Skip to content
Snippets Groups Projects

Compare revisions

Changes are shown as if the source revision was being merged into the target revision. Learn more about comparing revisions.

Source

Select target project
No results found

Target

Select target project
  • mdm-lab/wiki
  • hvaysset/wiki
  • jsousa/wiki
  • tclabby/wiki
4 results
Show changes
Showing
with 342 additions and 202 deletions
......@@ -3,35 +3,49 @@ title: AbiU
layout: article
tableColumns:
article:
doi: 10.1016/j.mib.2005.06.006
doi: 10.1128/AEM.67.11.5225-5232.2001
abstract: |
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
This study reports on the identification and characterization of a novel abortive infection system, AbiU, from Lactococcus lactis. AbiU confers resistance to phages from the three main industrially relevant lactococcal phage species: c2, 936, and P335. The presence of AbiU reduced the efficiency of plaquing against specific phage from each species as follows: 3.7 × 10−1, 1.0 × 10−2, and 1.0 × 10−1, respectively. abiU involves two open reading frames,abiU1 (1,772 bp) and abiU2 (1,019 bp). Evidence indicates that AbiU1 is responsible for phage resistance and that AbiU2 may downregulate phage resistance against 936 and P335 type phages but not c2 type phage. AbiU appeared to delay transcription of both phage 712 and c2, with the effect being more marked on phage c2.
Sensor: Unknown
Activator: Unknown
Effector: Unknown
PFAM: PF10592
contributors:
- Nathalie Bechon
relevantAbstracts:
- doi: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
- doi: 10.1128/AEM.67.11.5225-5232.2001
---
# AbiU
## Description
AbiU is a single-protein abortive infection defense system described in *Lactococcus*.
## Molecular mechanism
The molecular mechanism of AbiU is not well understood. It was shown that cells expressing AbiU showed delayed transcription of phage DNA, although how it is achieved, or how does it protect the bacterial culture is not understood. AbiU was shown to be encoded near another gene that seems to be an inhibitor of defense :ref{doi=10.1128/AEM.67.11.5225-5232.2001}.
## Example of genomic structure
The AbiU system is composed of one protein: AbiU.
The AbiU is composed of 1 protein: AbiU.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![abiu](/abiu/AbiU.svg){max-width=750px}
AbiU system in the genome of *Fulvivirga lutea* (GCF_017068455.1) is composed of 1 protein: AbiU (WP_205721428.1).
The AbiU system in *Bacillus subtilis* (GCF_001889385.1, NZ_CP018295) is composed of 1 protein: AbiU (WP_072589761.1)
## Distribution of the system among prokaryotes
The AbiU system is present in a total of 390 different species.
Among the 22,803 complete genomes of RefSeq, the AbiU is detected in 950 genomes (4.17 %).
Among the 22k complete genomes of RefSeq, this system is present in 1017 genomes (4.5 %).
The system was detected in 389 different species.
![abiu](/abiu/Distribution_AbiU.svg){max-width=750px}
*Proportion of genome encoding the AbiU system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the AbiU system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......@@ -70,14 +84,3 @@ 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: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
---
::
......@@ -15,23 +15,24 @@ tableColumns:
# AbiV
## Example of genomic structure
The AbiV system is composed of one protein: AbiV.
The AbiV is composed of 1 protein: AbiV.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![abiv](/abiv/AbiV.svg){max-width=750px}
AbiV system in the genome of *Lactococcus cremoris* (GCF_017376415.1) is composed of 1 protein: AbiV (WP_011834704.1).
The AbiV system in *Bacillus mycoides* (GCF_018739365.1, NZ_CP035984) is composed of 1 protein: AbiV (WP_070128168.1)
## Distribution of the system among prokaryotes
The AbiV system is present in a total of 76 different species.
Among the 22,803 complete genomes of RefSeq, the AbiV is detected in 97 genomes (0.43 %).
Among the 22k complete genomes of RefSeq, this system is present in 126 genomes (0.6 %).
The system was detected in 61 different species.
![abiv](/abiv/Distribution_AbiV.svg){max-width=750px}
*Proportion of genome encoding the AbiV system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the AbiV system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
......@@ -14,23 +14,24 @@ tableColumns:
# AbiZ
## Example of genomic structure
The AbiZ system is composed of one protein: AbiZ.
The AbiZ is composed of 1 protein: AbiZ.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![abiz](/abiz/AbiZ.svg){max-width=750px}
AbiZ system in the genome of *Streptococcus oralis* (GCF_019334565.1) is composed of 1 protein: AbiZ (WP_215804505.1).
The AbiZ system in *Fusobacterium pseudoperiodonticum* (GCF_002763695.1, NZ_CP024700) is composed of 1 protein: AbiZ (WP_099987858.1)
## Distribution of the system among prokaryotes
The AbiZ system is present in a total of 191 different species.
Among the 22,803 complete genomes of RefSeq, the AbiZ is detected in 118 genomes (0.52 %).
Among the 22k complete genomes of RefSeq, this system is present in 831 genomes (3.6 %).
The system was detected in 97 different species.
![abiz](/abiz/Distribution_AbiZ.svg){max-width=750px}
*Proportion of genome encoding the AbiZ system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the AbiZ system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
......@@ -15,23 +15,24 @@ tableColumns:
# Aditi
## Example of genomic structure
The Aditi system is composed of 2 proteins: DitB and, DitA.
The Aditi is composed of 2 proteins: DitA and DitB.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![aditi](/aditi/Aditi.svg){max-width=750px}
Aditi system in the genome of *Fusobacterium hwasookii* (GCF_001455105.1) is composed of 2 proteins: DitB (WP_029491896.1)and, DitA (WP_029491897.1).
The Aditi system in *Streptococcus suis* (GCF_003288175.1, NZ_CP025419) is composed of 2 proteins DitB (WP_002937368.1) DitA (WP_002937371.1)
## Distribution of the system among prokaryotes
The Aditi system is present in a total of 18 different species.
Among the 22,803 complete genomes of RefSeq, the Aditi is detected in 40 genomes (0.18 %).
Among the 22k complete genomes of RefSeq, this system is present in 40 genomes (0.2 %).
The system was detected in 19 different species.
![aditi](/aditi/Distribution_Aditi.svg){max-width=750px}
*Proportion of genome encoding the Aditi system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Aditi system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
......@@ -30,39 +30,40 @@ Upon binding to their cognate phage protein, Avs1-4 assemble into tetramers that
## Example of genomic structure
The Avs system have been describe in a total of 5 subsystems.
A total of 5 subsystems have been described for the Avs system.
Here is some example found in the RefSeq database:
Here is some examples found in the RefSeq database:
![avs](/avs/Avs_I.svg){max-width=750px}
![avs_i](/avs/Avs_I.svg){max-width=750px}
Avs_I subsystem in the genome of *Vibrio sp.* (GCF_905175355.1) is composed of 3 proteins: Avs1A (WP_208445041.1), Avs1B (WP_208445042.1)and, Avs1C (WP_108173272.1).
The Avs_I system in *Priestia aryabhattai* (GCF_022811825.1, NZ_CP064098) is composed of 3 proteins Avs1C (WP_243495694.1) Avs1B (WP_243495695.1) Avs1A (WP_243495696.1)
![avs](/avs/Avs_II.svg){max-width=750px}
![avs_ii](/avs/Avs_II.svg){max-width=750px}
Avs_II subsystem in the genome of *Escherichia coli* (GCF_018884505.1) is composed of 1 protein: Avs2A (WP_032199984.1).
The Avs_II system in *Haloferax volcanii* (GCF_000025685.1, NC_013967) is composed of 1 protein: Avs2A (WP_013035348.1)
![avs](/avs/Avs_III.svg){max-width=750px}
![avs_iii](/avs/Avs_III.svg){max-width=750px}
Avs_III subsystem in the genome of *Enterobacter cancerogenus* (GCF_002850575.1) is composed of 2 proteins: Avs3B (WP_199559884.1)and, Avs3A (WP_101737373.1).
The Avs_III system in *Chryseobacterium indologenes* (GCF_002208925.2, NZ_CP022058) is composed of 2 proteins Avs3B (WP_002978689.1) Avs3A (WP_088583894.1)
![avs](/avs/Avs_IV.svg){max-width=750px}
![avs_iv](/avs/Avs_IV.svg){max-width=750px}
Avs_IV subsystem in the genome of *Escherichia coli* (GCF_016903595.1) is composed of 1 protein: Avs4A (WP_000240574.1).
The Avs_IV system in *Dysosmobacter welbionis* (GCF_005121165.3, NZ_CP034413) is composed of 1 protein: Avs4A (WP_136890703.1)
![avs](/avs/Avs_V.svg){max-width=750px}
![avs_v](/avs/Avs_V.svg){max-width=750px}
Avs_V subsystem in the genome of *Leclercia adecarboxylata* (GCF_006171285.1) is composed of 1 protein: Avs5A (WP_139565349.1).
The Avs_V system in *Klebsiella variicola* (GCF_015287155.1, NZ_CP063912) is composed of 1 protein: Avs5A (WP_131026359.1)
## Distribution of the system among prokaryotes
The Avs system is present in a total of 363 different species.
Among the 22,803 complete genomes of RefSeq, the Avs is detected in 978 genomes (4.29 %).
Among the 22k complete genomes of RefSeq, this system is present in 1046 genomes (4.6 %).
The system was detected in 366 different species.
![avs](/avs/Distribution_Avs.svg){max-width=750px}
*Proportion of genome encoding the Avs system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.*
Proportion of genome encoding the Avs system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......@@ -80,61 +81,6 @@ dataUrls:
::
## Structure
### Avs_I
::molstar-pdbe-plugin
---
height: 700
dataUrls:
- /avs/AVAST_I,AVAST_I__Avs1A,0,V-plddts_85.07081.pdb
- /avs/AVAST_I,AVAST_I__Avs1B,0,V-plddts_80.96481.pdb
- /avs/AVAST_I,AVAST_I__Avs1C,0,V-plddts_81.74849.pdb
---
::
### Avs_II
::molstar-pdbe-plugin
---
height: 700
dataUrls:
- /avs/AVAST_II__Avs2A-plddts_86.07393.pdb
---
::
### Avs_III
::molstar-pdbe-plugin
---
height: 700
dataUrls:
- /avs/AVAST_III,AVAST_III__Avs3A,0,V-plddts_81.87773.pdb
- /avs/AVAST_III,AVAST_III__Avs3B,0,V-plddts_71.16048.pdb
---
::
### Avs_IV
::molstar-pdbe-plugin
---
height: 700
dataUrls:
- /avs/AVAST_IV__Avs4A-plddts_87.35544.pdb
---
::
### Avs_V
::molstar-pdbe-plugin
---
height: 700
dataUrls:
- /avs/AVAST_V__Avs5A-plddts_89.56857.pdb
---
::
## Experimental validation
<mermaid>
......
......@@ -15,23 +15,24 @@ tableColumns:
# Azaca
## Example of genomic structure
The Azaca system is composed of 3 proteins: ZacA, ZacB and, ZacC.
The Azaca is composed of 3 proteins: ZacA, ZacB and ZacC.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![azaca](/azaca/Azaca.svg){max-width=750px}
Azaca system in the genome of *Ornithinimicrobium sp.* (GCF_023923205.1) is composed of 3 proteins: ZacA (WP_252620090.1), ZacB (WP_252620091.1)and, ZacC (WP_252620092.1).
The Azaca system in *Gordonia polyisoprenivorans* (GCF_018135605.1, NZ_CP073075) is composed of 3 proteins ZacC (WP_006372053.1) ZacB (WP_006372052.1) ZacA (WP_006372051.1)
## Distribution of the system among prokaryotes
The Azaca system is present in a total of 156 different species.
Among the 22,803 complete genomes of RefSeq, the Azaca is detected in 203 genomes (0.89 %).
Among the 22k complete genomes of RefSeq, this system is present in 206 genomes (0.9 %).
The system was detected in 166 different species.
![azaca](/azaca/Distribution_Azaca.svg){max-width=750px}
*Proportion of genome encoding the Azaca system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Azaca system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
......@@ -10,28 +10,43 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF12770
contributors:
- Héloïse Georjon
relevantAbstracts:
- doi: 10.1016/j.chom.2022.09.017
- doi: 10.1016/j.cell.2023.02.029
---
# Borvo
## Description
Borvo is a single-gene anti-phage system that was identify through bioinformatic prediction and experimental validation :ref{doi=10.1016/j.chom.2022.09.017}.
## Molecular mechanisms
Mutations in the phage DNA polymerase can allow phages to escape Borvo defense, indicating that it could be the trigger of the system :ref{doi=10.1016/j.cell.2023.02.029}. Borvo is a suspected abortive infection :ref{doi=10.1016/j.cell.2023.02.029}. However as far as we are aware, the precise molecular mechanism of Borvo is unknown.
## Example of genomic structure
The Borvo system is composed of one protein: BovA.
The Borvo is composed of 1 protein: BovA.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![borvo](/borvo/Borvo.svg){max-width=750px}
Borvo system in the genome of *Brevundimonas sp.* (GCF_002002865.1) is composed of 1 protein: BovA_addition (WP_077354142.1).
The Borvo system in *Enterobacter cloacae complex sp. ECL78* (GCF_019056615.1, NZ_CP077660) is composed of 1 protein: BovA (WP_126517459.1)
## Distribution of the system among prokaryotes
The Borvo system is present in a total of 348 different species.
Among the 22,803 complete genomes of RefSeq, the Borvo is detected in 177 genomes (0.78 %).
Among the 22k complete genomes of RefSeq, this system is present in 650 genomes (2.9 %).
The system was detected in 79 different species.
![borvo](/borvo/Distribution_Borvo.svg){max-width=750px}
*Proportion of genome encoding the Borvo system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Borvo system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......@@ -71,13 +86,4 @@ 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
---
::
......@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00069, PF00176, PF00270, PF00271, PF01507, PF01555, PF02384, PF04851, PF07669, PF07714, PF08378, PF08665, PF08747, PF08849, PF10923, PF13337, PF16565
contributors:
- Marian Dominguez-Mirazo
relevantAbstracts:
- doi: 10.1093/nar/gkaa290
- doi: 10.1093/nar/gky1125
......@@ -20,50 +22,67 @@ relevantAbstracts:
## Description
BREX (for Bacteriophage Exclusion) is a family of anti-phage defense systems. BREX systems are active against both lytic and lysogenic phages. They allow phage adsorption but block phage DNA replication, and are considered to be [RM](/defense-systems/rm)-like systems (1,2). BREX systems are found in around 10% of sequenced microbial genomes (1).
BREX (for Bacteriophage Exclusion) is a family of anti-phage defense systems. BREX systems are active against both lytic and lysogenic phages. They allow phage adsorption but block phage DNA replication, and are considered to be [RM](/defense-systems/rm)-like systems :ref{doi=10.15252/embj.201489455,10.1093/nar/gkaa290}. BREX systems are found in around 10% of sequenced microbial genomes :ref{doi=10.15252/embj.201489455}.
BREX systems can be divided into six subtypes, and are encoded by 4 to 8 genes, some of these genes being mandatory while others are subtype-specific (1).
BREX systems can be divided into six subtypes, and are encoded by 4 to 8 genes, some of these genes being mandatory while others are subtype-specific :ref{doi=10.15252/embj.201489455}.
## Molecular mechanism
*B. cereus* BREX Type 1 system was reported to methylate target motifs in the bacterial genome (1). The methylation activity of this system has been hypothesized to allow for self from non-self discrimination, as it is the case for Restriction-Modification ([RM)](/defense-systems/rm) systems.
*B. cereus* BREX Type 1 system was reported to methylate target motifs in the bacterial genome :ref{doi=10.15252/embj.201489455}. The methylation activity of this system has been hypothesized to allow for self from non-self discrimination, as it is the case for Restriction-Modification ([RM)](/defense-systems/rm) systems.
However, the mechanism through which BREX Type 1 systems defend against phages is distinct from RM systems, and does not seem to degrade phage nucleic acids (1).
However, the mechanism through which BREX Type 1 systems defend against phages is distinct from RM systems, and does not seem to degrade phage nucleic acids :ref{doi=10.15252/embj.201489455}.
To date, BREX molecular mechanism remains to be described.
## Example of genomic structure
The BREX system have been describe in a total of 6 subsystems.
BREX systems necessarily include the pglZ gene (encoding for a putative alkaline phosphatase), which is accompanied by either brxC or pglY. These two genes share only a distant homology but have been hypothesized to fulfill the same function among the different BREX subtypes :ref{doi=10.15252/embj.201489455}.
BREX systems necessarily include the pglZ gene (encoding for a putative alkaline phosphatase), which is accompanied by either brxC or pglY. These two genes share only a distant homology but have been hypothesized to fulfill the same function among the different BREX subtypes (1).
Goldfarb and colleagues reported a 6-gene cassette from *Bacillus cereus* as being the model for BREX Type 1. BREX Type 1 are the most widespread BREX systems, and present two core genes (pglZ and brxC). Four other genes are associated with BREX Type 1 : *pglX (*encoding for a putative methyltransferase), *brxA (*encoding an RNA-binding anti-termination protein)*, brxB (*unknown functio*n), brxC (*encoding for a protein with ATP-binding domain) and *brxL* (encoding for a putative protease) :ref{doi=10.15252/embj.201489455,10.1093/nar/gkaa290}.
Goldfarb and colleagues reported a 6-gene cassette from *Bacillus cereus* as being the model for BREX Type 1. BREX Type 1 are the most widespread BREX systems, and present two core genes (pglZ and brxC). Four other genes are associated with BREX Type 1 : *pglX (*encoding for a putative methyltransferase), *brxA (*encoding an RNA-binding anti-termination protein)*, brxB (*unknown functio*n), brxC (*encoding for a protein with ATP-binding domain) and *brxL* (encoding for a putative protease) (1,2).
Type 2 BREX systems include the system formerly known as Pgl, which is comprised of four genes (pglW, X, Y, and Z) :ref{doi=10.1093/nar/gky1125}, to which :ref{doi=10.15252/embj.201489455} found often associated two additional genes (brxD, and brxHI).
Type 2 BREX systems include the system formerly known as Pgl , which is comprised of four genes (pglW, X, Y, and Z) (3), to which Goldfarb and colleagues found often associated two additional genes (brxD, and brxHI).
Although 4 additional BREX subtypes have been proposed, BREX Type 1 and Type 2 remain the only ones to be experimentally validated. A detailed description of the other subtypes can be found in :ref{doi=10.15252/embj.201489455}.
Although 4 additional BREX subtypes have been proposed, BREX Type 1 and Type 2 remain the only ones to be experimentally validated. A detailed description of the other subtypes can be found in Goldfarb *et al*., 2015.
A total of 6 subsystems have been described for the BREX system.
Here is some example found in the RefSeq database:
Here is some examples found in the RefSeq database:
![brex](/brex/BREX_I.svg){max-width=750px}
![brex_i](/brex/BREX_I.svg){max-width=750px}
BREX_I subsystem in the genome of *Kaistella sp.* (GCF_020410745.1) is composed of 6 proteins: brxL (WP_226063319.1), pglZA (WP_226063320.1), pglX1 (WP_226063321.1), brxC (WP_226063322.1), brxB_DUF1788 (WP_226063323.1)and, brxA_DUF1819 (WP_226063324.1).
The BREX_I system in *Mycobacterium kubicae* (GCF_015689175.1, NZ_CP065047) is composed of 6 proteins brxA_DUF1819 (WP_241007777.1) brxB_DUF1788 (WP_174814228.1) brxC (WP_085074024.1) pglX1 (WP_085074003.1) pglZA (WP_085074004.1) brxL (WP_085074005.1)
![brex](/brex/BREX_II.svg){max-width=750px}
![brex_ii](/brex/BREX_II.svg){max-width=750px}
BREX_II subsystem in the genome of *Streptomyces hygroscopicus* (GCF_001447075.1) is composed of 5 proteins: brxD (WP_058082289.1), pglZ2 (WP_058082290.1), pglY (WP_058082291.1), pglX2 (WP_058082292.1)and, pglW (WP_237280966.1).
The BREX_II system in *Nocardia terpenica* (GCF_002568625.1, NZ_CP023778) is composed of 6 proteins pglW (WP_232535326.1) pglX2 (WP_098693854.1) pglY (WP_098693855.1) pglZ2 (WP_098693856.1) brxD (WP_098693857.1) brxHI (WP_098693858.1)
![brex_iii](/brex/BREX_III.svg){max-width=750px}
The BREX_III system in *Rubinisphaera brasiliensis* (GCF_000165715.2, NC_015174) is composed of 5 proteins pglZ3 (WP_013627487.1) brxHII (WP_013627488.1) pglXI (WP_013627489.1) brxC (WP_041397812.1) brxF (WP_218916504.1)
![brex_iv](/brex/BREX_IV.svg){max-width=750px}
The BREX_IV system in *Olsenella sp. oral taxon 807* (GCF_001189515.2, NZ_CP012069) is composed of 4 proteins brxL (WP_050344523.1) pglZ4 (WP_172674480.1) brxC4 (WP_050340978.1) brxP (WP_050340980.1)
![brex_v](/brex/BREX_V.svg){max-width=750px}
The BREX_V system in *Heyndrickxia vini* (GCF_016772275.1, NZ_CP065425) is composed of 7 proteins brxHII (WP_202780866.1) pglZA (WP_202778092.1) pglX1 (WP_202778093.1) pglX1 (WP_202778094.1) brxC (WP_202778095.1) brxB_DUF1788 (WP_246483846.1) brxA_DUF1819 (WP_202778096.1)
![brex_vi](/brex/BREX_VI.svg){max-width=750px}
The BREX_VI system in *Virgibacillus halodenitrificans* (GCF_001878675.1, NZ_CP017962) is composed of 8 proteins brxE (WP_071648637.1) brxA_DUF1819 (WP_071648638.1) brxB_DUF1788 (WP_071648639.1) brxC (WP_197035844.1) pglX1 (WP_071648641.1) pglZA (WP_071648642.1) brxD (WP_071648643.1) brxHI (WP_071648644.1)
## Distribution of the system among prokaryotes
The BREX system is present in a total of 732 different species.
Among the 22,803 complete genomes of RefSeq, the BREX is detected in 1658 genomes (7.27 %).
Among the 22k complete genomes of RefSeq, this system is present in 1612 genomes (7.1 %).
The system was detected in 888 different species.
![brex](/brex/Distribution_BREX.svg){max-width=750px}
*Proportion of genome encoding the BREX system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.*
Proportion of genome encoding the BREX system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
......@@ -24,23 +24,24 @@ Interestingly, part of the BstA locus appears to encode an anti-BstA genetic ele
## Example of genomic structure
The BstA system is composed of one protein: BstA.
The BstA is composed of 1 protein: BstA.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![bsta](/bsta/BstA.svg){max-width=750px}
BstA system in the genome of *Providencia rustigianii* (GCF_900635875.1) is composed of 1 protein: BstA (WP_126437212.1).
The BstA system in *Vibrio harveyi* (GCF_021397735.1, NZ_CP090179) is composed of 1 protein: BstA (WP_038899043.1)
## Distribution of the system among prokaryotes
The BstA system is present in a total of 81 different species.
Among the 22,803 complete genomes of RefSeq, the BstA is detected in 236 genomes (1.03 %).
Among the 22k complete genomes of RefSeq, this system is present in 236 genomes (1.0 %).
The system was detected in 88 different species.
![bsta](/bsta/Distribution_BstA.svg){max-width=750px}
*Proportion of genome encoding the BstA system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the BstA system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
......@@ -26,23 +26,24 @@ As far as we are aware, the molecular mechanism is unknown.
## Example of genomic structure
The Bunzi system is composed of 2 proteins: BnzB and, BnzA.
The Bunzi is composed of 2 proteins: BnzA and BnzB.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![bunzi](/bunzi/Bunzi.svg){max-width=750px}
Bunzi system in the genome of *Mammaliicoccus lentus* (GCF_014070215.1) is composed of 2 proteins: BnzB (WP_107556517.1)and, BnzA (WP_107556516.1).
The Bunzi system in *Shewanella loihica* (GCF_000016065.1, NC_009092) is composed of 2 proteins BnzB (WP_011866821.1) BnzA (WP_011866822.1)
## Distribution of the system among prokaryotes
The Bunzi system is present in a total of 86 different species.
Among the 22,803 complete genomes of RefSeq, the Bunzi is detected in 103 genomes (0.45 %).
Among the 22k complete genomes of RefSeq, this system is present in 286 genomes (1.3 %).
The system was detected in 58 different species.
![bunzi](/bunzi/Distribution_Bunzi.svg){max-width=750px}
*Proportion of genome encoding the Bunzi system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Bunzi system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
......@@ -12,6 +12,27 @@ tableColumns:
## To do
## Example of genomic structure
The Butters_gp30_gp31 is composed of 2 proteins: Butters_gp30 and Butters_gp31.
Here is an example found in the RefSeq database:
![butters_gp30_gp31](/butters_gp30_gp31/Butters_gp30_gp31.svg){max-width=750px}
The Butters_gp30_gp31 system in *Snodgrassella alvi* (GCF_022870965.1, NZ_CP091515) is composed of 2 proteins Butters_gp31 (WP_025330184.1) CarolAnn_gp44 (WP_144353282.1)
## Distribution of the system among prokaryotes
Among the 22,803 complete genomes of RefSeq, the Butters_gp30_gp31 is detected in 38 genomes (0.17 %).
The system was detected in 34 different species.
![butters_gp30_gp31](/butters_gp30_gp31/Distribution_Butters_gp30_gp31.svg){max-width=750px}
Proportion of genome encoding the Butters_gp30_gp31 system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
### Butters_gp30_gp31
......
......@@ -12,6 +12,27 @@ tableColumns:
## To do
## Example of genomic structure
The Butters_gp57r is composed of 1 protein: gp57r.
Here is an example found in the RefSeq database:
![butters_gp57r](/butters_gp57r/Butters_gp57r.svg){max-width=750px}
The Butters_gp57r system in *Mycobacteroides immunogenum* (GCF_001605725.1, NZ_CP011530) is composed of 1 protein: gp57r (WP_043080133.1)
## Distribution of the system among prokaryotes
Among the 22,803 complete genomes of RefSeq, the Butters_gp57r is detected in 10 genomes (0.04 %).
The system was detected in 7 different species.
![butters_gp57r](/butters_gp57r/Distribution_Butters_gp57r.svg){max-width=750px}
Proportion of genome encoding the Butters_gp57r system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
### Butters_gp57r
......
......@@ -27,23 +27,24 @@ Different CapRel homologues confer defense against different phages, suggesting
## Example of genomic structure
The CapRel system is composed of one protein: CapRel.
The CapRel is composed of 1 protein: CapRel.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![caprel](/caprel/CapRel.svg){max-width=750px}
CapRel system in the genome of *Escherichia coli* (GCF_003856995.1) is composed of 1 protein: CapRel (WP_000526244.1).
The CapRel system in *Campylobacter sp. RM12175* (GCF_002139875.1, NZ_CP018793) is composed of 1 protein: CapRel (WP_086315994.1)
## Distribution of the system among prokaryotes
The CapRel system is present in a total of 202 different species.
Among the 22,803 complete genomes of RefSeq, the CapRel is detected in 398 genomes (1.75 %).
Among the 22k complete genomes of RefSeq, this system is present in 407 genomes (1.8 %).
The system was detected in 217 different species.
![caprel](/caprel/Distribution_CapRel.svg){max-width=750px}
*Proportion of genome encoding the CapRel system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the CapRel system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
......@@ -6,19 +6,56 @@ tableColumns:
doi: 10.1101/2023.05.28.542683
abstract: |
Caspase recruitment domains (CARDs) and pyrin domains are important facilitators of inflammasome activity and pyroptosis. Upon pathogen recognition by NLR proteins, CARDs recruit and activate caspases, which, in turn, activate gasdermin pore forming proteins to and induce pyroptotic cell death. Here we show that CARD-like domains are present in defense systems that protect bacteria against phage. The bacterial CARD is essential for protease-mediated activation of certain bacterial gasdermins, which promote cell death once phage infection is recognized. We further show that multiple anti-phage defense systems utilize CARD-like domains to activate a variety of cell death effectors. We find that these systems are triggered by a conserved immune evasion protein that phages use to overcome the bacterial defense system RexAB, demonstrating that phage proteins inhibiting one defense system can activate another. We also detect a phage protein with a predicted CARD-like structure that can inhibit the CARD-containing bacterial gasdermin system. Our results suggest that CARD domains represent an ancient component of innate immune systems conserved from bacteria to humans, and that CARD-dependent activation of gasdermins is conserved in organisms across the tree of life.
Sensor: Unknown
Activator: Unknown
Effector: Membrane disrupting or other
PFAM: PF00082, PF00089, PF00614, PF01223, PF13091, PF13191, PF13365
contributors:
- Marian Dominguez-Mirazo
relevantAbstract:
- doi: 10.1101/2023.05.28.542683
---
# CARD_NLR
## Description
Pore-forming proteins called gasdermins control cell-death response to infection in animals. Gasdermins are also present in bacteria where they have been shown to act as an abortive infection system that permeabilizes the cell membrane before phage release :ref{doi=10.1126/science.abj8432,10.1101/2023.05.28.542683}. In *Lysobacter*, the gasdermin operon includes two genes encoding trypsin-like protease domains, and a gene encoding an ATPase domain :ref{doi=10.1101/2023.05.28.542683}. Intact active sites for the second protease and the ATPase, but not the first protease, are required for succesful phage defense :ref{doi=10.1126/science.abj8432}. The domain architecture of the ATPase suggests it belongs to a protein family that is considered the ancestor of the eukaryotic nucleotide oligomerization domain (NOD)-like receptor (NLR) protein family :ref{doi=10.1101/2023.05.28.542683}. In animals, NLR initiates the formation of the inflammasome complex :ref{doi=10.1126/science.abe3069}. The second protease contains a region with similar structure to human CARD domain :ref{doi=10.1101/2023.05.28.542683}. The CARD domain takes part on the assembly of immune protein complexes :ref{doi=10.1038/sj.cdd.4401890}. The CARD-like domain in the *Lysobacter* system is required for succesful phage defense :ref{doi=10.1101/2023.05.28.542683}. Homology searches recovered multiple bacterial operons that include two proteases, one of them containing a CARD-like domain, and a NLR-like protein. In most cases, the effector gasdermin gene was replaced by another gene:ref{doi=10.1101/2023.05.28.542683}. The operon found in *Pedobacter rhizosphaerae* exhibits phage defense capabilities and contains a protein with phospholipase and endonuclease domains replacing the gasdermin gene. This system confers protection against the same phages as the *Lysobacter* gasdermin containing system, suggesting that the proteases and ATPase participate in phage specificity and recognition.
## To do
## Molecular mechanisms
For the *Lysobacter* system, the effector has been described as a pore-formin protein that disrupts the cell membrane :ref{doi=10.1101/2023.05.28.542683}. To our knowledge, other parts of the molecular mechanisms have yet to be elucidated.
## Relevant abstract
::relevant-abstracts
---
items:
- doi: 10.1101/2023.05.28.542683
## Example of genomic structure
---
::
A total of 5 subsystems have been described for the CARD_NLR system.
Here is some examples found in the RefSeq database:
![card_nlr_endonuclease](/card_nlr/CARD_NLR_Endonuclease.svg){max-width=750px}
The CARD_NLR_Endonuclease system in *Spirosoma montaniterrae* (GCF_001988955.1, NZ_CP014263) is composed of 4 proteins Trypsin (WP_077131797.1) CARD_Protease_new (WP_077131798.1) NLR_new (WP_157579217.1) Endonuclease (WP_083732853.1)
![card_nlr_gasdermin](/card_nlr/CARD_NLR_GasderMIN.svg){max-width=750px}
The CARD_NLR_GasderMIN system in *Lysobacter enzymogenes* (GCF_005954665.1, NZ_CP040656) is composed of 4 proteins bGSDM (WP_057949280.1) Trypsin_new (WP_158229849.1) CARD_Protease (WP_175429318.1) NLR_new (WP_057949283.1)
![card_nlr_phospho](/card_nlr/CARD_NLR_Phospho.svg){max-width=750px}
The CARD_NLR_Phospho system in *Achromobacter deleyi* (GCF_013116765.2, NZ_CP074375) is composed of 4 proteins Trypsin_Phospho (WP_171663676.1) Trypsin_new (WP_171663675.1) CARD_Protease_supposed (WP_171663674.1) NLR_new (WP_171663673.1)
![card_nlr_subtilase](/card_nlr/CARD_NLR_Subtilase.svg){max-width=750px}
The CARD_NLR_Subtilase system in *Mesorhizobium sp. L-8-3* (GCF_016756615.1, NZ_AP023262) is composed of 4 proteins Subtilase (WP_202329294.1) Trypsin_new (WP_202305630.1) CARD_Protease_supposed (WP_202305632.1) NLR_IMG (WP_202329295.1)
![card_nlr_like](/card_nlr/CARD_NLR_like.svg){max-width=750px}
The CARD_NLR_like system in *Sphingomonas sanguinis* (GCF_019297835.1, NZ_CP079203) is composed of 4 proteins Subtilase (WP_219018701.1) CARD_Protease_new (WP_219018702.1) NLR_new (WP_219018703.1) Endonuclease (WP_219021412.1)
## Distribution of the system among prokaryotes
Among the 22,803 complete genomes of RefSeq, the CARD_NLR is detected in 80 genomes (0.35 %).
The system was detected in 57 different species.
![card_nlr](/card_nlr/Distribution_CARD_NLR.svg){max-width=750px}
Proportion of genome encoding the CARD_NLR system for the 14 phyla with more than 50 genomes in the RefSeq database.
---
title: CRISPR-Cas
layout: article
tableColumns:
article:
doi: 10.1038/nrmicro3569
abstract: |
The evolution of CRISPR-cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR-cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR-Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized.
---
# CRISPR-Cas
For the CRISPR-Cas system, a good place to start is the [Wikipedia page](https://en.wikipedia.org/wiki/CRISPR)
## Example of genomic structure
CRISPR-Cas systems have been classified in 6 different families :ref{doi=10.1038/s41579-019-0299-x}.
Each family is composed of different subtypes. For example, Type I CRISPR is composed of 7 subtypes: I-A to I-G.
Here is example of each of the 6 family found in the RefSeq database:
![cas_class1-subtype-i-e](/cas/CAS_Class1-Subtype-I-E.svg){max-width=750px}
The CAS_Class1-Subtype-I-E system in *Citrobacter sp. RHBSTW-00017* (GCF_013797615.1, NZ_CP056899) is composed of 8 proteins cas3_I_5 (WP_103284157.1) cas8e_I-E_1 (HV037_RS05730) cse2gr11_I-E_2 (HV037_RS05735) cas7_I-E_2 (HV037_RS05740) cas5_I-E_3 (HV037_RS05745) cas6e_I_II_III_IV_V_VI_1 (HV037_RS05750) cas1_I-E_1 (HV037_RS05755) cas2_I-E_2 (HV037_RS05760)
![cas_class2-subtype-ii-a](/cas/CAS_Class2-Subtype-II-A.svg){max-width=750px}
The CAS_Class2-Subtype-II-A system in *Streptococcus agalactiae* (GCF_001190885.1, NZ_CP011329) is composed of 4 proteins cas9_II-A_II-B_II-C_3 (SAH002_RS04760) cas1_I_II_III_IV_V_VI_5 (SAH002_RS04765) cas2_I_II_III_IV_V_VI_6 (SAH002_RS04770) csn2_II-A_4 (SAH002_RS04775)
![cas_class1-subtype-iii-a](/cas/CAS_Class1-Subtype-III-A.svg){max-width=750px}
The CAS_Class1-Subtype-III-A system in *Mycobacterium tuberculosis* (GCF_014900005.1, NZ_CP041828) is composed of 9 proteins cas2_I_II_III_IV_V_VI_5 (FPJ80_RS14760) cas1_I_II_III_IV_V_VI_8 (FPJ80_RS14765) csm6_III_2 (FPJ80_RS14770) csm5gr7_III-A_3 (FPJ80_RS14775) csm4gr5_III-A_3 (FPJ80_RS14780) csm3gr7_III-A_1 (FPJ80_RS14785) csm2gr11_III-A_1 (FPJ80_RS14790) cas10_III_7 (FPJ80_RS14795) cas6_I_II_III_IV_V_VI_15 (FPJ80_RS14800)
![cas_class1-subtype-iv-a](/cas/CAS_Class1-Subtype-IV-A.svg){max-width=750px}
The CAS_Class1-Subtype-IV-A system in *Shigella flexneri* (GCF_022353685.1, NZ_CP054978) is composed of 5 proteins csf1gr8_IV-A_3 (WP_038989757.1) cas6e_I_II_III_IV_V_VI_3 (WP_038989755.1) csf4_IV-A_1 (WP_016947078.1) csf3gr5_IV-A_1 (WP_004181864.1) csf2gr7_IV-A_1 (WP_029505552.1)
![cas_class2-subtype-v-a](/cas/CAS_Class2-Subtype-V-A.svg){max-width=750px}
The CAS_Class2-Subtype-V-A system in *Francisella tularensis* (GCF_001865695.1, NZ_CP016635) is composed of 4 proteins cas2_I_II_III_IV_V_VI_3 (N894_RS07580) cas1_I_II_III_IV_V_VI_1 (N894_RS07585) cas4_V_1 (N894_RS07590) cas12a_V-A_4 (N894_RS07595)
![cas_class2-subtype-vi-a](/cas/CAS_Class2-Subtype-VI-A.svg){max-width=750px}
The CAS_Class2-Subtype-VI-A system in *Leptotrichia shahii* (GCF_008327825.1, NZ_AP019827) is composed of 3 proteins cas13a_VI-A_1 (F1564_RS00570) cas1_I_II_III_IV_V_VI_5 (F1564_RS00575) cas2_I_II_III_IV_V_VI_11 (F1564_RS00580)
## Distribution of the system among prokaryotes
Among the 22,803 complete genomes of RefSeq, the AbiC is detected in 8581 genomes (37.63 %).
The system was detected in 2905 different species.
![cas](/cas/Distribution_Cas.svg){max-width=750px}
Proportion of genome encoding the AbiC system for the 14 phyla with more than 50 genomes in the RefSeq database.
......@@ -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
......
......@@ -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
......
......@@ -31,23 +31,24 @@ DarT uses NAD+ to ADP-ribosylates tymidines on ssDNA, while DarG catalyses the r
## Example of genomic structure
The DarTG system is composed of 2 proteins: DarT and, DarG.
The DarTG is composed of 2 proteins: DarT and DarG.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![dartg](/dartg/DarTG.svg){max-width=750px}
DarTG system in the genome of *Mycobacterium tuberculosis* (GCF_904810345.1) is composed of 2 proteins: DarT (WP_003400548.1)and, DarG (WP_003400551.1).
The DarTG system in *Leptodesmis sichuanensis* (GCF_021379005.1, NZ_CP075171) is composed of 2 proteins DarT (WP_233744308.1) DarG (WP_233744309.1)
## Distribution of the system among prokaryotes
The DarTG system is present in a total of 356 different species.
Among the 22,803 complete genomes of RefSeq, the DarTG is detected in 952 genomes (4.17 %).
Among the 22k complete genomes of RefSeq, this system is present in 955 genomes (4.2 %).
The system was detected in 386 different species.
![dartg](/dartg/Distribution_DarTG.svg){max-width=750px}
*Proportion of genome encoding the DarTG system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the DarTG system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
......@@ -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
......
......@@ -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
......