.
-
-![abij](/abij/Distribution_AbiJ.svg){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
-### AbiJ
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
-   - /abij/AbiJ__AbiJ.cif
 
----
+::article-structure
 ::
 
 ## Experimental validation

content/3.defense-systems/abik.md

@@ -48,27 +48,12 @@ 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.
-
-![abik](/abik/Distribution_AbiK.svg){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
-### AbiK
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
-   - /abik/AbiK__AbiK.cif
 
----
+::article-structure
 ::
 
 ## Experimental validation

content/3.defense-systems/abil.md

@@ -40,28 +40,12 @@ 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.
-
-![abil](/abil/Distribution_AbiL.svg){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
-### AbiL
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
-   - /abil/AbiL.AbiL__AbiLi.0.V.cif
-   - /abil/AbiL.AbiL__AbiLii.0.V.cif
 
----
+::article-structure
 ::
 
 ## Experimental validation

content/3.defense-systems/abin.md

@@ -42,27 +42,12 @@ 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.
-
-![abin](/abin/Distribution_AbiN.svg){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
-### AbiN
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
-   - /abin/AbiN__AbiN.cif
 
----
+::article-structure
 ::
 
 ## Experimental validation

content/3.defense-systems/abio.md

@@ -45,27 +45,12 @@ 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.
-
-![abio](/abio/Distribution_AbiO.svg){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
-### AbiO
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
-   - /abio/AbiO__AbiO.cif
 
----
+::article-structure
 ::
 
 ## Experimental validation

content/3.defense-systems/abip2.md

@@ -50,27 +50,12 @@ 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.
-
-![abip2](/abip2/Distribution_AbiP2.svg){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
-### AbiP2
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
-   - /abip2/AbiP2__AbiP2.cif
 
----
+::article-structure
 ::
 
 ## Experimental validation

content/3.defense-systems/abiq.md

@@ -49,39 +49,12 @@ 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.
-
-![abiq](/abiq/Distribution_AbiQ.svg){max-width=750px}
-
-Proportion of genome encoding the AbiQ system for the 14 phyla with more than 50 genomes in the RefSeq database.
-
-
-## Structure
-### Experimentally determined structure
-
-From :ref{doi=10.1111/mmi.12129} in *Lactococcus lactis*:
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /abiq/4glk_LlAbiQ_1mer.cif
----
+::article-system-distribution-plot
 ::
 
-
 ## Structure
-### AbiQ
-##### Example 1
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
-   - /abiq/AbiQ__AbiQ.cif
-
----
+::article-structure
 ::
 
 ## Experimental validation

content/3.defense-systems/abir.md

@@ -45,29 +45,12 @@ 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.
-
-![abir](/abir/Distribution_AbiR.svg){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
-### AbiR
-##### Example 1
-
-::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
 
----
+::article-structure
 ::
 
 ## Experimental validation

content/3.defense-systems/abit.md

@@ -44,28 +44,12 @@ 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.
-
-![abit](/abit/Distribution_AbiT.svg){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
-### AbiT
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
-   - /abit/AbiT.AbiT__AbiTi.0.V.cif
-   - /abit/AbiT.AbiT__AbiTii.0.V.cif
 
----
+::article-structure
 ::
 
 ## Experimental validation

content/3.defense-systems/abiu.md

@@ -38,27 +38,12 @@ 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.
-
-![abiu](/abiu/Distribution_AbiU.svg){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
-### AbiU
-##### Example 1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls:
-   - /abiu/AbiU__AbiU.cif
 
----
+::article-structure
 ::
 
 ## Experimental validation