content/3.defense-systems/abir.md

@@ -15,23 +15,24 @@ tableColumns:
 # AbiR
 ## Example of genomic structure
 
-The AbiR system is composed of 3 proteins: AbiRc, AbiRb and, AbiRa.
+The AbiR is composed of 3 proteins: AbiRa, AbiRb and AbiRc.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![abir](/abir/AbiR.svg){max-width=750px}
 
-AbiR system in the genome of *Pediococcus pentosaceus* (GCF_019614475.1) is composed of 3 proteins: AbiRa (WP_220689027.1), AbiRb (WP_011673124.1)and, AbiRc (WP_011673125.1).
+The AbiR system in *Clostridium perfringens* (GCF_016027155.1, NZ_CP065677) is composed of 3 proteins AbiRc (WP_049039794.1) AbiRb (WP_049039795.1) AbiRa (WP_049039796.1) 
 
 ## Distribution of the system among prokaryotes
 
-The AbiR system is present in a total of 31 different species.
+Among the 22,803 complete genomes of RefSeq, the AbiR is detected in 51 genomes (0.22 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 56 genomes (0.2 %).
+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.* 
+Proportion of genome encoding the AbiR system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/abit.md

@@ -15,23 +15,24 @@ tableColumns:
 # AbiT
 ## Example of genomic structure
 
-The AbiT system is composed of 2 proteins: AbiTii and, AbiTi.
+The AbiT is composed of 2 proteins: AbiTi and AbiTii.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![abit](/abit/AbiT.svg){max-width=750px}
 
-AbiT system in the genome of *Sphaerochaeta associata* (GCF_022869165.1) is composed of 2 proteins: AbiTi (WP_244771454.1)and, AbiTii (WP_244771455.1).
+The AbiT system in *Bdellovibrio bacteriovorus* (GCF_000317895.1, NC_019567) is composed of 2 proteins AbiTii (WP_051026283.1) AbiTi (WP_041577337.1) 
 
 ## Distribution of the system among prokaryotes
 
-The AbiT system is present in a total of 5 different species.
+Among the 22,803 complete genomes of RefSeq, the AbiT is detected in 8 genomes (0.04 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 8 genomes (0.0 %).
+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.* 
+Proportion of genome encoding the AbiT system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/abiu.md

@@ -28,23 +28,24 @@ The molecular mechanism of AbiU is not well understood. It was shown that cells
 
 ## Example of genomic structure
 
-The AbiU system is composed of one protein: AbiU.
+The AbiU is composed of 1 protein: AbiU.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![abiu](/abiu/AbiU.svg){max-width=750px}
 
-AbiU system in the genome of *Fulvivirga lutea* (GCF_017068455.1) is composed of 1 protein: AbiU (WP_205721428.1).
+The AbiU system in *Bacillus subtilis* (GCF_001889385.1, NZ_CP018295) is composed of 1 protein: AbiU (WP_072589761.1) 
 
 ## Distribution of the system among prokaryotes
 
-The AbiU system is present in a total of 390 different species.
+Among the 22,803 complete genomes of RefSeq, the AbiU is detected in 950 genomes (4.17 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 1017 genomes (4.5 %).
+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.* 
+Proportion of genome encoding the AbiU system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/abiv.md

@@ -15,23 +15,24 @@ tableColumns:
 # AbiV
 ## Example of genomic structure
 
-The AbiV system is composed of one protein: AbiV.
+The AbiV is composed of 1 protein: AbiV.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![abiv](/abiv/AbiV.svg){max-width=750px}
 
-AbiV system in the genome of *Lactococcus cremoris* (GCF_017376415.1) is composed of 1 protein: AbiV (WP_011834704.1).
+The AbiV system in *Bacillus mycoides* (GCF_018739365.1, NZ_CP035984) is composed of 1 protein: AbiV (WP_070128168.1) 
 
 ## Distribution of the system among prokaryotes
 
-The AbiV system is present in a total of 76 different species.
+Among the 22,803 complete genomes of RefSeq, the AbiV is detected in 97 genomes (0.43 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 126 genomes (0.6 %).
+The system was detected in 61 different species.
 
 ![abiv](/abiv/Distribution_AbiV.svg){max-width=750px}
 
-*Proportion of genome encoding the AbiV system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the AbiV system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/abiz.md

@@ -14,23 +14,24 @@ tableColumns:
 # AbiZ
 ## Example of genomic structure
 
-The AbiZ system is composed of one protein: AbiZ.
+The AbiZ is composed of 1 protein: AbiZ.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![abiz](/abiz/AbiZ.svg){max-width=750px}
 
-AbiZ system in the genome of *Streptococcus oralis* (GCF_019334565.1) is composed of 1 protein: AbiZ (WP_215804505.1).
+The AbiZ system in *Fusobacterium pseudoperiodonticum* (GCF_002763695.1, NZ_CP024700) is composed of 1 protein: AbiZ (WP_099987858.1) 
 
 ## Distribution of the system among prokaryotes
 
-The AbiZ system is present in a total of 191 different species.
+Among the 22,803 complete genomes of RefSeq, the AbiZ is detected in 118 genomes (0.52 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 831 genomes (3.6 %).
+The system was detected in 97 different species.
 
 ![abiz](/abiz/Distribution_AbiZ.svg){max-width=750px}
 
-*Proportion of genome encoding the AbiZ system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the AbiZ system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/aditi.md

@@ -15,23 +15,24 @@ tableColumns:
 # Aditi
 ## Example of genomic structure
 
-The Aditi system is composed of 2 proteins: DitB and, DitA.
+The Aditi is composed of 2 proteins: DitA and DitB.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![aditi](/aditi/Aditi.svg){max-width=750px}
 
-Aditi system in the genome of *Fusobacterium hwasookii* (GCF_001455105.1) is composed of 2 proteins: DitB (WP_029491896.1)and, DitA (WP_029491897.1).
+The Aditi system in *Streptococcus suis* (GCF_003288175.1, NZ_CP025419) is composed of 2 proteins DitB (WP_002937368.1) DitA (WP_002937371.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Aditi system is present in a total of 18 different species.
+Among the 22,803 complete genomes of RefSeq, the Aditi is detected in 40 genomes (0.18 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 40 genomes (0.2 %).
+The system was detected in 19 different species.
 
 ![aditi](/aditi/Distribution_Aditi.svg){max-width=750px}
 
-*Proportion of genome encoding the Aditi system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the Aditi system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/avs.md

@@ -30,39 +30,40 @@ Upon binding to their cognate phage protein, Avs1-4 assemble into tetramers that
 
 ## Example of genomic structure
 
-The Avs system have been describe in a total of 5 subsystems.
+A total of 5 subsystems have been described for the Avs system.
 
-Here is some example found in the RefSeq database:
+Here is some examples found in the RefSeq database:
 
-![avs](/avs/Avs_I.svg){max-width=750px}
+![avs_i](/avs/Avs_I.svg){max-width=750px}
 
-Avs_I subsystem in the genome of *Vibrio sp.* (GCF_905175355.1) is composed of 3 proteins: Avs1A (WP_208445041.1), Avs1B (WP_208445042.1)and, Avs1C (WP_108173272.1).
+The Avs_I system in *Priestia aryabhattai* (GCF_022811825.1, NZ_CP064098) is composed of 3 proteins Avs1C (WP_243495694.1) Avs1B (WP_243495695.1) Avs1A (WP_243495696.1) 
 
-![avs](/avs/Avs_II.svg){max-width=750px}
+![avs_ii](/avs/Avs_II.svg){max-width=750px}
 
-Avs_II subsystem in the genome of *Escherichia coli* (GCF_018884505.1) is composed of 1 protein: Avs2A (WP_032199984.1).
+The Avs_II system in *Haloferax volcanii* (GCF_000025685.1, NC_013967) is composed of 1 protein: Avs2A (WP_013035348.1) 
 
-![avs](/avs/Avs_III.svg){max-width=750px}
+![avs_iii](/avs/Avs_III.svg){max-width=750px}
 
-Avs_III subsystem in the genome of *Enterobacter cancerogenus* (GCF_002850575.1) is composed of 2 proteins: Avs3B (WP_199559884.1)and, Avs3A (WP_101737373.1).
+The Avs_III system in *Chryseobacterium indologenes* (GCF_002208925.2, NZ_CP022058) is composed of 2 proteins Avs3B (WP_002978689.1) Avs3A (WP_088583894.1) 
 
-![avs](/avs/Avs_IV.svg){max-width=750px}
+![avs_iv](/avs/Avs_IV.svg){max-width=750px}
 
-Avs_IV subsystem in the genome of *Escherichia coli* (GCF_016903595.1) is composed of 1 protein: Avs4A (WP_000240574.1).
+The Avs_IV system in *Dysosmobacter welbionis* (GCF_005121165.3, NZ_CP034413) is composed of 1 protein: Avs4A (WP_136890703.1) 
 
-![avs](/avs/Avs_V.svg){max-width=750px}
+![avs_v](/avs/Avs_V.svg){max-width=750px}
 
-Avs_V subsystem in the genome of *Leclercia adecarboxylata* (GCF_006171285.1) is composed of 1 protein: Avs5A (WP_139565349.1).
+The Avs_V system in *Klebsiella variicola* (GCF_015287155.1, NZ_CP063912) is composed of 1 protein: Avs5A (WP_131026359.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Avs system is present in a total of 363 different species.
+Among the 22,803 complete genomes of RefSeq, the Avs is detected in 978 genomes (4.29 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 1046 genomes (4.6 %).
+The system was detected in 366 different species.
 
 ![avs](/avs/Distribution_Avs.svg){max-width=750px}
 
-*Proportion of genome encoding the Avs system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.*
+Proportion of genome encoding the Avs system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 
@@ -80,61 +81,6 @@ dataUrls:
 ::
 
 
-## Structure
-
-### Avs_I
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls: 
-    - /avs/AVAST_I,AVAST_I__Avs1A,0,V-plddts_85.07081.pdb
-    - /avs/AVAST_I,AVAST_I__Avs1B,0,V-plddts_80.96481.pdb
-    - /avs/AVAST_I,AVAST_I__Avs1C,0,V-plddts_81.74849.pdb
----
-::
-
-### Avs_II
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls: 
-    - /avs/AVAST_II__Avs2A-plddts_86.07393.pdb
----
-::
-
-### Avs_III
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls: 
-    - /avs/AVAST_III,AVAST_III__Avs3A,0,V-plddts_81.87773.pdb
-    - /avs/AVAST_III,AVAST_III__Avs3B,0,V-plddts_71.16048.pdb
----
-::
-
-### Avs_IV
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls: 
-    - /avs/AVAST_IV__Avs4A-plddts_87.35544.pdb
----
-::
-
-### Avs_V
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrls: 
-    - /avs/AVAST_V__Avs5A-plddts_89.56857.pdb
----
-::
-
 ## Experimental validation
 
 <mermaid>

content/3.defense-systems/azaca.md

@@ -15,23 +15,24 @@ tableColumns:
 # Azaca
 ## Example of genomic structure
 
-The Azaca system is composed of 3 proteins: ZacA, ZacB and, ZacC.
+The Azaca is composed of 3 proteins: ZacA, ZacB and ZacC.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![azaca](/azaca/Azaca.svg){max-width=750px}
 
-Azaca system in the genome of *Ornithinimicrobium sp.* (GCF_023923205.1) is composed of 3 proteins: ZacA (WP_252620090.1), ZacB (WP_252620091.1)and, ZacC (WP_252620092.1).
+The Azaca system in *Gordonia polyisoprenivorans* (GCF_018135605.1, NZ_CP073075) is composed of 3 proteins ZacC (WP_006372053.1) ZacB (WP_006372052.1) ZacA (WP_006372051.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Azaca system is present in a total of 156 different species.
+Among the 22,803 complete genomes of RefSeq, the Azaca is detected in 203 genomes (0.89 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 206 genomes (0.9 %).
+The system was detected in 166 different species.
 
 ![azaca](/azaca/Distribution_Azaca.svg){max-width=750px}
 
-*Proportion of genome encoding the Azaca system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the Azaca system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/borvo.md

@@ -29,23 +29,24 @@ Mutations in the phage DNA polymerase can allow phages to escape Borvo defense,
 
 ## Example of genomic structure
 
-The Borvo system is composed of one protein: BovA.
+The Borvo is composed of 1 protein: BovA.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![borvo](/borvo/Borvo.svg){max-width=750px}
 
-Borvo system in the genome of *Brevundimonas sp.* (GCF_002002865.1) is composed of 1 protein: BovA_addition (WP_077354142.1).
+The Borvo system in *Enterobacter cloacae complex sp. ECL78* (GCF_019056615.1, NZ_CP077660) is composed of 1 protein: BovA (WP_126517459.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Borvo system is present in a total of 348 different species.
+Among the 22,803 complete genomes of RefSeq, the Borvo is detected in 177 genomes (0.78 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 650 genomes (2.9 %).
+The system was detected in 79 different species.
 
 ![borvo](/borvo/Distribution_Borvo.svg){max-width=750px}
 
-*Proportion of genome encoding the Borvo system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the Borvo system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/brex.md

@@ -37,8 +37,6 @@ To date, BREX molecular mechanism remains to be described.
 
 ## Example of genomic structure
 
-There are 6 subsystems described for the BREX system.
-
 BREX systems necessarily include the pglZ gene (encoding for a putative alkaline phosphatase), which is accompanied by either brxC or pglY. These two genes share only a distant homology but have been hypothesized to fulfill the same function among the different BREX subtypes :ref{doi=10.15252/embj.201489455}.
 
 Goldfarb and colleagues reported a 6-gene cassette from *Bacillus cereus* as being the model for BREX Type 1. BREX Type 1 are the most widespread BREX systems, and present two core genes (pglZ and brxC).  Four other genes  are associated with BREX Type 1 : *pglX (*encoding for a putative methyltransferase),  *brxA (*encoding an RNA-binding anti-termination protein)*, brxB (*unknown functio*n), brxC (*encoding for a protein with ATP-binding domain) and *brxL* (encoding for a putative protease) :ref{doi=10.15252/embj.201489455,10.1093/nar/gkaa290}.
@@ -47,25 +45,44 @@ Type 2 BREX systems include the system formerly known as Pgl, which is comprised
 
 Although 4 additional BREX subtypes have been proposed, BREX Type 1 and Type 2 remain the only ones to be experimentally validated. A detailed description of the other subtypes can be found in :ref{doi=10.15252/embj.201489455}.
 
-Here is some example found in the RefSeq database:
+A total of 6 subsystems have been described for the BREX system.
+
+Here is some examples found in the RefSeq database:
+
+![brex_i](/brex/BREX_I.svg){max-width=750px}
+
+The BREX_I system in *Mycobacterium kubicae* (GCF_015689175.1, NZ_CP065047) is composed of 6 proteins brxA_DUF1819 (WP_241007777.1) brxB_DUF1788 (WP_174814228.1) brxC (WP_085074024.1) pglX1 (WP_085074003.1) pglZA (WP_085074004.1) brxL (WP_085074005.1) 
+
+![brex_ii](/brex/BREX_II.svg){max-width=750px}
+
+The BREX_II system in *Nocardia terpenica* (GCF_002568625.1, NZ_CP023778) is composed of 6 proteins pglW (WP_232535326.1) pglX2 (WP_098693854.1) pglY (WP_098693855.1) pglZ2 (WP_098693856.1) brxD (WP_098693857.1) brxHI (WP_098693858.1) 
 
-![brex](/brex/BREX_I.svg){max-width=750px}
+![brex_iii](/brex/BREX_III.svg){max-width=750px}
 
-BREX_I subsystem in the genome of *Kaistella sp.* (GCF_020410745.1) is composed of 6 proteins: brxL (WP_226063319.1), pglZA (WP_226063320.1), pglX1 (WP_226063321.1), brxC (WP_226063322.1), brxB_DUF1788 (WP_226063323.1)and, brxA_DUF1819 (WP_226063324.1).
+The BREX_III system in *Rubinisphaera brasiliensis* (GCF_000165715.2, NC_015174) is composed of 5 proteins pglZ3 (WP_013627487.1) brxHII (WP_013627488.1) pglXI (WP_013627489.1) brxC (WP_041397812.1) brxF (WP_218916504.1) 
 
-![brex](/brex/BREX_II.svg){max-width=750px}
+![brex_iv](/brex/BREX_IV.svg){max-width=750px}
 
-BREX_II subsystem in the genome of *Streptomyces hygroscopicus* (GCF_001447075.1) is composed of 5 proteins: brxD (WP_058082289.1), pglZ2 (WP_058082290.1), pglY (WP_058082291.1), pglX2 (WP_058082292.1)and, pglW (WP_237280966.1).
+The BREX_IV system in *Olsenella sp. oral taxon 807* (GCF_001189515.2, NZ_CP012069) is composed of 4 proteins brxL (WP_050344523.1) pglZ4 (WP_172674480.1) brxC4 (WP_050340978.1) brxP (WP_050340980.1) 
+
+![brex_v](/brex/BREX_V.svg){max-width=750px}
+
+The BREX_V system in *Heyndrickxia vini* (GCF_016772275.1, NZ_CP065425) is composed of 7 proteins brxHII (WP_202780866.1) pglZA (WP_202778092.1) pglX1 (WP_202778093.1) pglX1 (WP_202778094.1) brxC (WP_202778095.1) brxB_DUF1788 (WP_246483846.1) brxA_DUF1819 (WP_202778096.1) 
+
+![brex_vi](/brex/BREX_VI.svg){max-width=750px}
+
+The BREX_VI system in *Virgibacillus halodenitrificans* (GCF_001878675.1, NZ_CP017962) is composed of 8 proteins brxE (WP_071648637.1) brxA_DUF1819 (WP_071648638.1) brxB_DUF1788 (WP_071648639.1) brxC (WP_197035844.1) pglX1 (WP_071648641.1) pglZA (WP_071648642.1) brxD (WP_071648643.1) brxHI (WP_071648644.1) 
 
 ## Distribution of the system among prokaryotes
 
-The BREX system is present in a total of 732 different species.
+Among the 22,803 complete genomes of RefSeq, the BREX is detected in 1658 genomes (7.27 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 1612 genomes (7.1 %).
+The system was detected in 888 different species.
 
 ![brex](/brex/Distribution_BREX.svg){max-width=750px}
 
-*Proportion of genome encoding the BREX system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.*
+Proportion of genome encoding the BREX system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/bsta.md

@@ -24,23 +24,24 @@ Interestingly, part of the BstA locus appears to encode an anti-BstA genetic ele
 
 ## Example of genomic structure
 
-The BstA system is composed of one protein: BstA.
+The BstA is composed of 1 protein: BstA.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![bsta](/bsta/BstA.svg){max-width=750px}
 
-BstA system in the genome of *Providencia rustigianii* (GCF_900635875.1) is composed of 1 protein: BstA (WP_126437212.1).
+The BstA system in *Vibrio harveyi* (GCF_021397735.1, NZ_CP090179) is composed of 1 protein: BstA (WP_038899043.1) 
 
 ## Distribution of the system among prokaryotes
 
-The BstA system is present in a total of 81 different species.
+Among the 22,803 complete genomes of RefSeq, the BstA is detected in 236 genomes (1.03 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 236 genomes (1.0 %).
+The system was detected in 88 different species.
 
 ![bsta](/bsta/Distribution_BstA.svg){max-width=750px}
 
-*Proportion of genome encoding the BstA system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the BstA system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/bunzi.md

@@ -26,23 +26,24 @@ As far as we are aware, the molecular mechanism is unknown.
 
 ## Example of genomic structure
 
-The Bunzi system is composed of 2 proteins: BnzB and, BnzA.
+The Bunzi is composed of 2 proteins: BnzA and BnzB.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![bunzi](/bunzi/Bunzi.svg){max-width=750px}
 
-Bunzi system in the genome of *Mammaliicoccus lentus* (GCF_014070215.1) is composed of 2 proteins: BnzB (WP_107556517.1)and, BnzA (WP_107556516.1).
+The Bunzi system in *Shewanella loihica* (GCF_000016065.1, NC_009092) is composed of 2 proteins BnzB (WP_011866821.1) BnzA (WP_011866822.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Bunzi system is present in a total of 86 different species.
+Among the 22,803 complete genomes of RefSeq, the Bunzi is detected in 103 genomes (0.45 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 286 genomes (1.3 %).
+The system was detected in 58 different species.
 
 ![bunzi](/bunzi/Distribution_Bunzi.svg){max-width=750px}
 
-*Proportion of genome encoding the Bunzi system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the Bunzi system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/butters_gp30_gp31.md

@@ -12,6 +12,27 @@ tableColumns:
 
 ## To do 
 
+## Example of genomic structure
+
+The Butters_gp30_gp31 is composed of 2 proteins: Butters_gp30 and Butters_gp31.
+
+Here is an example found in the RefSeq database:
+
+![butters_gp30_gp31](/butters_gp30_gp31/Butters_gp30_gp31.svg){max-width=750px}
+
+The Butters_gp30_gp31 system in *Snodgrassella alvi* (GCF_022870965.1, NZ_CP091515) is composed of 2 proteins Butters_gp31 (WP_025330184.1) CarolAnn_gp44 (WP_144353282.1) 
+
+## 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.
+
+![butters_gp30_gp31](/butters_gp30_gp31/Distribution_Butters_gp30_gp31.svg){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.
+
+
 ## Structure
 
 ### Butters_gp30_gp31

content/3.defense-systems/butters_gp57r.md

@@ -12,6 +12,27 @@ tableColumns:
 
 ## To do 
 
+## Example of genomic structure
+
+The Butters_gp57r is composed of 1 protein: gp57r.
+
+Here is an example found in the RefSeq database:
+
+![butters_gp57r](/butters_gp57r/Butters_gp57r.svg){max-width=750px}
+
+The Butters_gp57r system in *Mycobacteroides immunogenum* (GCF_001605725.1, NZ_CP011530) is composed of 1 protein: gp57r (WP_043080133.1) 
+
+## 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.
+
+![butters_gp57r](/butters_gp57r/Distribution_Butters_gp57r.svg){max-width=750px}
+
+Proportion of genome encoding the Butters_gp57r system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
+
 ## Structure
 
 ### Butters_gp57r

content/3.defense-systems/caprel.md

@@ -27,23 +27,24 @@ Different CapRel homologues confer defense against different phages, suggesting
 
 ## Example of genomic structure
 
-The CapRel system is composed of one protein: CapRel.
+The CapRel is composed of 1 protein: CapRel.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![caprel](/caprel/CapRel.svg){max-width=750px}
 
-CapRel system in the genome of *Escherichia coli* (GCF_003856995.1) is composed of 1 protein: CapRel (WP_000526244.1).
+The CapRel system in *Campylobacter sp. RM12175* (GCF_002139875.1, NZ_CP018793) is composed of 1 protein: CapRel (WP_086315994.1) 
 
 ## Distribution of the system among prokaryotes
 
-The CapRel system is present in a total of 202 different species.
+Among the 22,803 complete genomes of RefSeq, the CapRel is detected in 398 genomes (1.75 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 407 genomes (1.8 %).
+The system was detected in 217 different species.
 
 ![caprel](/caprel/Distribution_CapRel.svg){max-width=750px}
 
-*Proportion of genome encoding the CapRel system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the CapRel system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/card_nlr.md

@@ -13,6 +13,43 @@ tableColumns:
 
 ## To do 
 
+## Example of genomic structure
+
+A total of 5 subsystems have been described for the CARD_NLR system.
+
+Here is some examples found in the RefSeq database:
+
+![card_nlr_endonuclease](/card_nlr/CARD_NLR_Endonuclease.svg){max-width=750px}
+
+The CARD_NLR_Endonuclease system in *Spirosoma montaniterrae* (GCF_001988955.1, NZ_CP014263) is composed of 4 proteins Trypsin (WP_077131797.1) CARD_Protease_new (WP_077131798.1) NLR_new (WP_157579217.1) Endonuclease (WP_083732853.1) 
+
+![card_nlr_gasdermin](/card_nlr/CARD_NLR_GasderMIN.svg){max-width=750px}
+
+The CARD_NLR_GasderMIN system in *Lysobacter enzymogenes* (GCF_005954665.1, NZ_CP040656) is composed of 4 proteins bGSDM (WP_057949280.1) Trypsin_new (WP_158229849.1) CARD_Protease (WP_175429318.1) NLR_new (WP_057949283.1) 
+
+![card_nlr_phospho](/card_nlr/CARD_NLR_Phospho.svg){max-width=750px}
+
+The CARD_NLR_Phospho system in *Achromobacter deleyi* (GCF_013116765.2, NZ_CP074375) is composed of 4 proteins Trypsin_Phospho (WP_171663676.1) Trypsin_new (WP_171663675.1) CARD_Protease_supposed (WP_171663674.1) NLR_new (WP_171663673.1) 
+
+![card_nlr_subtilase](/card_nlr/CARD_NLR_Subtilase.svg){max-width=750px}
+
+The CARD_NLR_Subtilase system in *Mesorhizobium sp. L-8-3* (GCF_016756615.1, NZ_AP023262) is composed of 4 proteins Subtilase (WP_202329294.1) Trypsin_new (WP_202305630.1) CARD_Protease_supposed (WP_202305632.1) NLR_IMG (WP_202329295.1) 
+
+![card_nlr_like](/card_nlr/CARD_NLR_like.svg){max-width=750px}
+
+The CARD_NLR_like system in *Sphingomonas sanguinis* (GCF_019297835.1, NZ_CP079203) is composed of 4 proteins Subtilase (WP_219018701.1) CARD_Protease_new (WP_219018702.1) NLR_new (WP_219018703.1) Endonuclease (WP_219021412.1) 
+
+## Distribution of the system among prokaryotes
+
+Among the 22,803 complete genomes of RefSeq, the CARD_NLR is detected in 80 genomes (0.35 %).
+
+The system was detected in 57 different species.
+
+![card_nlr](/card_nlr/Distribution_CARD_NLR.svg){max-width=750px}
+
+Proportion of genome encoding the CARD_NLR system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
+
 ## Relevant abstract
 ::relevant-abstracts
 ---

content/3.defense-systems/cas.md

+---
+title: CRISPR-Cas
+layout: article
+tableColumns:
+    article:
+      doi: 10.1038/nrmicro3569
+      abstract: |
+        The evolution of CRISPR-cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR-cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR-Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized.
+---
+
+# CRISPR-Cas
+
+For the CRISPR-Cas system, a good place to start is the [Wikipedia page](https://en.wikipedia.org/wiki/CRISPR)
+
+## Example of genomic structure
+
+CRISPR-Cas systems have been classified in 6 different families :ref{doi=10.1038/s41579-019-0299-x}.
+Each family is composed of different subtypes. For example, Type I CRISPR is composed of 7 subtypes: I-A to I-G.
+
+Here is example of each of the 6 family found in the RefSeq database:
+
+![cas_class1-subtype-i-e](/cas/CAS_Class1-Subtype-I-E.svg){max-width=750px}
+
+The CAS_Class1-Subtype-I-E system in *Citrobacter sp. RHBSTW-00017* (GCF_013797615.1, NZ_CP056899) is composed of 8 proteins cas3_I_5 (WP_103284157.1) cas8e_I-E_1 (HV037_RS05730) cse2gr11_I-E_2 (HV037_RS05735) cas7_I-E_2 (HV037_RS05740) cas5_I-E_3 (HV037_RS05745) cas6e_I_II_III_IV_V_VI_1 (HV037_RS05750) cas1_I-E_1 (HV037_RS05755) cas2_I-E_2 (HV037_RS05760) 
+
+![cas_class2-subtype-ii-a](/cas/CAS_Class2-Subtype-II-A.svg){max-width=750px}
+
+The CAS_Class2-Subtype-II-A system in *Streptococcus agalactiae* (GCF_001190885.1, NZ_CP011329) is composed of 4 proteins cas9_II-A_II-B_II-C_3 (SAH002_RS04760) cas1_I_II_III_IV_V_VI_5 (SAH002_RS04765) cas2_I_II_III_IV_V_VI_6 (SAH002_RS04770) csn2_II-A_4 (SAH002_RS04775) 
+
+![cas_class1-subtype-iii-a](/cas/CAS_Class1-Subtype-III-A.svg){max-width=750px}
+
+The CAS_Class1-Subtype-III-A system in *Mycobacterium tuberculosis* (GCF_014900005.1, NZ_CP041828) is composed of 9 proteins cas2_I_II_III_IV_V_VI_5 (FPJ80_RS14760) cas1_I_II_III_IV_V_VI_8 (FPJ80_RS14765) csm6_III_2 (FPJ80_RS14770) csm5gr7_III-A_3 (FPJ80_RS14775) csm4gr5_III-A_3 (FPJ80_RS14780) csm3gr7_III-A_1 (FPJ80_RS14785) csm2gr11_III-A_1 (FPJ80_RS14790) cas10_III_7 (FPJ80_RS14795) cas6_I_II_III_IV_V_VI_15 (FPJ80_RS14800) 
+
+![cas_class1-subtype-iv-a](/cas/CAS_Class1-Subtype-IV-A.svg){max-width=750px}
+
+The CAS_Class1-Subtype-IV-A system in *Shigella flexneri* (GCF_022353685.1, NZ_CP054978) is composed of 5 proteins csf1gr8_IV-A_3 (WP_038989757.1) cas6e_I_II_III_IV_V_VI_3 (WP_038989755.1) csf4_IV-A_1 (WP_016947078.1) csf3gr5_IV-A_1 (WP_004181864.1) csf2gr7_IV-A_1 (WP_029505552.1) 
+
+
+![cas_class2-subtype-v-a](/cas/CAS_Class2-Subtype-V-A.svg){max-width=750px}
+
+The CAS_Class2-Subtype-V-A system in *Francisella tularensis* (GCF_001865695.1, NZ_CP016635) is composed of 4 proteins cas2_I_II_III_IV_V_VI_3 (N894_RS07580) cas1_I_II_III_IV_V_VI_1 (N894_RS07585) cas4_V_1 (N894_RS07590) cas12a_V-A_4 (N894_RS07595) 
+
+![cas_class2-subtype-vi-a](/cas/CAS_Class2-Subtype-VI-A.svg){max-width=750px}
+
+The CAS_Class2-Subtype-VI-A system in *Leptotrichia shahii* (GCF_008327825.1, NZ_AP019827) is composed of 3 proteins cas13a_VI-A_1 (F1564_RS00570) cas1_I_II_III_IV_V_VI_5 (F1564_RS00575) cas2_I_II_III_IV_V_VI_11 (F1564_RS00580) 
+
+## Distribution of the system among prokaryotes
+
+Among the 22,803 complete genomes of RefSeq, the AbiC is detected in 8581 genomes (37.63 %).
+
+The system was detected in 2905 different species.
+
+![cas](/cas/Distribution_Cas.svg){max-width=750px}
+
+Proportion of genome encoding the AbiC system for the 14 phyla with more than 50 genomes in the RefSeq database.

content/3.defense-systems/cbass.md

@@ -15,35 +15,36 @@ tableColumns:
 # CBASS
 ## Example of genomic structure
 
-The CBASS system have been describe in a total of 5 subsystems.
+A total of 4 subsystems have been described for the CBASS system.
 
-Here is some example found in the RefSeq database:
+Here is some examples found in the RefSeq database:
 
-![cbass](/cbass/CBASS_I.svg){max-width=750px}
+![cbass_i](/cbass/CBASS_I.svg){max-width=750px}
 
-CBASS_I subsystem in the genome of *Rhizobium leguminosarum* (GCF_002243365.1) is composed of 2 proteins: 4TM_new (WP_094230678.1)and, Cyclase_SMODS (WP_094230679.1).
+The CBASS_I system in *Vibrio fluvialis* (GCF_018140575.1, NZ_CP073273) is composed of 2 proteins Effector_4TM_S_4TM (WP_212571187.1) Cyclase_SMODS (WP_203534033.1) 
 
-![cbass](/cbass/CBASS_II.svg){max-width=750px}
+![cbass_ii](/cbass/CBASS_II.svg){max-width=750px}
 
-CBASS_II subsystem in the genome of *Parvularcula bermudensis* (GCF_000152825.2) is composed of 3 proteins: 4TM_new (WP_013299178.1), Cyclase_II (WP_148235131.1)and, AG_E2_Prok-E2_B (WP_013299180.1).
+The CBASS_II system in *Klebsiella oxytoca* (GCF_002072655.1, NZ_CP020358) is composed of 4 proteins Sensing_SAVED (WP_080528222.1) Jab (WP_071681958.1) AG_E1_ThiF (WP_080528223.1) Cyclase_II (WP_061351239.1) 
 
-![cbass](/cbass/CBASS_III.svg){max-width=750px}
+![cbass_iii](/cbass/CBASS_III.svg){max-width=750px}
 
-CBASS_III subsystem in the genome of *Methylocella tundrae* (GCF_900749825.1) is composed of 5 proteins: Endonuc_small (WP_134490779.1), Cyclase_SMODS (WP_134490781.1), bacHORMA_2 (WP_134490783.1), HORMA (WP_134490785.1)and, TRIP13 (WP_134490787.1).
+The CBASS_III system in *Conexibacter sp. DBS9H8* (GCF_023330685.1, NZ_CP097128) is composed of 5 proteins Sensing_SAVED (WP_249010498.1) Cyclase_II (WP_249010499.1) bacHORMA_2 (WP_249010500.1) HORMA (WP_249010501.1) TRIP13 (WP_249010502.1) 
 
-![cbass](/cbass/CBASS_IV.svg){max-width=750px}
+![cbass_iv](/cbass/CBASS_IV.svg){max-width=750px}
 
-CBASS_IV subsystem in the genome of *Bacillus sp.* (GCF_022809835.1) is composed of 4 proteins: 2TM_type_IV (WP_243501124.1), QueC (WP_206906219.1), TGT (WP_243501126.1)and, Cyclase_SMODS (WP_243501127.1).
+The CBASS_IV system in *Flavobacterium alkalisoli* (GCF_008000935.1, NZ_CP042831) is composed of 5 proteins OGG (WP_147582669.1) Cyclase_II (WP_147582670.1) TGT (WP_147582671.1) QueC (WP_147582672.1) Effector_2TM_Sa_NUDIX (WP_147582673.1) 
 
 ## Distribution of the system among prokaryotes
 
-The CBASS system is present in a total of 1062 different species.
+Among the 22,803 complete genomes of RefSeq, the CBASS is detected in 2914 genomes (12.78 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 2938 genomes (12.9 %).
+The system was detected in 1290 different species.
 
 ![cbass](/cbass/Distribution_CBASS.svg){max-width=750px}
 
-*Proportion of genome encoding the CBASS system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.*
+Proportion of genome encoding the CBASS system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/charlie_gp32.md

@@ -12,6 +12,27 @@ tableColumns:
 
 ## To do 
 
+## Example of genomic structure
+
+The Charlie_gp32 is composed of 1 protein: gp32.
+
+Here is an example found in the RefSeq database:
+
+![charlie_gp32](/charlie_gp32/Charlie_gp32.svg){max-width=750px}
+
+The Charlie_gp32 system in *Mycobacterium liflandii* (GCF_000026445.2, NC_020133) is composed of 1 protein: gp32 (WP_015355567.1) 
+
+## 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.
+
+![charlie_gp32](/charlie_gp32/Distribution_Charlie_gp32.svg){max-width=750px}
+
+Proportion of genome encoding the Charlie_gp32 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
+
 ## Structure
 
 ### Charlie_gp32

content/3.defense-systems/dartg.md

@@ -31,23 +31,24 @@ DarT uses NAD+ to ADP-ribosylates tymidines on ssDNA, while DarG catalyses the r
 
 ## Example of genomic structure
 
-The DarTG system is composed of 2 proteins: DarT and, DarG.
+The DarTG is composed of 2 proteins: DarT and DarG.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![dartg](/dartg/DarTG.svg){max-width=750px}
 
-DarTG system in the genome of *Mycobacterium tuberculosis* (GCF_904810345.1) is composed of 2 proteins: DarT (WP_003400548.1)and, DarG (WP_003400551.1).
+The DarTG system in *Leptodesmis sichuanensis* (GCF_021379005.1, NZ_CP075171) is composed of 2 proteins DarT (WP_233744308.1) DarG (WP_233744309.1) 
 
 ## Distribution of the system among prokaryotes
 
-The DarTG system is present in a total of 356 different species.
+Among the 22,803 complete genomes of RefSeq, the DarTG is detected in 952 genomes (4.17 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 955 genomes (4.2 %).
+The system was detected in 386 different species.
 
 ![dartg](/dartg/Distribution_DarTG.svg){max-width=750px}
 
-*Proportion of genome encoding the DarTG system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the DarTG system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure