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content/3.defense-systems/sspbcde.md
View file @ f741a518
...@@ -10,6 +10,9 @@ tableColumns: ...@@ -10,6 +10,9 @@ tableColumns:
Activator: Direct Activator: Direct
Effector: Nucleic acid degrading Effector: Nucleic acid degrading
PFAM: PF01507, PF01580, PF03235, PF07510, PF13182 PFAM: PF01507, PF01580, PF03235, PF07510, PF13182
relevantAbstracts:
- doi: 10.1128/mBio.00613-21
- doi: 10.1128/mBio.00613-21
--- ---
# SspBCDE # SspBCDE
...@@ -34,83 +37,40 @@ The system was detected in 299 different species. ...@@ -34,83 +37,40 @@ The system was detected in 299 different species.
Proportion of genome encoding the SspBCDE system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the SspBCDE system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### SspBCDE ### SspBCDE
##### Example 1
Example 1:
::molstar-pdbe-plugin
---
height: 700
dataUrl: /sspbcde/SspBCDE,SspBCDE__SspB,0,V-plddts_92.59451.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /sspbcde/SspBCDE,SspBCDE__SspC,0,V-plddts_85.51697.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /sspbcde/SspBCDE,SspBCDE__SspD,0,V-plddts_87.41069.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /sspbcde/SspBCDE,SspBCDE__SspE,0,V-plddts_88.74902.pdb
---
::
Example 2:
::molstar-pdbe-plugin
---
height: 700
dataUrl: /sspbcde/SspBCDE,SspBCDE__SspB,0,V-plddts_92.59451.pdb
---
::
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /sspbcde/SspBCDE,SspBCDE__SspC,0,V-plddts_85.51697.pdb dataUrls:
--- - /sspbcde/SspBCDE.SspBCDE__SspC.1.V.cif
:: - /sspbcde/SspBCDE.SspBCDE__SspD.0.V.cif
- /sspbcde/SspBCDE.SspBCDE__SspE.0.V.cif
- /sspbcde/SspBCDE.SspBCDE__SspB.1.V.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /sspbcde/SspBCDE,SspBCDE__SspD,0,V-plddts_87.41069.pdb
--- ---
:: ::
##### Example 2
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /sspbcde/SspBCDE,SspBCDE__SspE,0,V-plddts_88.74902.pdb dataUrls:
--- - /sspbcde/SspBCDE.SspBCDE__SspH.1.V.cif
:: - /sspbcde/SspBCDE.SspBCDE__SspG.1.V.cif
- /sspbcde/SspBCDE.SspBCDE__SspF.1.V.cif
- /sspbcde/SspBCDE.SspBCDE__SspD.0.V.cif
- /sspbcde/SspBCDE.SspBCDE__SspC.1.V.cif
- /sspbcde/SspBCDE.SspBCDE__SspB.1.V.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /sspbcde/SspBCDE,SspBCDE__SspB,1,V-plddts_92.38727.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /sspbcde/SspBCDE,SspBCDE__SspC,1,V-plddts_84.03334.pdb
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Xiong_2020[<a href='https://doi.org/10.1038/s41564-020-0700-6'>Xiong et al., 2020</a>] --> Origin_0 Xiong_2020[<a href='https://doi.org/10.1038/s41564-020-0700-6'>Xiong et al., 2020</a>] --> Origin_0
...@@ -183,14 +143,4 @@ end ...@@ -183,14 +143,4 @@ end
style Title3 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 style Title4 fill:none,stroke:none,stroke-width:none
</mermaid> </mermaid>
## Relevant abstracts
::relevant-abstracts
---
items:
- doi: 10.1128/mBio.00613-21
- doi: 10.1128/mBio.00613-21
---
::
content/3.defense-systems/stk2.md
View file @ f741a518
...@@ -10,6 +10,8 @@ tableColumns: ...@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct Activator: Direct
Effector: Other (protein modifying) Effector: Other (protein modifying)
PFAM: PF00069, PF07714 PFAM: PF00069, PF07714
relevantAbstracts:
- doi: 10.1016/j.chom.2016.08.010
--- ---
# Stk2 # Stk2
...@@ -43,18 +45,22 @@ The system was detected in 29 different species. ...@@ -43,18 +45,22 @@ The system was detected in 29 different species.
Proportion of genome encoding the Stk2 system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the Stk2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### Stk2 ### Stk2
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /stk2/Stk2__Stk2-plddts_91.79541.pdb dataUrls:
- /stk2/Stk2__Stk2.cif
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Depardieu_2016[<a href='https://doi.org/10.1016/j.chom.2016.08.010'>Depardieu et al., 2016</a>] --> Origin_0 Depardieu_2016[<a href='https://doi.org/10.1016/j.chom.2016.08.010'>Depardieu et al., 2016</a>] --> Origin_0
...@@ -89,13 +95,4 @@ end ...@@ -89,13 +95,4 @@ end
style Title3 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 style Title4 fill:none,stroke:none,stroke-width:none
</mermaid> </mermaid>
## Relevant abstracts
::relevant-abstracts
---
items:
- doi: 10.1016/j.chom.2016.08.010
---
::
content/3.defense-systems/thoeris.md
View file @ f741a518
...@@ -10,6 +10,9 @@ tableColumns: ...@@ -10,6 +10,9 @@ tableColumns:
Activator: Signaling Activator: Signaling
Effector: Nucleotide modifying Effector: Nucleotide modifying
PFAM: PF08937, PF13289, PF18185 PFAM: PF08937, PF13289, PF18185
relevantAbstracts:
- doi: 10.1038/s41586-021-04098-7
- doi: 10.1126/science.aar4120
--- ---
# Thoeris # Thoeris
...@@ -34,41 +37,35 @@ The system was detected in 298 different species. ...@@ -34,41 +37,35 @@ The system was detected in 298 different species.
Proportion of genome encoding the Thoeris system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the Thoeris system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### Thoeris_I ### Thoeris_I
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /thoeris/Thoeris_I,Thoeris_I__ThsA_new_grand,0,V-plddts_93.92302.pdb dataUrls:
--- - /thoeris/Thoeris_I.Thoeris_I__ThsA_new_grand.0.V.cif
:: - /thoeris/Thoeris_I.Thoeris__ThsB_Global.0.V.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /thoeris/Thoeris_I,Thoeris__ThsB_Global,0,V-plddts_90.12702.pdb
--- ---
:: ::
### Thoeris_II ### Thoeris_II
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /thoeris/Thoeris_II,Thoeris_II__ThsA_new_petit,0,V-plddts_88.7532.pdb dataUrls:
--- - /thoeris/Thoeris_I.Thoeris__ThsB_Global.0.V.cif
:: - /thoeris/Thoeris_II.Thoeris_II__ThsA_new_petit.0.V.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /thoeris/Thoeris_II,Thoeris__ThsB_Global,0,V-plddts_93.32159.pdb
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0 Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
...@@ -127,14 +124,4 @@ end ...@@ -127,14 +124,4 @@ end
style Title3 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 style Title4 fill:none,stroke:none,stroke-width:none
</mermaid> </mermaid>
## Relevant abstracts
::relevant-abstracts
---
items:
- doi: 10.1038/s41586-021-04098-7
- doi: 10.1126/science.aar4120
---
::
content/3.defense-systems/tiamat.md
View file @ f741a518
...@@ -48,18 +48,22 @@ The system was detected in 251 different species. ...@@ -48,18 +48,22 @@ The system was detected in 251 different species.
Proportion of genome encoding the Tiamat system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the Tiamat system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### Tiamat ### Tiamat
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /tiamat/Tiamat__TmtA-plddts_86.46392.pdb dataUrls:
- /tiamat/Tiamat__TmtA.cif
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0 Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
...@@ -87,3 +91,4 @@ end ...@@ -87,3 +91,4 @@ end
--- ---
content/3.defense-systems/uzume.md
View file @ f741a518
...@@ -9,6 +9,8 @@ tableColumns: ...@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown Sensor: Unknown
Activator: Unknown Activator: Unknown
Effector: Unknown Effector: Unknown
relevantAbstracts:
- doi: 10.1016/j.chom.2022.09.017
--- ---
# Uzume # Uzume
...@@ -33,18 +35,22 @@ The system was detected in 87 different species. ...@@ -33,18 +35,22 @@ The system was detected in 87 different species.
Proportion of genome encoding the Uzume system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the Uzume system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### Uzume ### Uzume
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /uzume/Uzume__UzmA-plddts_94.2491.pdb dataUrls:
- /uzume/Uzume__UzmA.cif
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0 Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
...@@ -70,12 +76,4 @@ end ...@@ -70,12 +76,4 @@ end
style Title3 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 style Title4 fill:none,stroke:none,stroke-width:none
</mermaid> </mermaid>
## Relevant abstracts
::relevant-abstracts
---
items:
- doi: 10.1016/j.chom.2022.09.017
---
::
content/3.defense-systems/viperin.md
View file @ f741a518
...@@ -55,18 +55,22 @@ The system was detected in 95 different species. ...@@ -55,18 +55,22 @@ The system was detected in 95 different species.
Proportion of genome encoding the Viperin system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the Viperin system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### Viperin ### Viperin
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /viperin/Viperin__pVip-plddts_95.08271.pdb dataUrls:
- /viperin/Viperin__pVip.cif
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_0 Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_0
...@@ -228,3 +232,4 @@ end ...@@ -228,3 +232,4 @@ end
style Title4 fill:none,stroke:none,stroke-width:none style Title4 fill:none,stroke:none,stroke-width:none
</mermaid> </mermaid>
content/3.defense-systems/wadjet.md
View file @ f741a518
...@@ -10,6 +10,8 @@ tableColumns: ...@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct Activator: Direct
Effector: Nucleic acid degrading Effector: Nucleic acid degrading
PFAM: PF09660, PF09661, PF09664, PF09983, PF11795, PF11796, PF11855, PF13555, PF13558, PF13835 PFAM: PF09660, PF09661, PF09664, PF09983, PF11795, PF11796, PF11855, PF13555, PF13558, PF13835
relevantAbstracts:
- doi: 10.1126/science.aar4120
--- ---
# Wadjet # Wadjet
...@@ -42,105 +44,47 @@ The system was detected in 1467 different species. ...@@ -42,105 +44,47 @@ The system was detected in 1467 different species.
Proportion of genome encoding the Wadjet system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the Wadjet system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### Wadjet_I ### Wadjet_I
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /wadjet/Wadjet_I,Wadjet__JetA_I,0,V-plddts_85.26647.pdb dataUrls:
--- - /wadjet/Wadjet_I.Wadjet__JetA_I.0.V.cif
:: - /wadjet/Wadjet_I.Wadjet__JetB_I.0.V.cif
- /wadjet/Wadjet_I.Wadjet__JetC_I.0.V.cif
::molstar-pdbe-plugin - /wadjet/Wadjet_I.Wadjet__JetD_I.0.V.cif
---
height: 700
dataUrl: /wadjet/Wadjet_I,Wadjet__JetB_I,0,V-plddts_87.82736.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /wadjet/Wadjet_I,Wadjet__JetC_I,0,V-plddts_84.15592.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /wadjet/Wadjet_I,Wadjet__JetD_I,0,V-plddts_93.08112.pdb
--- ---
:: ::
### Wadjet_II ### Wadjet_II
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /wadjet/Wadjet_II,Wadjet__JetA_II,0,V-plddts_85.37749.pdb dataUrls:
--- - /wadjet/Wadjet_II.Wadjet__JetD_II.0.V.cif
:: - /wadjet/Wadjet_II.Wadjet__JetC_II.0.V.cif
- /wadjet/Wadjet_II.Wadjet__JetB_II.0.V.cif
::molstar-pdbe-plugin - /wadjet/Wadjet_II.Wadjet__JetA_II.0.V.cif
---
height: 700
dataUrl: /wadjet/Wadjet_II,Wadjet__JetB_II,0,V-plddts_94.08089.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /wadjet/Wadjet_II,Wadjet__JetC_II,0,V-plddts_84.09293.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /wadjet/Wadjet_II,Wadjet__JetD_II,0,V-plddts_92.28569.pdb
--- ---
:: ::
### Wadjet_III ### Wadjet_III
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /wadjet/Wadjet_III,Wadjet__JetA_III,0,V-plddts_80.48148.pdb dataUrls:
--- - /wadjet/Wadjet_III.Wadjet__JetD_III.0.V.cif
:: - /wadjet/Wadjet_III.Wadjet__JetA_III.0.V.cif
- /wadjet/Wadjet_III.Wadjet__JetB_III.0.V.cif
::molstar-pdbe-plugin - /wadjet/Wadjet_III.Wadjet__JetC_III.0.V.cif
---
height: 700
dataUrl: /wadjet/Wadjet_III,Wadjet__JetB_III,0,V-plddts_80.7136.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /wadjet/Wadjet_III,Wadjet__JetC_III,0,V-plddts_83.96933.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /wadjet/Wadjet_III,Wadjet__JetD_III,0,V-plddts_91.07357.pdb
---
::
## Relevant abstracts
::relevant-abstracts
---
items:
- doi: 10.1126/science.aar4120
--- ---
:: ::
content/3.defense-systems/zorya.md
View file @ f741a518
...@@ -10,6 +10,9 @@ tableColumns: ...@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown Activator: Unknown
Effector: Unknown Effector: Unknown
PFAM: PF00176, PF00271, PF00691, PF04851, PF15611 PFAM: PF00176, PF00271, PF00691, PF04851, PF15611
relevantAbstracts:
- doi: 10.1093/nar/gkab883
- doi: 10.1126/science.aar4120
--- ---
# Zorya # Zorya
...@@ -38,62 +41,38 @@ The system was detected in 310 different species. ...@@ -38,62 +41,38 @@ The system was detected in 310 different species.
Proportion of genome encoding the Zorya system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the Zorya system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### Zorya_TypeI ### Zorya_TypeI
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /zorya/Zorya_TypeI,Zorya_TypeI__ZorC,0,V-plddts_85.7807.pdb dataUrls:
--- - /zorya/Zorya_TypeI.Zorya_TypeI__ZorC.0.V.cif
:: - /zorya/Zorya_TypeI.Zorya_TypeI__ZorD.0.V.cif
- /zorya/Zorya_TypeII.Zorya__ZorA.0.V.cif
- /zorya/Zorya_TypeI.Zorya__ZorB.0.V.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /zorya/Zorya_TypeI,Zorya_TypeI__ZorD,0,V-plddts_80.74261.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /zorya/Zorya_TypeI,Zorya__ZorA,0,V-plddts_72.58295.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /zorya/Zorya_TypeI,Zorya__ZorB,0,V-plddts_88.9782.pdb
--- ---
:: ::
### Zorya_TypeII ### Zorya_TypeII
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /zorya/Zorya_TypeII,Zorya_TypeII__ZorE,0,V-plddts_88.59937.pdb dataUrls:
--- - /zorya/Zorya_TypeII.Zorya__ZorA.0.V.cif
:: - /zorya/Zorya_TypeI.Zorya__ZorB.0.V.cif
- /zorya/Zorya_TypeII.Zorya_TypeII__ZorE.0.V.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /zorya/Zorya_TypeII,Zorya__ZorA,0,V-plddts_77.19519.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /zorya/Zorya_TypeII,Zorya__ZorB,0,V-plddts_91.39341.pdb
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0 Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
...@@ -145,14 +124,4 @@ end ...@@ -145,14 +124,4 @@ end
style Title3 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 style Title4 fill:none,stroke:none,stroke-width:none
</mermaid> </mermaid>
## Relevant abstracts
::relevant-abstracts
---
items:
- doi: 10.1093/nar/gkab883
- doi: 10.1126/science.aar4120
---
::
data/all_predictions_statistics_clean.csv LFS
View file @ f741a518
source diff could not be displayed: it is stored in LFS. Options to address this: view the blob.
data/all_predictions_statistics_clean.tsv
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source diff could not be displayed: it is too large. Options to address this: view the blob.
packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py
View file @ f741a518
...@@ -161,6 +161,8 @@ def update_structure( ...@@ -161,6 +161,8 @@ def update_structure(
"prediction_type", "prediction_type",
"plddts", "plddts",
"iptm+ptm", "iptm+ptm",
"proteins_in_the_prediction",
"system_genes",
"pDockQ", "pDockQ",
] ]
) )
......