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content/3.defense-systems/dgtpase.md
View file @ f741a518
......@@ -45,18 +45,22 @@ The system was detected in 449 different species.
Proportion of genome encoding the dGTPase system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### dGTPase
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dgtpase/dGTPase__Sp_dGTPase-plddts_94.35719.pdb
dataUrls:
- /dgtpase/dGTPase__Sp_dGTPase.cif
---
::
## Experimental validation
<mermaid>
graph LR;
Tal_2022[<a href='https://doi.org/10.1038/s41564-022-01158-0'>Tal et al., 2022</a>] --> Origin_0
......@@ -123,3 +127,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
content/3.defense-systems/disarm.md
View file @ f741a518
......@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00145, PF00176, PF00271, PF04851, PF09369, PF13091
relevantAbstracts:
- doi: 10.1038/s41467-022-30673-1
- doi: 10.1038/s41564-017-0051-0
---
# DISARM
......@@ -59,7 +62,40 @@ The system was detected in 201 different species.
Proportion of genome encoding the DISARM system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
### DISARM_1
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrls:
- /disarm/DISARM_2.DISARM__drmC.0.V.cif
- /disarm/DISARM_2.DISARM__drmB.0.V.cif
- /disarm/DISARM_1.DISARM__drmA.0.DF.cif
- /disarm/DISARM_1.DISARM_1__drmMI.0.DF.cif
- /disarm/DISARM_1.DISARM_1__drmD.0.DF.cif
---
::
### DISARM_2
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrls:
- /disarm/DISARM_1.DISARM__drmA.0.DF.cif
- /disarm/DISARM_2.DISARM__drmC.0.V.cif
- /disarm/DISARM_2.DISARM_2__drmMII.0.V.cif
- /disarm/DISARM_2.DISARM__drmB.0.V.cif
- /disarm/DISARM_2.DISARM_2__drmE.0.V.cif
---
::
## Experimental validation
<mermaid>
graph LR;
Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
......@@ -120,14 +156,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
## Relevant abstracts
::relevant-abstracts
---
items:
- doi: 10.1038/s41467-022-30673-1
- doi: 10.1038/s41564-017-0051-0
---
::
content/3.defense-systems/dnd.md
View file @ f741a518
......@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Nucleic acid degrading
PFAM: PF00266, PF01507, PF01935, PF08870, PF13476, PF14072
relevantAbstracts:
- doi: 10.1038/nchembio.2007.39
- doi: 10.1038/s41467-019-09390-9
---
# Dnd
......@@ -38,104 +41,45 @@ The system was detected in 237 different species.
Proportion of genome encoding the Dnd system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### Dnd_ABCDE
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dnd/Dnd_ABCDE,Dnd__DndA,0,DF-plddts_93.47347.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dnd/Dnd_ABCDE,Dnd__DndB,0,DF-plddts_92.88424.pdb
---
::
dataUrls:
- /dnd/Dnd_ABCDE.Dnd__DndD.0.DF.cif
- /dnd/Dnd_ABCDE.Dnd__DndE.0.DF.cif
- /dnd/Dnd_ABCDE.Dnd__DndD.0.DF.cif
- /dnd/Dnd_ABCDE.Dnd__DndC.0.DF.cif
- /dnd/Dnd_ABCDEFGH.Dnd__DndB.0.DF.cif
- /dnd/Dnd_ABCDE.Dnd__DndA.0.DF.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dnd/Dnd_ABCDE,Dnd__DndC,0,DF-plddts_88.29934.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dnd/Dnd_ABCDE,Dnd__DndD,0,DF-plddts_86.40104.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dnd/Dnd_ABCDE,Dnd__DndE,0,DF-plddts_94.0153.pdb
---
::
### Dnd_ABCDEFGH
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dnd/Dnd_ABCDEFGH,Dnd_ABCDEFGH__DptF,0,DF-plddts_90.5398.pdb
---
::
dataUrls:
- /dnd/Dnd_ABCDE.Dnd__DndA.0.DF.cif
- /dnd/Dnd_ABCDEFGH.Dnd__DndB.0.DF.cif
- /dnd/Dnd_ABCDE.Dnd__DndC.0.DF.cif
- /dnd/Dnd_ABCDE.Dnd__DndD.0.DF.cif
- /dnd/Dnd_ABCDE.Dnd__DndE.0.DF.cif
- /dnd/Dnd_ABCDEFGH.Dnd_ABCDEFGH__DptH.0.DF.cif
- /dnd/Dnd_ABCDEFGH.Dnd_ABCDEFGH__DptG.0.DF.cif
- /dnd/Dnd_ABCDEFGH.Dnd_ABCDEFGH__DptF.0.DF.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dnd/Dnd_ABCDEFGH,Dnd_ABCDEFGH__DptG,0,DF-plddts_92.29053.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dnd/Dnd_ABCDEFGH,Dnd_ABCDEFGH__DptH,0,DF-plddts_83.00895.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dnd/Dnd_ABCDEFGH,Dnd__DndA,0,DF-plddts_95.7234.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dnd/Dnd_ABCDEFGH,Dnd__DndB,0,DF-plddts_94.63597.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dnd/Dnd_ABCDEFGH,Dnd__DndC,0,DF-plddts_90.06321.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dnd/Dnd_ABCDEFGH,Dnd__DndD,0,DF-plddts_85.70431.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dnd/Dnd_ABCDEFGH,Dnd__DndE,0,DF-plddts_95.24932.pdb
---
::
## Experimental validation
<mermaid>
graph LR;
Xiong_2019[<a href='https://doi.org/10.1038/s41467-019-09390-9'>Xiong et al., 2019</a>] --> Origin_0
......@@ -159,14 +103,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
## Relevant abstracts
::relevant-abstracts
---
items:
- doi: 10.1038/nchembio.2007.39
- doi: 10.1038/s41467-019-09390-9
---
::
content/3.defense-systems/dodola.md
View file @ f741a518
......@@ -47,25 +47,23 @@ The system was detected in 91 different species.
Proportion of genome encoding the Dodola system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### Dodola
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dodola/Dodola,Dodola__DolA,0,V-plddts_78.91796.pdb
---
::
dataUrls:
- /dodola/Dodola.Dodola__DolB.0.V.cif
- /dodola/Dodola.Dodola__DolA.0.V.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dodola/Dodola,Dodola__DolB,0,V-plddts_92.53304.pdb
---
::
## Experimental validation
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
......@@ -91,3 +89,4 @@ end
</mermaid>
content/3.defense-systems/dpd.md
View file @ f741a518
......@@ -7,6 +7,8 @@ tableColumns:
abstract: |
The discovery of ?20-kb gene clusters containing a family of paralogs of tRNA guanosine transglycosylase genes, called tgtA5, alongside 7-cyano-7-deazaguanine (preQ0) synthesis and DNA metabolism genes, led to the hypothesis that 7-deazaguanine derivatives are inserted in DNA. This was established by detecting 2’-deoxy-preQ0 and 2’-deoxy-7-amido-7-deazaguanosine in enzymatic hydrolysates of DNA extracted from the pathogenic, Gram-negative bacteria Salmonella enterica serovar Montevideo. These modifications were absent in the closely related S. enterica serovar Typhimurium LT2 and from a mutant of S. Montevideo, each lacking the gene cluster. This led us to rename the genes of the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA. Similar gene clusters were analyzed in ?150 phylogenetically diverse bacteria, and the modifications were detected in DNA from other organisms containing these clusters, including Kineococcus radiotolerans, Comamonas testosteroni, and Sphingopyxis alaskensis. Comparative genomic analysis shows that, in Enterobacteriaceae, the cluster is a genomic island integrated at the leuX locus, and the phylogenetic analysis of the TgtA5 family is consistent with widespread horizontal gene transfer. Comparison of transformation efficiencies of modified or unmodified plasmids into isogenic S. Montevideo strains containing or lacking the cluster strongly suggests a restriction-modification role for the cluster in Enterobacteriaceae. Another preQ0 derivative, 2’-deoxy-7-formamidino-7-deazaguanosine, was found in the Escherichia coli bacteriophage 9g, as predicted from the presence of homologs of genes involved in the synthesis of the archaeosine tRNA modification. These results illustrate a deep and unexpected evolutionary connection between DNA and tRNA metabolism.
PFAM: PF00176, PF00270, PF00271, PF01227, PF01242, PF04055, PF04851, PF06508, PF13091, PF13353, PF13394, PF14072
relevantAbstracts:
- doi: 10.1073/pnas.1518570113
---
# Dpd
......@@ -31,103 +33,27 @@ The system was detected in 103 different species.
Proportion of genome encoding the Dpd system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### Dpd
Example 1:
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dpd/Dpd.Dpd__DpdF.0.DF-plddts_89.51241.pdb
---
::
Example 2:
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dpd/Dpd.Dpd__DpdF.0.DF-plddts_89.51241.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dpd/Dpd,Dpd__DpdA,0,DF-plddts_94.55021.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dpd/Dpd,Dpd__DpdB,0,DF-plddts_93.00056.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dpd/Dpd,Dpd__DpdC,0,DF-plddts_93.71712.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dpd/Dpd,Dpd__DpdD,0,DF-plddts_85.62349.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dpd/Dpd,Dpd__DpdE,0,DF-plddts_88.00382.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dpd/Dpd,Dpd__DpdG,0,DF-plddts_91.59671.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dpd/Dpd,Dpd__DpdH,0,DF-plddts_85.20178.pdb
---
::
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dpd/Dpd,Dpd__DpdI,0,DF-plddts_83.71254.pdb
---
::
dataUrls:
- /dpd/Dpd.Dpd__QueD.0.DF.cif
- /dpd/Dpd.Dpd__DpdD.0.DF.cif
- /dpd/Dpd.Dpd__DpdK.0.DF.cif
- /dpd/Dpd.Dpd__DpdJ.0.DF.cif
- /dpd/Dpd.Dpd__DpdI.0.DF.cif
- /dpd/Dpd.Dpd__DpdH.0.DF.cif
- /dpd/Dpd.Dpd__DpdG.0.DF.cif
- /dpd/Dpd.Dpd__DpdF.0.DF.cif
- /dpd/Dpd.Dpd__DpdE.0.DF.cif
- /dpd/Dpd.Dpd__DpdB.0.DF.cif
- /dpd/Dpd.Dpd__DpdA.0.DF.cif
- /dpd/Dpd.Dpd__DpdC.0.DF.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dpd/Dpd,Dpd__DpdJ,0,DF-plddts_89.00672.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dpd/Dpd,Dpd__DpdK,0,DF-plddts_93.96529.pdb
---
::
## Relevant abstracts
::relevant-abstracts
---
items:
- doi: 10.1073/pnas.1518570113
---
::
content/3.defense-systems/drt.md
View file @ f741a518
......@@ -94,104 +94,112 @@ The system was detected in 577 different species.
Proportion of genome encoding the DRT system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### DRT6
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /drt/DRT6__DRT6-plddts_92.73056.pdb
dataUrls:
- /drt/DRT6__DRT6.cif
---
::
### DRT7
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /drt/DRT7__DRT7-plddts_85.85621.pdb
dataUrls:
- /drt/DRT7__DRT7.cif
---
::
### DRT8
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /drt/DRT8__DRT8-plddts_92.44735.pdb
dataUrls:
- /drt/DRT8__DRT8.cif
---
::
### DRT9
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /drt/DRT9__DRT9-plddts_91.47402.pdb
dataUrls:
- /drt/DRT9__DRT9.cif
---
::
### DRT_1
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /drt/DRT_1,DRT_1__drt1a,0,V-plddts_88.59974.pdb
---
::
dataUrls:
- /drt/DRT_1.DRT_1__drt1b.0.V.cif
- /drt/DRT_1.DRT_1__drt1a.0.V.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /drt/DRT_1,DRT_1__drt1b,0,V-plddts_92.26985.pdb
---
::
### DRT_2
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /drt/DRT_2__drt2-plddts_95.09027.pdb
dataUrls:
- /drt/DRT_2__drt2.cif
---
::
### DRT_3
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /drt/DRT_3,DRT_3__drt3a,0,V-plddts_91.16835.pdb
---
::
dataUrls:
- /drt/DRT_3.DRT_3__drt3b.0.V.cif
- /drt/DRT_3.DRT_3__drt3a.0.V.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /drt/DRT_3,DRT_3__drt3b,0,V-plddts_87.11665.pdb
---
::
### DRT_4
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /drt/DRT_4__drt4-plddts_92.79751.pdb
dataUrls:
- /drt/DRT_4__drt4.cif
---
::
### DRT_5
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /drt/DRT_5__drt5-plddts_90.89502.pdb
dataUrls:
- /drt/DRT_5__drt5.cif
---
::
## Experimental validation
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
......@@ -302,3 +310,4 @@ end
</mermaid>
content/3.defense-systems/druantia.md
View file @ f741a518
......@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00145, PF00270, PF00271, PF04851, PF09369, PF14236
relevantAbstracts:
- doi: 10.1126/science.aar4120
---
# Druantia
......@@ -42,92 +44,52 @@ The system was detected in 303 different species.
Proportion of genome encoding the Druantia system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### Druantia_I
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /druantia/Druantia_I,Druantia_I__DruA,0,V-plddts_88.89293.pdb
---
::
dataUrls:
- /druantia/Druantia_I.Druantia_I__DruA.0.V.cif
- /druantia/Druantia_I.Druantia_I__DruB.0.V.cif
- /druantia/Druantia_I.Druantia_I__DruC.0.V.cif
- /druantia/Druantia_I.Druantia_I__DruD.0.V.cif
- /druantia/Druantia_I.Druantia__DruE.0.V.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /druantia/Druantia_I,Druantia_I__DruB,0,V-plddts_82.83057.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /druantia/Druantia_I,Druantia_I__DruC,0,V-plddts_85.18836.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /druantia/Druantia_I,Druantia_I__DruD,0,V-plddts_91.26112.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /druantia/Druantia_I,Druantia__DruE,0,V-plddts_86.11628.pdb
---
::
### Druantia_II
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /druantia/Druantia_II,Druantia_II__DruF,0,DF-plddts_86.11001.pdb
---
::
dataUrls:
- /druantia/Druantia_II.Druantia_II__DruM.0.DF.cif
- /druantia/Druantia_II.Druantia_II__DruF.0.DF.cif
- /druantia/Druantia_II.Druantia_II__DruG.0.DF.cif
- /druantia/Druantia_II.Druantia__DruE_2.0.DF.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /druantia/Druantia_II,Druantia_II__DruG,0,DF-plddts_80.40261.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /druantia/Druantia_II,Druantia_II__DruM,0,DF-plddts_90.00131.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /druantia/Druantia_II,Druantia__DruE_2,0,DF-plddts_84.77074.pdb
---
::
### Druantia_III
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /druantia/Druantia_III,Druantia_III__DruH,0,DF-plddts_82.87318.pdb
---
::
dataUrls:
- /druantia/Druantia_III.Druantia_III__DruH.0.DF.cif
- /druantia/Druantia_III.Druantia__DruE_3.0.DF.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /druantia/Druantia_III,Druantia__DruE_3,0,DF-plddts_83.26091.pdb
---
::
## Experimental validation
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
......@@ -178,13 +140,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
## Relevant abstracts
::relevant-abstracts
---
items:
- doi: 10.1126/science.aar4120
---
::
content/3.defense-systems/dsr.md
View file @ f741a518
......@@ -10,6 +10,9 @@ tableColumns:
Activator: Direct
Effector: Nucleotide modifying
PFAM: PF13289
relevantAbstracts:
- doi: 10.1038/s41564-022-01207-8
- doi: 10.1126/science.aba0372
---
# Dsr
......@@ -38,27 +41,33 @@ The system was detected in 162 different species.
Proportion of genome encoding the Dsr system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### Dsr_I
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dsr/Dsr_I__Dsr1-plddts_87.99578.pdb
dataUrls:
- /dsr/Dsr_I__Dsr1.cif
---
::
### Dsr_II
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /dsr/Dsr_II__Dsr2-plddts_86.62203.pdb
dataUrls:
- /dsr/Dsr_II__Dsr2.cif
---
::
## Experimental validation
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
......@@ -110,14 +119,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
## Relevant abstracts
::relevant-abstracts
---
items:
- doi: 10.1038/s41564-022-01207-8
- doi: 10.1126/science.aba0372
---
::
content/3.defense-systems/eleos.md
View file @ f741a518
......@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00350, PF01926, PF18709
relevantAbstracts:
- doi: 10.1016/j.chom.2022.09.017
---
# Eleos
......@@ -36,25 +38,23 @@ The system was detected in 223 different species.
Proportion of genome encoding the Eleos system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### Eleos
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /eleos/Eleos,Eleos__LeoA,0,V-plddts_81.66314.pdb
---
::
dataUrls:
- /eleos/Eleos.Eleos__LeoBC.0.V.cif
- /eleos/Eleos.Eleos__LeoA.0.V.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /eleos/Eleos,Eleos__LeoBC,0,V-plddts_83.32056.pdb
---
::
## Experimental validation
<mermaid>
graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
......@@ -79,13 +79,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
## Relevant abstracts
::relevant-abstracts
---
items:
- doi: 10.1016/j.chom.2022.09.017
---
::
content/3.defense-systems/fs_giy_yig.md
View file @ f741a518
......@@ -6,6 +6,8 @@ tableColumns:
doi: 10.1016/j.cell.2022.07.014
abstract: |
Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
relevantAbstracts:
- doi: 10.1016/j.cell.2022.07.014
---
# FS_GIY_YIG
......@@ -33,18 +35,22 @@ The system was detected in 87 different species.
Proportion of genome encoding the FS_GIY_YIG system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### FS_GIY_YIG
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /fs_giy_yig/FS_GIY_YIG__GIY_YIG-plddts_93.05664.pdb
dataUrls:
- /fs_giy_yig/FS_GIY_YIG__GIY_YIG.cif
---
::
## Experimental validation
<mermaid>
graph LR;
Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
......@@ -77,11 +83,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
## Relevant abstract
::relevant-abstracts
---
items:
- doi: 10.1016/j.cell.2022.07.014
---
::
content/3.defense-systems/fs_hepn_tm.md
View file @ f741a518
......@@ -6,31 +6,31 @@ tableColumns:
doi: 10.1016/j.cell.2022.07.014
abstract: |
Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
relevantAbstracts:
- doi: 10.1016/j.cell.2022.07.014
---
# FS_HEPN_TM
## To do
## Structure
## Structure
### FS_HEPN_TM
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /fs_hepn_tm/FS_HEPN_TM__HEPN-plddts_69.12248.pdb
---
::
dataUrls:
- /fs_hepn_tm/FS_HEPN_TM__TM.cif
- /fs_hepn_tm/FS_HEPN_TM__HEPN.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /fs_hepn_tm/FS_HEPN_TM__TM-plddts_90.28126.pdb
---
::
## Experimental validation
<mermaid>
graph LR;
Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
......@@ -56,11 +56,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
## Relevant abstract
::relevant-abstracts
---
items:
- doi: 10.1016/j.cell.2022.07.014
---
::
content/3.defense-systems/fs_hp.md
View file @ f741a518
......@@ -43,18 +43,22 @@ The system was detected in 29 different species.
Proportion of genome encoding the FS_HP system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### FS_HP
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /fs_hp/FS_HP__HP-plddts_94.44828.pdb
dataUrls:
- /fs_hp/FS_HP__HP.cif
---
::
## Experimental validation
<mermaid>
graph LR;
Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
......@@ -86,3 +90,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
content/3.defense-systems/fs_hp_sdh_sah.md
View file @ f741a518
......@@ -7,6 +7,8 @@ tableColumns:
abstract: |
Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
PFAM: PF01972
relevantAbstracts:
- doi: 10.1016/j.cell.2022.07.014
---
# FS_HP_SDH_sah
......@@ -34,25 +36,23 @@ The system was detected in 3 different species.
Proportion of genome encoding the FS_HP_SDH_sah system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### FS_HP_SDH_sah
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /fs_hp_sdh_sah/FS_HP_SDH_sah__HP-plddts_58.30935.pdb
---
::
dataUrls:
- /fs_hp_sdh_sah/FS_HP_SDH_sah__SDH_sah.cif
- /fs_hp_sdh_sah/FS_HP_SDH_sah__HP.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /fs_hp_sdh_sah/FS_HP_SDH_sah__SDH_sah-plddts_95.32024.pdb
---
::
## Experimental validation
<mermaid>
graph LR;
Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
......@@ -76,12 +76,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
## Relevant abstract
::relevant-abstracts
---
items:
- doi: 10.1016/j.cell.2022.07.014
---
::
content/3.defense-systems/fs_hsdr_like.md
View file @ f741a518
......@@ -6,6 +6,8 @@ tableColumns:
doi: 10.1016/j.cell.2022.07.014
abstract: |
Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
relevantAbstracts:
- doi: 10.1016/j.cell.2022.07.014
---
# FS_HsdR_like
......@@ -33,25 +35,33 @@ The system was detected in 15 different species.
Proportion of genome encoding the FS_HsdR_like system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
### FS_HsdR_like
## Structure
### FS_HsdR_like_HP-plddts_74.75219.html
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /fs_hsdr_like/FS_HsdR_like__HP-plddts_74.75219.pdb
dataUrls:
- /fs_hsdr_like/FS_HsdR_like_HP.cif
---
::
### FS_HsdR_like_HdrR-plddts_88.7069.html
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /fs_hsdr_like/FS_HsdR_like__HdrR-plddts_88.7069.pdb
dataUrls:
- /fs_hsdr_like/FS_HsdR_like_HdrR.cif
---
::
## Experimental validation
<mermaid>
graph LR;
Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
......@@ -90,11 +100,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
## Relevant abstract
::relevant-abstracts
---
items:
- doi: 10.1016/j.cell.2022.07.014
---
::
content/3.defense-systems/fs_sma.md
View file @ f741a518
......@@ -7,6 +7,8 @@ tableColumns:
abstract: |
Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
PFAM: PF02452
relevantAbstracts:
- doi: 10.1016/j.cell.2022.07.014
---
# FS_Sma
......@@ -34,18 +36,22 @@ The system was detected in 20 different species.
Proportion of genome encoding the FS_Sma system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### FS_Sma
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /fs_sma/FS_Sma__Sma-plddts_94.14969.pdb
dataUrls:
- /fs_sma/FS_Sma__Sma.cif
---
::
## Experimental validation
<mermaid>
graph LR;
Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
......@@ -86,12 +92,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
## Relevant abstract
::relevant-abstracts
---
items:
- doi: 10.1016/j.cell.2022.07.014
---
::
content/3.defense-systems/gabija.md
View file @ f741a518
......@@ -54,25 +54,23 @@ The system was detected in 1375 different species.
Proportion of genome encoding the Gabija system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### Gabija
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /gabija/Gabija,Gabija_GajB,0,V-plddts_91.3911.pdb
---
::
dataUrls:
- /gabija/Gabija.Gabija__GajA.0.V.cif
- /gabija/Gabija.Gabija_GajB.0.V.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /gabija/Gabija,Gabija__GajA,0,V-plddts_86.08162.pdb
---
::
## Experimental validation
<mermaid>
graph LR;
Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
......@@ -116,3 +114,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
content/3.defense-systems/gao_ape.md
View file @ f741a518
......@@ -47,18 +47,22 @@ The system was detected in 45 different species.
Proportion of genome encoding the Gao_Ape system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### Gao_Ape
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /gao_ape/Gao_Ape__ApeA-plddts_90.44181.pdb
dataUrls:
- /gao_ape/Gao_Ape__ApeA.cif
---
::
## Experimental validation
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
......@@ -87,3 +91,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
content/3.defense-systems/gao_her.md
View file @ f741a518
......@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF01935, PF10412, PF13289
relevantAbstracts:
- doi: 10.1126/science.aba0372
---
# Gao_Her
......@@ -38,41 +40,35 @@ The system was detected in 134 different species.
Proportion of genome encoding the Gao_Her system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### Gao_Her_DUF
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /gao_her/Gao_Her_DUF,Gao_Her_DUF__DUF4297,0,V-plddts_91.87572.pdb
---
::
dataUrls:
- /gao_her/Gao_Her_DUF.Gao_Her_DUF__DUF4297.0.V.cif
- /gao_her/Gao_Her_DUF.Gao_Her_DUF__HerA_DUF.0.V.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /gao_her/Gao_Her_DUF,Gao_Her_DUF__HerA_DUF,0,V-plddts_88.91697.pdb
---
::
### Gao_Her_SIR
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /gao_her/Gao_Her_SIR,Gao_Her_SIR__HerA_SIR2,0,V-plddts_86.52691.pdb
---
::
dataUrls:
- /gao_her/Gao_Her_SIR.Gao_Her_SIR__HerA_SIR2.0.V.cif
- /gao_her/Gao_Her_SIR.Gao_Her_SIR__SIR2.0.V.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /gao_her/Gao_Her_SIR,Gao_Her_SIR__SIR2,0,V-plddts_87.76893.pdb
---
::
## Experimental validation
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
......@@ -112,13 +108,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
## Relevant abstracts
::relevant-abstracts
---
items:
- doi: 10.1126/science.aba0372
---
::
content/3.defense-systems/gao_hhe.md
View file @ f741a518
......@@ -45,18 +45,22 @@ The system was detected in 56 different species.
Proportion of genome encoding the Gao_Hhe system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### Gao_Hhe
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /gao_hhe/Gao_Hhe__HheA-plddts_81.41701.pdb
dataUrls:
- /gao_hhe/Gao_Hhe__HheA.cif
---
::
## Experimental validation
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
......@@ -85,3 +89,4 @@ end
</mermaid>
content/3.defense-systems/gao_iet.md
View file @ f741a518
......@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00004, PF00082
relevantAbstracts:
- doi: 10.1126/science.aba0372
---
# Gao_Iet
......@@ -34,25 +36,23 @@ The system was detected in 185 different species.
Proportion of genome encoding the Gao_Iet system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### Gao_Iet
##### Example 1
::molstar-pdbe-plugin
---
height: 700
dataUrl: /gao_iet/Gao_Iet,Gao_Iet__IetA,0,V-plddts_85.57017.pdb
---
::
dataUrls:
- /gao_iet/Gao_Iet.Gao_Iet__IetA.0.V.cif
- /gao_iet/Gao_Iet.Gao_Iet__IetS.0.V.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /gao_iet/Gao_Iet,Gao_Iet__IetS,0,V-plddts_90.4167.pdb
---
::
## Experimental validation
<mermaid>
graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
......@@ -79,13 +79,4 @@ end
style Title3 fill:none,stroke:none,stroke-width:none
style Title4 fill:none,stroke:none,stroke-width:none
</mermaid>
## Relevant abstracts
::relevant-abstracts
---
items:
- doi: 10.1126/science.aba0372
---
::