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

@@ -7,31 +7,48 @@ tableColumns:
       abstract: |
         Toxin-antitoxin (TA) systems are broadly distributed, yet poorly conserved, genetic elements whose biological functions are unclear and controversial. Some TA systems may provide bacteria with immunity to infection by their ubiquitous viral predators, bacteriophages. To identify such TA systems, we searched bioinformatically for those frequently encoded near known phage defence genes in bacterial genomes. This search identified homologues of DarTG, a recently discovered family of TA systems whose biological functions and natural activating conditions were unclear. Representatives from two different subfamilies, DarTG1 and DarTG2, strongly protected E. coli MG1655 against different phages. We demonstrate that for each system, infection with either RB69 or T5 phage, respectively, triggers release of the DarT toxin, a DNA ADP-ribosyltransferase, that then modifies viral DNA and prevents replication, thereby blocking the production of mature virions. Further, we isolated phages that have evolved to overcome DarTG defence either through mutations to their DNA polymerase or to an anti-DarT factor, gp61.2, encoded by many T-even phages. Collectively, our results indicate that phage defence may be a common function for TA systems and reveal the mechanism by which DarTG systems inhibit phage infection.
     Sensor: Unknown
-    Activator: Unknown
+    Activator: Direct binding to ssDNA
     Effector: Nucleic acid degrading (ADP-ribosylation)
     PFAM: PF01661, PF14487
+contributors: 
+    - Ernest Mordret
+relevantAbstracts:
+    - doi: 10.1038/s41564-022-01153-5
+    - doi: 10.1016/j.molcel.2016.11.014
+    - doi: 10.1016/j.celrep.2020.01.014 
+    - doi: 10.1038/s41586-021-03825-4
 ---
 
 # DarTG
+
+## Description
+
+The DarTG defense system is a toxin-antitoxin (TA) system that provides defense against bacteriophages by ADP-ribosylating viral DNA, thereby preventing replication and the production of mature virions. This system consists of two subfamilies, DarTG1 and DarTG2, which protect against different phages. When infected by specific phages, the DarT toxin, a DNA ADP-ribosyltransferase, is released, modifying viral DNA and inhibiting replication.
+
+## Molecular mechanism
+
+DarT uses NAD+ to ADP-ribosylates tymidines on ssDNA, while DarG catalyses the reverse reaction. ADP-ribosylation of ssDNA prevents DNA replication and triggers the cell's SOS response. While initially proposed to work on bacterial ssDNA as a TA system :ref{doi=10.1016/j.molcel.2016.11.014}, Leroux et al. :ref{doi=10.1038/s41564-022-01153-5} show that it mostly modifies viral DNA and therefore block viral replication and perturb the transcription of phage genes. They conclude that "DarTG does not ultimately kill the host cell as in a conventional Abi mechanism, but instead acts to thwart phage replication directly."
+
 ## 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
 
@@ -77,13 +94,5 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
-    - doi: 10.1038/s41564-022-01153-5
-
----
 ::
 

content/3.defense-systems/dazbog.md

@@ -26,23 +26,24 @@ As far as we are aware, the molecular mechanism is unknown.
 
 ## Example of genomic structure
 
-The Dazbog system is composed of 2 proteins: DzbB and, DzbA.
+The Dazbog is composed of 2 proteins: DzbA and DzbB.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![dazbog](/dazbog/Dazbog.svg){max-width=750px}
 
-Dazbog system in the genome of *Bacillus cereus* (GCF_001518875.1) is composed of 2 proteins: DzbA (WP_082188833.1)and, DzbB (WP_059303380.1).
+The Dazbog system in *Cyanobium gracile* (GCF_000316515.1, NC_019675) is composed of 2 proteins DzbA (WP_015108896.1) DzbB (WP_156818401.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Dazbog system is present in a total of 66 different species.
+Among the 22,803 complete genomes of RefSeq, the Dazbog is detected in 55 genomes (0.24 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 73 genomes (0.3 %).
+The system was detected in 50 different species.
 
 ![dazbog](/dazbog/Distribution_Dazbog.svg){max-width=750px}
 
-*Proportion of genome encoding the Dazbog system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the Dazbog system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/dctpdeaminase.md

@@ -31,23 +31,24 @@ The trigger for dCTPdeaminase may be linked to the shutoff of RNAP ($\sigma$ S-d
 
 ## Example of genomic structure
 
-The dCTPdeaminase system is composed of one protein: dCTPdeaminase.
+The dCTPdeaminase is composed of 1 protein: dCTPdeaminase.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![dctpdeaminase](/dctpdeaminase/dCTPdeaminase.svg){max-width=750px}
 
-dCTPdeaminase system in the genome of *Vibrio parahaemolyticus* (GCF_009883855.1) is composed of 1 protein: dCTPdeaminase (WP_029845369.1).
+The dCTPdeaminase system in *Pseudomonas entomophila* (GCF_023277925.1, NZ_CP063832) is composed of 1 protein: dCTPdeaminase (WP_248918739.1) 
 
 ## Distribution of the system among prokaryotes
 
-The dCTPdeaminase system is present in a total of 269 different species.
+Among the 22,803 complete genomes of RefSeq, the dCTPdeaminase is detected in 501 genomes (2.2 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 501 genomes (2.2 %).
+The system was detected in 294 different species.
 
 ![dctpdeaminase](/dctpdeaminase/Distribution_dCTPdeaminase.svg){max-width=750px}
 
-*Proportion of genome encoding the dCTPdeaminase system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the dCTPdeaminase system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/dmdde.md → content/3.defense-systems/ddmde.md

 ---
-title: DmdDE
+title: DdmDE
 layout: article
 tableColumns:
     article:
@@ -8,26 +8,27 @@ tableColumns:
         Horizontal gene transfer can trigger rapid shifts in bacterial evolution. Driven by a variety of mobile genetic elements—in particular bacteriophages and plasmids—the ability to share genes within and across species underpins the exceptional adaptability of bacteria. Nevertheless, invasive mobile genetic elements can also present grave risks to the host; bacteria have therefore evolved a vast array of defences against these elements1. Here we identify two plasmid defence systems conserved in the Vibrio cholerae El Tor strains responsible for the ongoing seventh cholera pandemic2-4. These systems, termed DdmABC and DdmDE, are encoded on two major pathogenicity islands that are a hallmark of current pandemic strains. We show that the modules cooperate to rapidly eliminate small multicopy plasmids by degradation. Moreover, the DdmABC system is widespread and can defend against bacteriophage infection by triggering cell suicide (abortive infection, or Abi). Notably, we go on to show that, through an Abi-like mechanism, DdmABC increases the burden of large low-copy-number conjugative plasmids, including a broad-host IncC multidrug resistance plasmid, which creates a fitness disadvantage that counterselects against plasmid-carrying cells. Our results answer the long-standing question of why plasmids, although abundant in environmental strains, are rare in pandemic strains; have implications for understanding the dissemination of antibiotic resistance plasmids; and provide insights into how the interplay between two defence systems has shaped the evolution of the most successful lineage of pandemic V. cholerae.
 ---
 
-# DmdDE
+# DdmDE
 ## Example of genomic structure
 
-The DmdDE system is composed of 2 proteins: DdmE and, DdmD.
+The DmdDE is composed of 2 proteins: DdmE and DdmD.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
-![dmdde](/dmdde/DdmDE.svg){max-width=750px}
+![ddmde](/ddmde/DdmDE.svg){max-width=750px}
 
-DdmDE subsystem in the genome of *Vibrio vulnificus* (GCF_002850455.1) is composed of 2 proteins: DdmE (WP_101957190.1)and, DdmD (WP_101957191.1).
+The DdmDE system in *Vibrio coralliilyticus* (GCF_000772065.1, NZ_CP009617) is composed of 2 proteins DdmD (WP_043007104.1) DdmE (WP_043007106.1) 
 
 ## Distribution of the system among prokaryotes
 
-The DmdDE system is present in a total of 50 different species.
+Among the 22,803 complete genomes of RefSeq, the DdmDE is detected in 135 genomes (0.59 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 145 genomes (0.6 %).
+The system was detected in 50 different species.
 
-![dmdde](/dmdde/Distribution_DmdDE.svg){max-width=750px}
+![DdmDE](/ddmde/Distribution_DmdDE.svg){max-width=750px}
+
+Proportion of genome encoding the DdmDE system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
-*Proportion of genome encoding the DmdDE system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
 
 ## Structure
 

content/3.defense-systems/detocs.md

@@ -29,54 +29,39 @@ While the genetic architecture of Detocs is similar to that of regulatory two-co
 
 While 80% of Detocs operons encode PNP effectors, in a minority of these operons the PNP is replaced by other domains known to function as cell-killing effectors in bacterial defense systems, including endonuclease and transmembrane-spanning domains. A Detocs operon with a transmembrane α/β hydrolase effector from Enterobacter cloacae JD6301 was able to efficiently protect E. coli against diverse phages (Rousset et al., 2023).
 
+## Example of genomic structure
+
+A total of 4 subsystems have been described for the Detocs system.
+
+Here is some examples found in the RefSeq database:
+
+![detocs](/detocs/Detocs.svg){max-width=750px}
+
+The Detocs system in *Vibrio anguillarum* (GCF_002287545.1, NZ_CP023054) is composed of 3 proteins dtcC (WP_019283384.1) dtcB (WP_019283385.1) dtcA (WP_198303352.1) 
+
+![detocs_rease](/detocs/Detocs_REase.svg){max-width=750px}
+
+The Detocs_REase system in *Winogradskyella sp. HaHa_3_26* (GCF_019278425.1, NZ_CP058981) is composed of 3 proteins dtcA (WP_179313105.1) dtcB (WP_179313104.1) dtcC_REase (WP_179313103.1) 
+
+![detocs_toprim](/detocs/Detocs_TOPRIM.svg){max-width=750px}
+
+The Detocs_TOPRIM system in *Kaistella flava (ex Peng et al. 2021)* (GCF_015191005.1, NZ_CP040442) is composed of 3 proteins dtcA (WP_193813510.1) dtcB (WP_193813511.1) dtcC_TOPRIM (WP_193813512.1) 
+
+![detocs_hydrolase](/detocs/Detocs_hydrolase.svg){max-width=750px}
+
+The Detocs_hydrolase system in *Yersinia canariae* (GCF_009831415.1, NZ_CP043727) is composed of 3 proteins dtcA (WP_159677463.1) dtcB (WP_159677464.1) dtcC_hydrolase (WP_159677465.1) 
+
 ## Distribution of the system among prokaryotes
 
-Detocs is encoded in Proteobacteria, Bacteroidetes, Firmicutes, Planctomycetes and Chloroflexi phyla.
+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.
+
+![detocs](/detocs/Distribution_Detocs.svg){max-width=750px}
+
+Proportion of genome encoding the Detocs system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
-## Experimental validation
-<mermaid>
-graph LR;
-    Rousset_2023[<a href='https://doi.org/10.1016/j.cell.2023.07.020'>Rousset et al., 2023</a>] --> Origin_0
-    Origin_0[Vibrio alginolyticus 
-<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2645761408'>2645761408</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2645761407'>2645761407</a>,
-<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2645761406'>2645761406</a>] --> Expressed_0[Escherichia coli]
-    Expressed_0[Escherichia coli] ----> T2 & T4 & T5 & T6
-    Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_1
-    Origin_1[ Detocs Hydrolase
-Enterobacter cloacae 
-<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2540965173'>2540965173</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2540965172'>2540965172</a>,
-<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2540965171'>2540965171</a>] --> Expressed_1[Escherichia coli]
-    Expressed_1[Escherichia coli] ----> SECPhi27 & T5 & SECPhi18 & SECPhi6 & T2 & T4 & T7
-    subgraph Title1[Reference]
-        Rousset_2023
-        Millman_2022
-end
-    subgraph Title2[System origin]
-        Origin_0
-        Origin_1
-end
-    subgraph Title3[Expression species]
-        Expressed_0
-        Expressed_1
-end
-    subgraph Title4[Phage infected]
-        T2
-        T4
-        T5
-        T6
-        SECPhi27
-        T5
-        SECPhi18
-        SECPhi6
-        T2
-        T4
-        T7
-end
-    style Title1 fill:none,stroke:none,stroke-width:none
-    style Title2 fill:none,stroke:none,stroke-width:none
-    style Title3 fill:none,stroke:none,stroke-width:none
-    style Title4 fill:none,stroke:none,stroke-width:none
-</mermaid>
 ## Structure
 
 ### Detocs
@@ -125,3 +110,48 @@ dataUrl: /detocs/Detocs_hydrolase__dtcC-plddts_89.47253.pdb
 ---
 ::
 
+
+## Experimental validation
+<mermaid>
+graph LR;
+    Rousset_2023[<a href='https://doi.org/10.1016/j.cell.2023.07.020'>Rousset et al., 2023</a>] --> Origin_0
+    Origin_0[Vibrio alginolyticus 
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2645761408'>2645761408</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2645761407'>2645761407</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2645761406'>2645761406</a>] --> Expressed_0[Escherichia coli]
+    Expressed_0[Escherichia coli] ----> T2 & T4 & T5 & T6
+    Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_1
+    Origin_1[ Detocs Hydrolase
+Enterobacter cloacae 
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2540965173'>2540965173</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2540965172'>2540965172</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2540965171'>2540965171</a>] --> Expressed_1[Escherichia coli]
+    Expressed_1[Escherichia coli] ----> SECPhi27 & T5 & SECPhi18 & SECPhi6 & T2 & T4 & T7
+    subgraph Title1[Reference]
+        Rousset_2023
+        Millman_2022
+end
+    subgraph Title2[System origin]
+        Origin_0
+        Origin_1
+end
+    subgraph Title3[Expression species]
+        Expressed_0
+        Expressed_1
+end
+    subgraph Title4[Phage infected]
+        T2
+        T4
+        T5
+        T6
+        SECPhi27
+        T5
+        SECPhi18
+        SECPhi6
+        T2
+        T4
+        T7
+end
+    style Title1 fill:none,stroke:none,stroke-width:none
+    style Title2 fill:none,stroke:none,stroke-width:none
+    style Title3 fill:none,stroke:none,stroke-width:none
+    style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
\ No newline at end of file

content/3.defense-systems/dgtpase.md

@@ -3,35 +3,47 @@ title: dGTPase
 layout: article
 tableColumns:
     article:
-      doi: 10.1016/j.cell.2021.09.031
+      doi: 10.1038/s41564-022-01158-0
       abstract: |
-        The cyclic pyrimidines 3',5'-cyclic cytidine monophosphate (cCMP) and 3',5'-cyclic uridine monophosphate (cUMP) have been reported in multiple organisms and cell types. As opposed to the cyclic nucleotides 3',5'-cyclic adenosine monophosphate (cAMP) and 3',5'-cyclic guanosine monophosphate (cGMP), which are second messenger molecules with well-established regulatory roles across all domains of life, the biological role of cyclic pyrimidines has remained unclear. Here we report that cCMP and cUMP are second messengers functioning in bacterial immunity against viruses. We discovered a family of bacterial pyrimidine cyclase enzymes that specifically synthesize cCMP and cUMP following phage infection and demonstrate that these molecules activate immune effectors that execute an antiviral response. A crystal structure of a uridylate cyclase enzyme from this family explains the molecular mechanism of selectivity for pyrimidines as cyclization substrates. Defense systems encoding pyrimidine cyclases, denoted here Pycsar (pyrimidine cyclase system for antiphage resistance), are widespread in prokaryotes. Our results assign clear biological function to cCMP and cUMP as immunity signaling molecules in bacteria.
+        DNA viruses and retroviruses consume large quantities of deoxynucleotides (dNTPs) when replicating. The human antiviral factor SAMHD1 takes advantage of this vulnerability in the viral lifecycle, and inhibits viral replication by degrading dNTPs into their constituent deoxynucleosides and inorganic phosphate. Here, we report that bacteria use a similar strategy to defend against bacteriophage infection. We identify a family of defensive bacterial deoxycytidine triphosphate (dCTP) deaminase proteins that convert dCTP into deoxyuracil nucleotides in response to phage infection. We also identify a family of phage resistance genes that encode deoxyguanosine triphosphatase (dGTPase) enzymes, which degrade dGTP into phosphate-free deoxyguanosine and are distant homologues of human SAMHD1. Our results suggest that bacterial defensive proteins deplete specific deoxynucleotides (either dCTP or dGTP) from the nucleotide pool during phage infection, thus starving the phage of an essential DNA building block and halting its replication. Our study shows that manipulation of the dNTP pool is a potent antiviral strategy shared by both prokaryotes and eukaryotes.
     Sensor: Monitoring of the host cell machinery integrity
-    Activator: Direc
+    Activator: Direct
     Effector: Nucleotide modifying
     PFAM: PF01966, PF13286
+contributors: 
+  - Aude Bernheim
+relevantAbstracts:
+  - doi:  10.1038/s41564-022-01158-0 
 ---
 
 # dGTPase
+
+## Description
+dGTPase are a family of proteins discovered in :ref{doi=10.1038/s41564-022-01158-0}. It degrades dGTP into phosphate-free deoxyguanosine. It was suggested that these *"bacterial defensive proteins deplete  deoxynucleotides from the nucleotide pool during phage infection, thus starving the phage of an essential DNA building block and halting its replication"*. The mechanism is remindful of the mechanism of SAMHD1 in humans.
+
+## Molecular mechanism 
+dGTPase degrades dGTP into phosphate-free deoxyguanosine. Phage mutants which overcome this defense carry mutations in phage-RNAP-modifying proteins suggesting, that *"phage-mediated inhibition of host transcription may be involved in triggering the activation of bacterial dNTP-depletion"*. 
+
 ## Example of genomic structure
 
-The dGTPase system is composed of one protein: Sp_dGTPase.
+The dGTPase is composed of 1 protein: Sp_dGTPase.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
-![dGTPase](/dGTPase.svg){max-width=750px}
+![dgtpase](/dgtpase/dGTPase.svg){max-width=750px}
 
-dGTPase system in the genome of *Acinetobacter pittii* (GCF_002012285.1) is composed of 1 protein: Sp_dGTPase (WP_213033921.1).
+The dGTPase system in *Citrobacter sp. RHBSTW-00986* (GCF_013783065.1, NZ_CP056202) is composed of 1 protein: Sp_dGTPase (WP_048216953.1) 
 
 ## Distribution of the system among prokaryotes
 
-The dGTPase system is present in a total of 353 different species.
+Among the 22,803 complete genomes of RefSeq, the dGTPase is detected in 1531 genomes (6.71 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 1532 genomes (6.7 %).
+The system was detected in 449 different species.
 
-![Distribution_dGTPase](/Distribution_dGTPase.svg){max-width=750px}
+![dgtpase](/dgtpase/Distribution_dGTPase.svg){max-width=750px}
+
+Proportion of genome encoding the dGTPase system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
-*Proportion of genome encoding the dGTPase system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
 
 ## Structure
 
@@ -111,13 +123,3 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
-    - doi: 10.1038/s41564-022-01162-4
-
----
-::
-

content/3.defense-systems/disarm.md

@@ -31,29 +31,33 @@ Hints of these additional mechanisms can be found in recent structural studies,
 
 
 ## Example of genomic structure
+
 DISARM is encoded by three core genes: *drmA* (encoding for a protein containing a putative helicase domain)*,* *drmB* (encoding for a protein containing a putative helicase-associated domain), and *drmC* (encoding for a protein containing a phospholipase D/nuclease domain) (1)
 
 These three core genes are accompanied by a methyltransferase, which can be either an adenine methylase (*drmMI*) for class 1 DISARM systems or a cytosine methylase (*drmMII*) for DISARM class 2. Both classes also encode an additional gene (*drmD* for class 1, and *drmE* for class 2). 
 
-Here is some example found in the RefSeq database:
+A total of 2 subsystems have been described for the DISARM system.
+
+Here is some examples found in the RefSeq database:
 
-![disarm](/disarm/DISARM_1.svg){max-width=750px}
+![disarm_1](/disarm/DISARM_1.svg){max-width=750px}
 
-DISARM_1 subsystem in the genome of *Pseudomonas aeruginosa* (GCF_009676885.1) is composed of 6 proteins: drmD (WP_023093122.1), drmMI (WP_023115027.1), drmD (WP_023093126.1), drmA (WP_033993408.1), drmB (WP_023093129.1)and, drmC (WP_031637507.1).
+The DISARM_1 system in *Burkholderia pseudomallei* (GCF_001887555.1, NZ_CP016910) is composed of 5 proteins drmD (WP_043276582.1) drmMI (WP_071897987.1) drmA (WP_024430133.1) drmB (WP_043276578.1) drmC (WP_229202442.1) 
 
-![disarm](/disarm/DISARM_2.svg){max-width=750px}
+![disarm_2](/disarm/DISARM_2.svg){max-width=750px}
 
-DISARM_2 subsystem in the genome of *Bacillus paralicheniformis* (GCF_009497935.1) is composed of 5 proteins: drmMII (WP_020450482.1), drmC (WP_020450481.1), drmB (WP_025810358.1), drmA (WP_020450479.1)and, drmE (WP_020450478.1).
+The DISARM_2 system in *Bacillus halotolerans* (GCF_018417515.1, NZ_CP070976) is composed of 5 proteins drmMII (WP_213418185.1) drmC (WP_213418186.1) drmB (WP_213418187.1) drmA (WP_213418188.1) drmE (WP_213418189.1) 
 
 ## Distribution of the system among prokaryotes
 
-The DISARM system is present in a total of 214 different species.
+Among the 22,803 complete genomes of RefSeq, the DISARM is detected in 298 genomes (1.31 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 341 genomes (1.5 %).
+The system was detected in 201 different species.
 
 ![disarm](/disarm/Distribution_DISARM.svg){max-width=750px}
 
-*Proportion of genome encoding the DISARM 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 DISARM system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Experimental validation
 <mermaid>

content/3.defense-systems/dnd.md

@@ -15,27 +15,28 @@ tableColumns:
 # Dnd
 ## Example of genomic structure
 
-The Dnd system have been describe in a total of 2 subsystems.
+A total of 2 subsystems have been described for the Dnd system.
 
-Here is some example found in the RefSeq database:
+Here is some examples found in the RefSeq database:
 
-![dnd](/dnd/Dnd_ABCDE.svg){max-width=750px}
+![dnd_abcde](/dnd/Dnd_ABCDE.svg){max-width=750px}
 
-Dnd_ABCDE subsystem in the genome of *Vibrio tritonius* (GCF_001547935.1) is composed of 6 proteins: DndA (WP_068714508.1), DndB (WP_068714510.1), DndC (WP_068714512.1), DndD (WP_068714514.1), DndE (WP_068714516.1)and, DndD (WP_068714526.1).
+The Dnd_ABCDE system in *Streptomyces lividans* (GCF_000739105.1, NZ_CP009124) is composed of 5 proteins DndA (WP_016327563.1) DndB (WP_003972933.1) DndC (WP_003972934.1) DndD (WP_003972935.1) DndE (WP_003972936.1) 
 
-![dnd](/dnd/Dnd_ABCDEFGH.svg){max-width=750px}
+![dnd_abcdefgh](/dnd/Dnd_ABCDEFGH.svg){max-width=750px}
 
-Dnd_ABCDEFGH subsystem in the genome of *Vibrio sp.* (GCF_023716625.1) is composed of 8 proteins: DptF (WP_252041715.1), DptG (WP_252041716.1), DptH (WP_252041717.1), DndE (WP_252041720.1), DndD (WP_252041722.1), DndC (WP_252041723.1), DndB (WP_252041724.1)and, DndA (WP_252041725.1).
+The Dnd_ABCDEFGH system in *Shewanella acanthi* (GCF_019457475.1, NZ_CP080413) is composed of 9 proteins DndA (WP_220049638.1) DndB (WP_220049639.1) DndC (WP_220049640.1) DndD (WP_220049642.1) DndE (WP_220049643.1) DndB (WP_220049645.1) DptH (WP_220049650.1) DptG (WP_220052703.1) DptF (WP_220049651.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Dnd system is present in a total of 218 different species.
+Among the 22,803 complete genomes of RefSeq, the Dnd is detected in 376 genomes (1.65 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 388 genomes (1.7 %).
+The system was detected in 237 different species.
 
 ![dnd](/dnd/Distribution_Dnd.svg){max-width=750px}
 
-*Proportion of genome encoding the Dnd 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 Dnd system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/dodola.md

@@ -10,28 +10,42 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF00004, PF07724, PF07728
+contributors:
+    - Ernest Mordret
+relevantAbstracts:
+    - doi: 10.1016/j.chom.2022.09.017
 ---
 
 # Dodola
+
+## Description
+
+Dodola is named after a figure from Slavic mythology, often associated with rain and fertility. The Dodola defense system was first discovered through its common association with known defense systems, and characterized in B. subtilis, demonstrating its efficacy against the SPP1 phage. It is composed of two proteins, DolA and DolB
+
+## Molecular mechanisms
+
+The molecular mechanism is unknown. DolA contains a DUF6414 domain, and DolB contains a ClpB-like domain.
+
 ## Example of genomic structure
 
-The Dodola system is composed of 2 proteins: DolA and, DolB.
+The Dodola is composed of 2 proteins: DolA and DolB.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![dodola](/dodola/Dodola.svg){max-width=750px}
 
-Dodola system in the genome of *Streptococcus thermophilus* (GCF_015190465.1) is composed of 2 proteins: DolA (WP_084825722.1)and, DolB (WP_084825723.1).
+The Dodola system in *Lacrimispora saccharolytica* (GCF_000144625.1, NC_014376) is composed of 2 proteins DolA (WP_012104148.1) DolB (WP_012104147.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Dodola system is present in a total of 91 different species.
+Among the 22,803 complete genomes of RefSeq, the Dodola is detected in 312 genomes (1.37 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 313 genomes (1.4 %).
+The system was detected in 91 different species.
 
 ![dodola](/dodola/Distribution_Dodola.svg){max-width=750px}
 
-*Proportion of genome encoding the Dodola system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the Dodola system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 
@@ -75,13 +89,5 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
-    - doi: 10.1016/j.chom.2022.09.017
 
----
-::
 

content/3.defense-systems/dpd.md

@@ -12,23 +12,24 @@ tableColumns:
 # Dpd
 ## Example of genomic structure
 
-The Dpd system is composed of 15 proteins: FolE, QueD, DpdC, DpdA, DpdB, QueC, DpdD, DpdK, DpdJ, DpdI, DpdH, DpdG, DpdF, DpdE and, QueE.
+The Dpd is composed of 15 proteins: DpdA, DpdB, DpdC, DpdD, DpdE, DpdF, DpdG, DpdH, DpdI, DpdJ, DpdK, QueC, QueD, QueE and FolE.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![dpd](/dpd/Dpd.svg){max-width=750px}
 
-Dpd system in the genome of *Thalassotalea crassostreae* (GCF_001831495.1) is composed of 15 proteins: QueE (WP_068546614.1), DpdE (WP_068546526.1), DpdF (WP_068546528.1), DpdG (WP_068546530.1), DpdH (WP_070795901.1), DpdI (WP_068546533.1), DpdJ (WP_068546534.1), DpdK (WP_082897170.1), DpdD (WP_068546535.1), QueC (WP_068546536.1), DpdB (WP_068546537.1), DpdA (WP_068546538.1), DpdC (WP_157726628.1), QueD (WP_068546540.1)and, FolE (WP_068546542.1).
+The Dpd system in *Colwellia sp. PAMC 20917* (GCF_001767295.1, NZ_CP014944) is composed of 15 proteins FolE (WP_070374315.1) QueD (WP_070374318.1) DpdC (WP_070374319.1) DpdA (WP_070374320.1) DpdB (WP_070374321.1) QueC (WP_070374322.1) DpdD (WP_083277897.1) DpdK (WP_070374324.1) DpdJ (WP_070374325.1) DpdI (WP_070374326.1) DpdH (WP_070374327.1) DpdG (WP_070374328.1) DpdF (WP_070374329.1) DpdE (WP_070374330.1) QueE (WP_197517659.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Dpd system is present in a total of 100 different species.
+Among the 22,803 complete genomes of RefSeq, the Dpd is detected in 225 genomes (0.99 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 226 genomes (1.0 %).
+The system was detected in 103 different species.
 
 ![dpd](/dpd/Distribution_Dpd.svg){max-width=750px}
 
-*Proportion of genome encoding the Dpd system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the Dpd system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/drt.md

@@ -15,51 +15,56 @@ tableColumns:
 # DRT
 ## Example of genomic structure
 
-The DRT system have been describe in a total of 9 subsystems.
+A total of 9 subsystems have been described for the DRT system.
 
-Here is some example found in the RefSeq database:
+Here is some examples found in the RefSeq database:
 
-![drt](/drt/DRT6.svg){max-width=750px}
+![drt6](/drt/DRT6.svg){max-width=750px}
 
-DRT6 subsystem in the genome of *Methylobacterium sp.* (GCF_003254375.1) is composed of 1 protein: DRT6 (WP_111474389.1).
+The DRT6 system in *Polaribacter sp. L3A8* (GCF_009796785.1, NZ_CP047026) is composed of 1 protein: DRT6 (WP_158838312.1) 
 
-![drt](/drt/DRT8.svg){max-width=750px}
+![drt7](/drt/DRT7.svg){max-width=750px}
 
-DRT8 subsystem in the genome of *Undibacterium sp.* (GCF_009937955.1) is composed of 2 proteins: DRT8b (WP_162060770.1)and, DRT8 (WP_162060771.1).
+The DRT7 system in *Bacillus thuringiensis* (GCF_020809145.1, NZ_CP083117) is composed of 1 protein: DRT7 (WP_016090556.1) 
 
-![drt](/drt/DRT9.svg){max-width=750px}
+![drt8](/drt/DRT8.svg){max-width=750px}
 
-DRT9 subsystem in the genome of *Pseudomonas aeruginosa* (GCF_016864415.1) is composed of 1 protein: DRT9 (WP_071567741.1).
+The DRT8 system in *Vibrio natriegens* (GCF_001680065.1, NZ_CP016349) is composed of 2 proteins DRT8 (WP_065299195.1) DRT8b (WP_155759966.1) 
 
-![drt](/drt/DRT_1.svg){max-width=750px}
+![drt9](/drt/DRT9.svg){max-width=750px}
 
-DRT_1 subsystem in the genome of *Vibrio parahaemolyticus* (GCF_000430405.1) is composed of 2 proteins: drt1a (WP_020841728.1)and, drt1b (WP_020841729.1).
+The DRT9 system in *Escherichia coli* (GCF_004801575.1, NZ_CP039298) is composed of 1 protein: DRT9 (WP_211092143.1) 
 
-![drt](/drt/DRT_2.svg){max-width=750px}
+![drt_1](/drt/DRT_1.svg){max-width=750px}
 
-DRT_2 subsystem in the genome of *Klebsiella variicola* (GCF_018324045.1) is composed of 1 protein: drt2 (WP_020244644.1).
+The DRT_1 system in *Vibrio parahaemolyticus* (GCF_013393865.1, NZ_CP040101) is composed of 2 proteins drt1a (WP_179000524.1) drt1b (WP_179000525.1) 
 
-![drt](/drt/DRT_3.svg){max-width=750px}
+![drt_2](/drt/DRT_2.svg){max-width=750px}
 
-DRT_3 subsystem in the genome of *Vibrio mimicus* (GCF_019048845.1) is composed of 2 proteins: drt3a (WP_217011272.1)and, drt3b (WP_217011273.1).
+The DRT_2 system in *Chryseobacterium indoltheticum* (GCF_003815915.1, NZ_CP033929) is composed of 1 protein: drt2 (WP_228421416.1) 
 
-![drt](/drt/DRT_4.svg){max-width=750px}
+![drt_3](/drt/DRT_3.svg){max-width=750px}
 
-DRT_4 subsystem in the genome of *Escherichia albertii* (GCF_003316815.1) is composed of 1 protein: drt4 (WP_103054060.1).
+The DRT_3 system in *Enterobacter sp. JBIWA008* (GCF_019968765.1, NZ_CP074149) is composed of 2 proteins drt3a (WP_223562544.1) drt3b (WP_223562545.1) 
 
-![drt](/drt/DRT_5.svg){max-width=750px}
+![drt_4](/drt/DRT_4.svg){max-width=750px}
 
-DRT_5 subsystem in the genome of *Escherichia coli* (GCF_016904115.1) is composed of 1 protein: drt5 (WP_001524904.1).
+The DRT_4 system in *Vibrio diabolicus* (GCF_002953355.1, NZ_CP014133) is composed of 1 protein: drt4 (WP_104973818.1) 
+
+![drt_5](/drt/DRT_5.svg){max-width=750px}
+
+The DRT_5 system in *Klebsiella pasteurii* (GCF_018139045.1, NZ_CP073236) is composed of 1 protein: drt5 (WP_211811523.1) 
 
 ## Distribution of the system among prokaryotes
 
-The DRT system is present in a total of 573 different species.
+Among the 22,803 complete genomes of RefSeq, the DRT is detected in 1195 genomes (5.24 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 1365 genomes (6.0 %).
+The system was detected in 577 different species.
 
 ![drt](/drt/Distribution_DRT.svg){max-width=750px}
 
-*Proportion of genome encoding the DRT 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 DRT system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/druantia.md

@@ -15,31 +15,32 @@ tableColumns:
 # Druantia
 ## Example of genomic structure
 
-The Druantia system have been describe in a total of 3 subsystems.
+A total of 3 subsystems have been described for the Druantia system.
 
-Here is some example found in the RefSeq database:
+Here is some examples found in the RefSeq database:
 
-![druantia](/druantia/Druantia_I.svg){max-width=750px}
+![druantia_i](/druantia/Druantia_I.svg){max-width=750px}
 
-Druantia_I subsystem in the genome of *Escherichia coli* (GCF_002220215.1) is composed of 5 proteins: DruA (WP_000549798.1), DruB (WP_001315973.1), DruC (WP_021520530.1), DruD (WP_000455180.1)and, DruE_1 (WP_089180326.1).
+The Druantia_I system in *Serratia fonticola* (GCF_005489985.1, NZ_CP040182) is composed of 5 proteins DruA (WP_071682717.1) DruB (WP_071682718.1) DruC (WP_071682719.1) DruD (WP_071682720.1) DruE_1 (WP_071682721.1) 
 
-![druantia](/druantia/Druantia_II.svg){max-width=750px}
+![druantia_ii](/druantia/Druantia_II.svg){max-width=750px}
 
-Druantia_II subsystem in the genome of *Collimonas pratensis* (GCF_001584185.1) is composed of 4 proteins: DruM (WP_082793204.1), DruE_2 (WP_061945149.1), DruG (WP_061945151.1)and, DruF (WP_150119800.1).
+The Druantia_II system in *Klebsiella michiganensis* (GCF_018604105.1, NZ_CP075881) is composed of 4 proteins DruM (WP_045338337.1) DruF (WP_152403866.1) DruG (WP_214632470.1) DruE_2 (WP_152403875.1) 
 
-![druantia](/druantia/Druantia_III.svg){max-width=750px}
+![druantia_iii](/druantia/Druantia_III.svg){max-width=750px}
 
-Druantia_III subsystem in the genome of *Acinetobacter baumannii* (GCF_012935125.1) is composed of 2 proteins: DruH (WP_005120035.1)and, DruE_3 (WP_002036795.1).
+The Druantia_III system in *Citrobacter werkmanii* (GCF_002025225.1, NZ_CP019986) is composed of 2 proteins DruE_3 (WP_079225583.1) DruH (WP_079225584.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Druantia system is present in a total of 284 different species.
+Among the 22,803 complete genomes of RefSeq, the Druantia is detected in 807 genomes (3.54 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 827 genomes (3.6 %).
+The system was detected in 303 different species.
 
 ![druantia](/druantia/Distribution_Druantia.svg){max-width=750px}
 
-*Proportion of genome encoding the Druantia 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 Druantia system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/dsr.md

@@ -15,27 +15,28 @@ tableColumns:
 # Dsr
 ## Example of genomic structure
 
-The Dsr system have been describe in a total of 2 subsystems.
+A total of 2 subsystems have been described for the Dsr system.
 
-Here is some example found in the RefSeq database:
+Here is some examples found in the RefSeq database:
 
-![dsr](/dsr/Dsr_I.svg){max-width=750px}
+![dsr_i](/dsr/Dsr_I.svg){max-width=750px}
 
-Dsr_I subsystem in the genome of *Escherichia coli* (GCF_016904235.1) is composed of 1 protein: Dsr1 (WP_204608492.1).
+The Dsr_I system in *Pseudohalocynthiibacter aestuariivivens* (GCF_011040495.1, NZ_CP049037) is composed of 1 protein: Dsr1 (WP_165194530.1) 
 
-![dsr](/dsr/Dsr_II.svg){max-width=750px}
+![dsr_ii](/dsr/Dsr_II.svg){max-width=750px}
 
-Dsr_II subsystem in the genome of *Escherichia coli* (GCF_009950125.1) is composed of 1 protein: Dsr2 (WP_178103017.1).
+The Dsr_II system in *Deinococcus deserti* (GCF_000020685.1, NC_012526) is composed of 1 protein: Dsr2 (WP_083764220.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Dsr system is present in a total of 246 different species.
+Among the 22,803 complete genomes of RefSeq, the Dsr is detected in 246 genomes (1.08 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 641 genomes (2.8 %).
+The system was detected in 162 different species.
 
 ![dsr](/dsr/Distribution_Dsr.svg){max-width=750px}
 
-*Proportion of genome encoding the Dsr 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 Dsr system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/eleos.md

@@ -16,23 +16,25 @@ tableColumns:
 The Eleos system was previously described as the Dynamins-like system in (Millman et al, 2022).
 
 ## Example of genomic structure
-The Eleos system is composed of 2 proteins: LeoA and, LeoBC. Sometimes, the systems is in three genes: LeoA, LeoB and LeoC.
 
-Here is an example found in the RefSeq database: 
+The Eleos is composed of 4 proteins: LeoA, LeoBC, LeoB and LeoC.
+
+Here is an example found in the RefSeq database:
 
 ![eleos](/eleos/Eleos.svg){max-width=750px}
 
-Dynamins system in the genome of *Pseudomonas aeruginosa* (GCF_002223805.1) is composed of 2 proteins: LeoBC (WP_024947442.1)and, LeoA (WP_024947443.1).
+The Eleos system in *Synechococcus sp. CBW1002* (GCF_015840915.1, NZ_CP060398) is composed of 2 proteins LeoBC (WP_197170386.1) LeoA (WP_197170387.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Eleos system is present in a total of 807 different species.
+Among the 22,803 complete genomes of RefSeq, the Eleos is detected in 414 genomes (1.82 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 2652 genomes (11.6 %).
+The system was detected in 223 different species.
 
 ![eleos](/eleos/Distribution_Eleos.svg){max-width=750px}
 
-*Proportion of genome encoding the Eleos system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the Eleos system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/fs_giy_yig.md

@@ -12,6 +12,27 @@ tableColumns:
 
 ## To do 
 
+## Example of genomic structure
+
+The FS_GIY_YIG is composed of 1 protein: GIY_YIG.
+
+Here is an example found in the RefSeq database:
+
+![fs_giy_yig](/fs_giy_yig/FS_GIY_YIG.svg){max-width=750px}
+
+The FS_GIY_YIG system in *Klebsiella pneumoniae* (GCF_021389995.1, NZ_CP089989) is composed of 1 protein: GIY_YIG (WP_053067640.1) 
+
+## 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.
+
+![fs_giy_yig](/fs_giy_yig/Distribution_FS_GIY_YIG.svg){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.
+
+
 ## Structure
 
 ### FS_GIY_YIG

content/3.defense-systems/fs_hp.md

@@ -12,6 +12,27 @@ tableColumns:
 
 ## To do 
 
+## Example of genomic structure
+
+The FS_HP is composed of 1 protein: HP.
+
+Here is an example found in the RefSeq database:
+
+![fs_hp](/fs_hp/FS_HP.svg){max-width=750px}
+
+The FS_HP system in *Escherichia coli* (GCF_016944735.1, NZ_CP063511) is composed of 1 protein: HP (WP_227456581.1) 
+
+## 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.
+
+![fs_hp](/fs_hp/Distribution_FS_HP.svg){max-width=750px}
+
+Proportion of genome encoding the FS_HP system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
+
 ## Structure
 
 ### FS_HP

content/3.defense-systems/fs_hp_sdh_sah.md

@@ -13,6 +13,27 @@ tableColumns:
 
 ## To do 
 
+## Example of genomic structure
+
+The FS_HP_SDH_sah is composed of 2 proteins: HP and SDH_sah.
+
+Here is an example found in the RefSeq database:
+
+![fs_hp_sdh_sah](/fs_hp_sdh_sah/FS_HP_SDH_sah.svg){max-width=750px}
+
+The FS_HP_SDH_sah system in *Escherichia coli* (GCF_904831805.1, NZ_LR882990) is composed of 2 proteins HP (WP_133302715.1) SDH_sah (WP_032201440.1) 
+
+## 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.
+
+![fs_hp_sdh_sah](/fs_hp_sdh_sah/Distribution_FS_HP_SDH_sah.svg){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.
+
+
 ## Structure
 
 ### FS_HP_SDH_sah

content/3.defense-systems/fs_hsdr_like.md

@@ -12,6 +12,27 @@ tableColumns:
 
 ## To do 
 
+## Example of genomic structure
+
+The FS_HsdR_like is composed of 3 proteins: HdrR, DUF6731 and HP.
+
+Here is an example found in the RefSeq database:
+
+![fs_hsdr_like](/fs_hsdr_like/FS_HsdR_like.svg){max-width=750px}
+
+The FS_HsdR_like system in *Klebsiella pneumoniae* (GCF_009661415.2, NZ_CP062997) is composed of 3 proteins DUF6731 (WP_048981062.1) HP (WP_048981064.1) HdrR (WP_153928365.1) 
+
+## 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.
+
+![fs_hsdr_like](/fs_hsdr_like/Distribution_FS_HsdR_like.svg){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.
+
+
 ## Structure
 
 ### FS_HsdR_like