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components/content/MolstarPdbePlugin.vue
View file @ f741a518
...@@ -107,7 +107,7 @@ const pdbeMolstarComponent = ref(null) ...@@ -107,7 +107,7 @@ const pdbeMolstarComponent = ref(null)
const selectedPdb: Ref<string | null> = ref(null) const selectedPdb: Ref<string | null> = ref(null)
const structureToDownload: Ref<string | null> = ref(null) const structureToDownload: Ref<string | null> = ref(null)
const selectedPaePath = computed(() => { const selectedPaePath = computed(() => {
return selectedPdb.value ? `${selectedPdb.value.split(".").slice(0, -1).join('.')}.png` : null return selectedPdb.value ? `${selectedPdb.value.split(".").slice(0, -1).join('.')}.png` : undefined
}) })
watch(selectedPdb, (newSelectedPdb, prevSelectPdb) => { watch(selectedPdb, (newSelectedPdb, prevSelectPdb) => {
...@@ -190,10 +190,9 @@ const moleculeFormat: Ref<string> = ref("pdb") ...@@ -190,10 +190,9 @@ const moleculeFormat: Ref<string> = ref("pdb")
<v-col :cols="mobile ? 12 : 'auto'"> <v-col :cols="mobile ? 12 : 'auto'">
<v-sheet v-if="selectedPdb" <v-sheet v-if="selectedPdb"
class="d-flex align-center justify-center flex-wrap text-center mx-auto px-4 my-3" class="d-flex align-center justify-center flex-wrap text-center mx-auto px-4 my-3"
:height="computedHeight" :width="computedWidth" position="relative"> :height="computedHeight" :width="computedWidth" style="position:relative;">
<pdbe-molstar ref="pdbeMolstarComponent" landscape="true" hide-controls="true" <pdbe-molstar ref="pdbeMolstarComponent" :custom-data-url="selectedPdb" alphafold-view
:custom-data-url="selectedPdb" alphafold-view="true" sequence-panel="true" landscape="false" :custom-data-format="moleculeFormat"></pdbe-molstar>
:custom-data-format="moleculeFormat"></pdbe-molstar>
</v-sheet> </v-sheet>
</v-col> </v-col>
<v-col :cols="mobile ? 12 : undefined"> <v-col :cols="mobile ? 12 : undefined">
...@@ -272,4 +271,4 @@ div.msp-plugin-content.msp-layout-expanded { ...@@ -272,4 +271,4 @@ div.msp-plugin-content.msp-layout-expanded {
height: 16px; height: 16px;
width: 16px; width: 16px;
} }
</style> </style>
\ No newline at end of file
components/content/StructureDb.vue
View file @ f741a518
...@@ -8,7 +8,8 @@ import { useNumericalFilter } from "@/composables/useNumericalfilter" ...@@ -8,7 +8,8 @@ import { useNumericalFilter } from "@/composables/useNumericalfilter"
import { ServerDbTable } from "#components" import { ServerDbTable } from "#components"
const sortBy: Ref<SortItem[]> = ref([{ key: 'System', order: "asc" }]) const sortBy: Ref<SortItem[]> = ref([{ key: 'System', order: "asc" }])
const itemValue = ref("id"); const itemValue = ref("id");
const facets: Ref<string[]> = ref(["System", "subtype", "gene_name", "completed", "prediction_type",]) const facets: Ref<string[]> = ref(["System", "subtype", "gene_name", "completed", "prediction_type", "proteins_in_the_prediction", "system_genes",
])
const headers: Ref<Object[]> = ref([ const headers: Ref<Object[]> = ref([
{ title: 'Structure', key: 'structure', sortable: false, removable: false }, { title: 'Structure', key: 'structure', sortable: false, removable: false },
{ title: "System", key: "System", removable: false }, { title: "System", key: "System", removable: false },
......
content/3.defense-systems/abia.md
View file @ f741a518
...@@ -44,35 +44,35 @@ The system was detected in 35 different species. ...@@ -44,35 +44,35 @@ The system was detected in 35 different species.
Proportion of genome encoding the AbiA system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the AbiA system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### AbiA_large ### AbiA_large
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /abia/AbiA_large__AbiA_large-plddts_90.82916.pdb dataUrls:
- /abia/AbiA_large__AbiA_large.cif
--- ---
:: ::
### AbiA_small ### AbiA_small
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /abia/AbiA_small,AbiA_small__AbiA_SLATT,0,DF-plddts_94.13374.pdb dataUrls:
--- - /abia/AbiA_small.AbiA_small__AbiA_small.0.DF.cif
:: - /abia/AbiA_small.AbiA_small__AbiA_SLATT.0.DF.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /abia/AbiA_small,AbiA_small__AbiA_small,0,DF-plddts_89.82347.pdb
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0 Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
...@@ -98,3 +98,4 @@ end ...@@ -98,3 +98,4 @@ 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>
content/3.defense-systems/abib.md
View file @ f741a518
...@@ -47,18 +47,22 @@ The system was detected in 5 different species. ...@@ -47,18 +47,22 @@ The system was detected in 5 different species.
Proportion of genome encoding the AbiB system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the AbiB system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### AbiB ### AbiB
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /abib/AbiB__AbiB-plddts_74.5545.pdb dataUrls:
- /abib/AbiB__AbiB.cif
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0 Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
...@@ -84,3 +88,4 @@ end ...@@ -84,3 +88,4 @@ end
</mermaid> </mermaid>
content/3.defense-systems/abic.md
View file @ f741a518
...@@ -10,6 +10,9 @@ tableColumns: ...@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown Activator: Unknown
Effector: Unknown Effector: Unknown
PFAM: PF16872 PFAM: PF16872
relevantAbstracts:
- doi: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
--- ---
# AbiC # AbiC
...@@ -35,18 +38,22 @@ The system was detected in 57 different species. ...@@ -35,18 +38,22 @@ The system was detected in 57 different species.
Proportion of genome encoding the AbiC system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the AbiC system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### AbiC ### AbiC
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /abic/AbiC__AbiC-plddts_83.80335.pdb dataUrls:
- /abic/AbiC__AbiC.cif
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; 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 Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
...@@ -102,14 +109,4 @@ end ...@@ -102,14 +109,4 @@ 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: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
---
::
content/3.defense-systems/abid.md
View file @ f741a518
...@@ -10,6 +10,9 @@ tableColumns: ...@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown Activator: Unknown
Effector: Unknown Effector: Unknown
PFAM: PF07751 PFAM: PF07751
relevantAbstracts:
- doi: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
--- ---
# AbiD # AbiD
...@@ -35,18 +38,22 @@ The system was detected in 964 different species. ...@@ -35,18 +38,22 @@ The system was detected in 964 different species.
Proportion of genome encoding the AbiD system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the AbiD system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### AbiD ### AbiD
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /abid/AbiD__AbiD-plddts_91.87407.pdb dataUrls:
- /abid/AbiD__AbiD.cif
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0 Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
...@@ -72,14 +79,4 @@ end ...@@ -72,14 +79,4 @@ 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: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
---
::
content/3.defense-systems/abie.md
View file @ f741a518
...@@ -10,6 +10,10 @@ tableColumns: ...@@ -10,6 +10,10 @@ tableColumns:
Activator: Unknown Activator: Unknown
Effector: Unknown Effector: Unknown
PFAM: PF08843, PF09407, PF09952, PF11459, PF13338, PF17194 PFAM: PF08843, PF09407, PF09952, PF11459, PF13338, PF17194
relevantAbstracts:
- doi: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
- doi: 10.1093/nar/gkt1419
--- ---
# AbiE # AbiE
...@@ -44,25 +48,23 @@ The system was detected in 1107 different species. ...@@ -44,25 +48,23 @@ The system was detected in 1107 different species.
Proportion of genome encoding the AbiE system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the AbiE system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### AbiE ### AbiE
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /abie/AbiE,AbiE__AbiEi,0,V-plddts_85.81224.pdb dataUrls:
--- - /abie/AbiE.AbiE__AbiEi.0.V.cif
:: - /abie/AbiE.AbiE__AbiEii.0.V.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /abie/AbiE,AbiE__AbiEii,0,V-plddts_90.73768.pdb
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0 Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
...@@ -86,15 +88,4 @@ end ...@@ -86,15 +88,4 @@ 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: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
- doi: 10.1093/nar/gkt1419
---
::
content/3.defense-systems/abig.md
View file @ f741a518
...@@ -10,6 +10,9 @@ tableColumns: ...@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown Activator: Unknown
Effector: Unknown Effector: Unknown
PFAM: PF10899, PF16873 PFAM: PF10899, PF16873
relevantAbstracts:
- doi: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
--- ---
# AbiG # AbiG
...@@ -35,25 +38,23 @@ The system was detected in 22 different species. ...@@ -35,25 +38,23 @@ The system was detected in 22 different species.
Proportion of genome encoding the AbiG system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the AbiG system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### AbiG ### AbiG
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /abig/AbiG,AbiG__AbiGi,0,V-plddts_92.08021.pdb dataUrls:
--- - /abig/AbiG.AbiG__AbiGi.0.V.cif
:: - /abig/AbiG.AbiG__AbiGii.0.V.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /abig/AbiG,AbiG__AbiGii,0,V-plddts_88.01846.pdb
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0 Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
...@@ -79,14 +80,4 @@ end ...@@ -79,14 +80,4 @@ 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: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
---
::
content/3.defense-systems/abih.md
View file @ f741a518
...@@ -46,18 +46,22 @@ The system was detected in 439 different species. ...@@ -46,18 +46,22 @@ The system was detected in 439 different species.
Proportion of genome encoding the AbiH system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the AbiH system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### AbiH ### AbiH
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /abih/AbiH__AbiH-plddts_91.3485.pdb dataUrls:
- /abih/AbiH__AbiH.cif
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0 Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
...@@ -85,3 +89,4 @@ end ...@@ -85,3 +89,4 @@ end
content/3.defense-systems/abii.md
View file @ f741a518
...@@ -9,6 +9,9 @@ tableColumns: ...@@ -9,6 +9,9 @@ tableColumns:
Sensor: Unknown Sensor: Unknown
Activator: Unknown Activator: Unknown
Effector: Unknown Effector: Unknown
relevantAbstracts:
- doi: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
--- ---
# AbiI # AbiI
...@@ -33,18 +36,22 @@ The system was detected in 6 different species. ...@@ -33,18 +36,22 @@ The system was detected in 6 different species.
Proportion of genome encoding the AbiI system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the AbiI system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### AbiI ### AbiI
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /abii/AbiI__AbiI-plddts_90.31131.pdb dataUrls:
- /abii/AbiI__AbiI.cif
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0 Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
...@@ -69,13 +76,4 @@ end ...@@ -69,13 +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: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
---
::
content/3.defense-systems/abij.md
View file @ f741a518
...@@ -10,6 +10,9 @@ tableColumns: ...@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown Activator: Unknown
Effector: Unknown Effector: Unknown
PFAM: PF14355 PFAM: PF14355
relevantAbstracts:
- doi: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
--- ---
# AbiJ # AbiJ
...@@ -34,18 +37,22 @@ The system was detected in 261 different species. ...@@ -34,18 +37,22 @@ The system was detected in 261 different species.
Proportion of genome encoding the AbiJ system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the AbiJ system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### AbiJ ### AbiJ
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /abij/AbiJ__AbiJ-plddts_85.12535.pdb dataUrls:
- /abij/AbiJ__AbiJ.cif
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0 Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
...@@ -69,14 +76,4 @@ end ...@@ -69,14 +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: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
---
::
content/3.defense-systems/abik.md
View file @ f741a518
...@@ -10,6 +10,10 @@ tableColumns: ...@@ -10,6 +10,10 @@ tableColumns:
Activator: Unknown Activator: Unknown
Effector: Unknown Effector: Unknown
PFAM: PF00078 PFAM: PF00078
relevantAbstracts:
- doi: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
- doi: 10.1093/nar/gkac467
--- ---
# AbiK # AbiK
...@@ -34,18 +38,22 @@ The system was detected in 32 different species. ...@@ -34,18 +38,22 @@ The system was detected in 32 different species.
Proportion of genome encoding the AbiK system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the AbiK system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### AbiK ### AbiK
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /abik/AbiK__AbiK-plddts_91.42521.pdb dataUrls:
- /abik/AbiK__AbiK.cif
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0 Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
...@@ -71,15 +79,4 @@ end ...@@ -71,15 +79,4 @@ 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: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
- doi: 10.1093/nar/gkac467
---
::
content/3.defense-systems/abil.md
View file @ f741a518
...@@ -49,25 +49,23 @@ The system was detected in 126 different species. ...@@ -49,25 +49,23 @@ The system was detected in 126 different species.
Proportion of genome encoding the AbiL system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the AbiL system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### AbiL ### AbiL
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /abil/AbiL,AbiL__AbiLi,0,V-plddts_89.17612.pdb dataUrls:
--- - /abil/AbiL.AbiL__AbiLi.0.V.cif
:: - /abil/AbiL.AbiL__AbiLii.0.V.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /abil/AbiL,AbiL__AbiLii,0,V-plddts_86.69766.pdb
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0 Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
...@@ -95,3 +93,4 @@ end ...@@ -95,3 +93,4 @@ end
content/3.defense-systems/abin.md
View file @ f741a518
...@@ -9,6 +9,9 @@ tableColumns: ...@@ -9,6 +9,9 @@ tableColumns:
Sensor: Unknown Sensor: Unknown
Activator: Unknown Activator: Unknown
Effector: Unknown Effector: Unknown
relevantAbstracts:
- doi: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
--- ---
# AbiN # AbiN
...@@ -33,18 +36,22 @@ The system was detected in 52 different species. ...@@ -33,18 +36,22 @@ The system was detected in 52 different species.
Proportion of genome encoding the AbiN system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the AbiN system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### AbiN ### AbiN
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /abin/AbiN__AbiN-plddts_84.27216.pdb dataUrls:
- /abin/AbiN__AbiN.cif
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0 Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
...@@ -69,13 +76,4 @@ end ...@@ -69,13 +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: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
---
::
content/3.defense-systems/abio.md
View file @ f741a518
...@@ -10,6 +10,9 @@ tableColumns: ...@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown Activator: Unknown
Effector: Unknown Effector: Unknown
PFAM: PF01443, PF09848 PFAM: PF01443, PF09848
relevantAbstracts:
- doi: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
--- ---
# AbiO # AbiO
...@@ -34,18 +37,22 @@ The system was detected in 61 different species. ...@@ -34,18 +37,22 @@ The system was detected in 61 different species.
Proportion of genome encoding the AbiO system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the AbiO system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### AbiO ### AbiO
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /abio/AbiO__AbiO-plddts_87.43501.pdb dataUrls:
- /abio/AbiO__AbiO.cif
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0 Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
...@@ -70,14 +77,4 @@ end ...@@ -70,14 +77,4 @@ 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: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
---
::
content/3.defense-systems/abip2.md
View file @ f741a518
...@@ -10,6 +10,10 @@ tableColumns: ...@@ -10,6 +10,10 @@ tableColumns:
Activator: Unknown Activator: Unknown
Effector: Unknown Effector: Unknown
PFAM: PF00078 PFAM: PF00078
relevantAbstracts:
- doi: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
- doi: 10.1093/nar/gkac467
--- ---
# AbiP2 # AbiP2
...@@ -34,18 +38,22 @@ The system was detected in 96 different species. ...@@ -34,18 +38,22 @@ The system was detected in 96 different species.
Proportion of genome encoding the AbiP2 system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the AbiP2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### AbiP2 ### AbiP2
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /abip2/AbiP2__AbiP2-plddts_93.08218.pdb dataUrls:
- /abip2/AbiP2__AbiP2.cif
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0 Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
...@@ -78,15 +86,4 @@ end ...@@ -78,15 +86,4 @@ 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: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
- doi: 10.1093/nar/gkac467
---
::
content/3.defense-systems/abiq.md
View file @ f741a518
...@@ -10,6 +10,10 @@ tableColumns: ...@@ -10,6 +10,10 @@ tableColumns:
Activator: Unknown Activator: Unknown
Effector: Unknown Effector: Unknown
PFAM: PF13958 PFAM: PF13958
relevantAbstracts:
- doi: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
- doi: 10.1128/AEM.64.12.4748-4756.1998
--- ---
# AbiQ # AbiQ
...@@ -34,18 +38,22 @@ The system was detected in 111 different species. ...@@ -34,18 +38,22 @@ The system was detected in 111 different species.
Proportion of genome encoding the AbiQ system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the AbiQ system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### AbiQ ### AbiQ
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /abiq/AbiQ__AbiQ-plddts_90.84212.pdb dataUrls:
- /abiq/AbiQ__AbiQ.cif
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0 Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
...@@ -70,15 +78,4 @@ end ...@@ -70,15 +78,4 @@ 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: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
- doi: 10.1128/AEM.64.12.4748-4756.1998
---
::
content/3.defense-systems/abir.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, PF04545, PF04851, PF13091 PFAM: PF00176, PF00271, PF04545, PF04851, PF13091
relevantAbstracts:
- doi: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
--- ---
# AbiR # AbiR
...@@ -34,32 +37,24 @@ The system was detected in 28 different species. ...@@ -34,32 +37,24 @@ The system was detected in 28 different species.
Proportion of genome encoding the AbiR system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the AbiR system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### AbiR ### AbiR
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /abir/AbiR,AbiR__AbiRa,0,V-plddts_88.45598.pdb dataUrls:
--- - /abir/AbiR.AbiR__AbiRc.0.V.cif
:: - /abir/AbiR.AbiR__AbiRb.0.V.cif
- /abir/AbiR.AbiR__AbiRa.0.V.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /abir/AbiR,AbiR__AbiRb,0,V-plddts_92.82829.pdb
---
::
::molstar-pdbe-plugin
---
height: 700
dataUrl: /abir/AbiR,AbiR__AbiRc,0,V-plddts_86.60767.pdb
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0 Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
...@@ -84,14 +79,4 @@ end ...@@ -84,14 +79,4 @@ 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: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
---
::
content/3.defense-systems/abit.md
View file @ f741a518
...@@ -10,6 +10,9 @@ tableColumns: ...@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown Activator: Unknown
Effector: Unknown Effector: Unknown
PFAM: PF18864 PFAM: PF18864
relevantAbstracts:
- doi: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
--- ---
# AbiT # AbiT
...@@ -34,25 +37,23 @@ The system was detected in 6 different species. ...@@ -34,25 +37,23 @@ The system was detected in 6 different species.
Proportion of genome encoding the AbiT system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the AbiT system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### AbiT ### AbiT
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /abit/AbiT,AbiT__AbiTi,0,V-plddts_81.84478.pdb dataUrls:
--- - /abit/AbiT.AbiT__AbiTi.0.V.cif
:: - /abit/AbiT.AbiT__AbiTii.0.V.cif
::molstar-pdbe-plugin
---
height: 700
dataUrl: /abit/AbiT,AbiT__AbiTii,0,V-plddts_88.46375.pdb
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0 Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
...@@ -77,14 +78,4 @@ end ...@@ -77,14 +78,4 @@ 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: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
---
::
content/3.defense-systems/abiu.md
View file @ f741a518
...@@ -47,18 +47,22 @@ The system was detected in 389 different species. ...@@ -47,18 +47,22 @@ The system was detected in 389 different species.
Proportion of genome encoding the AbiU system for the 14 phyla with more than 50 genomes in the RefSeq database. Proportion of genome encoding the AbiU system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
## Structure
### AbiU ### AbiU
##### Example 1
::molstar-pdbe-plugin ::molstar-pdbe-plugin
--- ---
height: 700 height: 700
dataUrl: /abiu/AbiU__AbiU-plddts_84.61928.pdb dataUrls:
- /abiu/AbiU__AbiU.cif
--- ---
:: ::
## Experimental validation ## Experimental validation
<mermaid> <mermaid>
graph LR; graph LR;
Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0 Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
...@@ -84,3 +88,4 @@ end ...@@ -84,3 +88,4 @@ 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>