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components/content/MolstarPdbePlugin.vue
View file @ 49298b16
......@@ -4,16 +4,18 @@ import { withTrailingSlash, withLeadingSlash, joinURL } from 'ufo'
import { useRuntimeConfig, computed } from '#imports'
import * as d3 from "d3";
import * as Plot from "@observablehq/plot";
import PlotFigure from "~/components/PlotFigure";
import { useDisplay } from "vuetify";
export interface Props {
height?: number
dataUrls?: string[]
dataUrl?: string
uniq?: boolean
}
const { mobile } = useDisplay()
// const selectedPdb = ref('')
const refinedDataUrls = computed(() => {
......@@ -32,10 +34,15 @@ const refinedDataUrls = computed(() => {
if (props?.dataUrls && props?.dataUrls?.length > 0) {
urls = [...props.dataUrls.map((dataUrl) => {
return refinedUrl(dataUrl)
// return dataUrl
})]
}
if (props?.dataUrl) {
urls = [...urls, refinedUrl(props.dataUrl)]
urls = [
...urls,
// props.dataUrl
refinedUrl(props.dataUrl)
]
}
return urls
......@@ -100,66 +107,63 @@ const pdbeMolstarComponent = ref(null)
const selectedPdb: Ref<string | null> = ref(null)
const selectedPaePath = computed(() => {
return selectedPdb.value ? `${selectedPdb.value.split(".").slice(0, -1).join('.')}.tsv` : null
return selectedPdb.value ? `${selectedPdb.value.split(".").slice(0, -1).join('.')}.png` : null
})
const paeData = ref([])
watch(selectedPaePath, async (newPaePath) => {
if (newPaePath !== null) {
try {
const data = await d3.tsv(newPaePath);
console.log(data.length)
console.log(data[0][0])
console.log(data?.[0]?.[0] !== undefined)
if (data.length > 500) {
paeError.value = `The PAE is too large to be displayed (${data.length} residus)`
paeData.value = []
}
else if (data?.[0]?.[0] === undefined) {
paeError.value = "The PAE cannot be downloaded"
paeData.value = []
}
else {
paeData.value = data
paeError.value = null
}
}
catch (error) {
console.log(error)
}
} else {
paeData.value = []
}
})
// const paeData = ref([])
// watch(selectedPaePath, async (newPaePath) => {
// if (newPaePath !== null) {
// try {
// const data = await d3.tsv(newPaePath);
// if (data.length > 500) {
// paeError.value = `The PAE is too large to be displayed (${data.length} residus)`
// paeData.value = []
// }
// else if (data?.[0]?.[0] === undefined) {
// paeError.value = "The PAE cannot be downloaded"
// paeData.value = []
// }
// else {
// paeData.value = data
// paeError.value = null
// }
// }
// catch (error) {
// console.log(error)
// }
// } else {
// paeData.value = []
// }
const sanitizedPaeData = computed(() => {
return paeData.value.reduce((acc, curr, index) => {
const scoredResidue = index
// let newAcc = [...acc]
for (const [alignedResidue, value] of Object.entries(curr)) {
// console.log(value)
acc.push({ alignedResidue: parseInt(alignedResidue), scoredResidue: parseInt(scoredResidue), value: parseFloat(value) })
// newAcc = [...newAcc, ...[{ alignedResidue: parseInt(alignedResidue), scoredResidue: parseInt(scoredResidue), value: parseFloat(value) }]]
}
// })
return acc
}, [])
})
// const sanitizedPaeData = computed(() => {
// return paeData.value.reduce((acc, curr, index) => {
// const scoredResidue = index
// // let newAcc = [...acc]
// for (const [alignedResidue, value] of Object.entries(curr)) {
// // console.log(value)
// acc.push({ alignedResidue: parseInt(alignedResidue), scoredResidue: parseInt(scoredResidue), value: parseFloat(value) })
// // newAcc = [...newAcc, ...[{ alignedResidue: parseInt(alignedResidue), scoredResidue: parseInt(scoredResidue), value: parseFloat(value) }]]
// }
// return acc
// }, [])
// })
const plotPaeOptions = computed(() => {
return {
width: 640,
height: 640,
color: { scheme: "Greens", legend: true, reverse: true, label: "Expected position error (Ångströms)" },
y: { reverse: true },
marks: [
Plot.dot(sanitizedPaeData.value, { x: "scoredResidue", y: "alignedResidue", stroke: "value" })
]
}
})
// const plotPaeOptions = computed(() => {
// return {
// width: 640,
// height: 640,
// color: { scheme: "Greens", legend: true, reverse: true, label: "Expected position error (Ångströms)" },
// y: { reverse: true },
// marks: [
// Plot.dot(sanitizedPaeData.value, { x: "scoredResidue", y: "alignedResidue", stroke: "value" })
// ]
// }
// })
watch(selectedPdb, (newSelectedPdb, prevSelectPdb) => {
viewPdb(newSelectedPdb)
......@@ -172,9 +176,11 @@ function viewPdb(pdbPath: string | null) {
const format = toValue(pdbPath)?.split(".").slice(-1)[0]?.toLowerCase() ?? "pdb"
moleculeFormat.value = format
if (pdbeMolstarComponent.value?.viewerInstance) {
console.log(pdbeMolstarComponent.value)
const viewerInstance = pdbeMolstarComponent.value.viewerInstance
const customData = { url: pdbPath, format: format, binary: false }
viewerInstance.visual.update({ customData })
}
}
}
......@@ -217,7 +223,7 @@ const moleculeFormat: Ref<string> = ref("pdb")
</v-toolbar>
<v-card-text>
<v-row>
<v-col cols="auto">
<v-col :cols="mobile ? 12 : 'auto'">
<v-sheet v-if="selectedPdb"
class="d-flex align-center justify-center flex-wrap text-center mx-auto px-4 my-3"
:height="computedHeight" :width="computedWidth" position="relative">
......@@ -226,12 +232,13 @@ const moleculeFormat: Ref<string> = ref("pdb")
:custom-data-format="moleculeFormat"></pdbe-molstar>
</v-sheet>
</v-col>
<v-col>
<PlotFigure v-if="sanitizedPaeData?.length > 0 && paeError === null" defer
<v-col :cols="mobile ? 12 : undefined">
<v-img :src="selectedPaePath"></v-img>
<!-- <PlotFigure v-if="sanitizedPaeData?.length > 0 && paeError === null" defer
:options="plotPaeOptions"></PlotFigure>
<v-alert v-else type="warning" variant="tonal">{{ paeError }}</v-alert>
<v-alert v-else type="warning" variant="tonal">{{ paeError }}</v-alert> -->
<v-card flat color="transparent">
<v-card-title>Model Confidence</v-card-title>
<v-card-text>
AlphaFold produces a per-residue model
......
content/0.index.md
View file @ 49298b16
......@@ -5,7 +5,7 @@ navigation:
icon: 'md:home'
relevantAbstracts:
- doi: 10.1128/jb.64.4.557-569.1952
- doi: 10.1128/jb.65.2.113-121.19
- doi: 10.1128/jb.65.2.113-121.1953
- doi: 10.1128/JB.05535-11
- doi: 10.1126/science.aar4120
- doi: 10.1038/s41579-023-00934-x
......@@ -14,6 +14,7 @@ relevantAbstracts:
- doi: 10.1016/j.cell.2021.12.029
- doi: 10.1038/nmicrobiol.2017.92
- doi: 10.1038/s41586-019-1894-8
---
## Introduction
......
content/2.general-concepts/1.abortive-infection.md
View file @ 49298b16
---
title: Abortive Infection
layout: article
contributors:
- Lucas Paoli
relevantAbstracts:
- doi: 10.1128/jb.68.1.36-42.1954
- doi: 10.1016/0006-3002(61)90455-3
- doi: 10.1016/0022-2836(68)90078-8
- doi: 10.1128/jvi.4.2.162-168.1969
- doi: 10.1128/jvi.13.4.870-880.1974
- doi: 10.1128/mr.45.1.52-71.1981
- doi: 10.3168/jds.S0022-0302(90)78904-7
- doi: 10.1016/S0960-9822(00)00124-X
- doi: 10.1111/j.1365-2958.1995.tb02255.x
- doi: 10.1016/j.mib.2005.06.006
- doi: 10.1146/annurev-virology-011620-040628
- doi: 10.1016/j.mib.2023.102312
- doi: 10.1038/s41579-023-00934-x
---
This section is empty. You can help by adding to it.
The term abortive infection was coined in the 1950s :ref{doi=10.1128/jb.68.1.36-42.1954} to describe the observations that a fraction of the bacterial population did not support phage replication. This phenomenon, also called phage exclusion, was identified in multiple systems across the following decades :ref{doi=10.1016/0006-3002(61)90455-3,10.1016/0022-2836(68)90078-8,10.1128/jvi.4.2.162-168.1969,10.1128/jvi.13.4.870-880.1974} and reviewed extensively :ref{doi=10.1128/mr.45.1.52-71.1981,10.3168/jds.S0022-0302(90)78904-7,10.1111/j.1365-2958.1995.tb02255.x}. In the following years, and through the resolution of molecular mechanisms of key defense systems such as Rex or Lit, abortive infection became synonymous with infection-induced controlled cell-death. Controlled cell death upon detection of the phage infection stops the propagation of the phage and protects the rest of the bacterial population :ref{doi=10.1016/S0960-9822(00)00124-X,10.1016/j.mib.2005.06.006}. Abortive infection can thus be thought of as a form of bacterial altruism.
With the recent developments in phage-defense systems and microbial immunity (see :ref{doi=10.1038/s41579-023-00934-x} for a review), many newly identifed anti-phage defense systems are thought to function through abortive infection. Abortive defense systems often detect the phage infection at the later stage through protein sensing or the monitoring of host integrity but can also be based on nucleic acid sensing. Upon sensing, a diverse set of effectors can be used to reduce metabolism or induce cell-death (e.g., NAD+ depletion, translation interruption or membrane depolarisation). The diversity of and mechanisms of abortive infection were recently reviewd here :ref{doi=10.1146/annurev-virology-011620-040628}, while the evolutionary success of this paradoxical altruistic form of immunity has recently been discussed here :ref{doi=10.1016/j.mib.2023.102312}.
Although abortive infection is currently often understood as leading to cell-death, it should be noted that its original definition appeared to be broader and that some mechanisms currently included as abortive infection may only lead to metabolic stalling or dormancy.
content/2.general-concepts/3.defense-systems_trigger.md
View file @ 49298b16
......@@ -2,6 +2,7 @@
title: Defense system triggers
contributors:
- Avigail Stokar-Avihail
- Alba Herrero del Valle
layout: article
---
......@@ -9,22 +10,11 @@ layout: article
Upon phage infection, the bacterial immune system senses a specific phage component or modification that the phage exerts on the cell to elicit the bacterial immune response. Understanding how bacteria sense phage infection is a fundamental question, which remains unanswered for the majority of recently discovered immune systems. There are dozens of cases in which the mechanism of immunity has been elucidated, but the phage trigger remains elusive. Understanding how antiphage systems are activated is key for a full understanding of bacterial immunity and for repurposing them as molecular tools as has been done for restriction enzymes and CRISPR-Cas.
## Diversity
Various determinants of the phage can elicit bacterial immunity either in a direct or indirect manner. The most common and well known prokaryotic anti-phage systems, restriction enzymes and CRISPR-Cas, recognize and cleave phage DNA or RNA. More recently, a CBASS system has been found to directly bind to a structured phage RNA that triggers immune activation1. In other cases, defense systems are activated by protein coding phage genes. In some cases, the phage protein is directly sensed by the defense systems, as has been beautifully demonstrated for the Avs systems that directly bind either the phage terminase or portal protein2. In other cases, the phage protein can be sensed indirectly by the defense system, for example by detecting its activity in the cell. Such an indirect mechanism has been found for example in the case of some retron defense systems that are triggered by phage tampering with the RecBCD protein complex3,4. For a comprehensive coverage of all recent phage detection mechanisms the recent review by Huiting and Bondy-Denomy5 is highly recommended.
Various determinants of the phage can elicit bacterial immunity either in a direct or indirect manner. The most common and well known prokaryotic anti-phage systems, restriction enzymes and CRISPR-Cas, recognize and cleave phage DNA or RNA. More recently, a CBASS system has been found to directly bind to a structured phage RNA that triggers immune activation :ref{doi=10.1101/2023.03.07.531596}. In other cases, defense systems are activated by protein coding phage genes. In some cases, the phage protein is directly sensed by the defense systems, as has been beautifully demonstrated for the Avs systems that directly bind either the phage terminase or portal protein :ref{doi=10.1126/science.abm4096}. In other cases, the phage protein can be sensed indirectly by the defense system, for example by detecting its activity in the cell. Such an indirect mechanism has been found for example in the case of some retron defense systems that are triggered by phage tampering with the RecBCD protein complex :ref{doi=10.1016/j.cell.2020.09.065,10.1016/j.cell.2023.02.029}. For a comprehensive coverage of all recent phage detection mechanisms the recent review by Huiting and Bondy-Denomy :ref{doi=10.1016/j.mib.2023.102325} is highly recommended.
## Method of discovery:
The main method used to pinpoint phage components that trigger a specific defense system of interest has been through a simple classic genetics approach, whereby mutant phages that overcome the defense system are examined. Such mutants often occur spontaneously and can thus be selected for by simply picking phage plaques that are able to form on a lawn of bacteria expressing the defense system4,5. The hypothesis is that the phage mutant escapes bacterial immunity due to a mutation in the component sensed by the system. Thus, sequencing these phage mutants and identification of the mutated locus is the first required step. To validate that the mutated phage component is indeed the actual trigger of the defense system, follow up experiments are required. For example, in some cases expression of this phage component without any other phage genes is sufficient to elicit the activity of bacterial immune system. This approach was used to identify Borvo activation by expression of the phage DNA polymerase4, Dazbog activation by expression of a phage DNA methylase4, retron activation by either phage SSB proteins4 or by proteins that inhibit the host RecBCD3, CapRel triggering by the phage Capsid protein6 and many more5. Additional biochemical pulldown assays can be used to assess binding of the defense system to the suspected phage trigger.
One major caveat in the above approach is that in some cases mutant phages that escape the immune system cannot be isolated. This can occur for example if the defense system senses a general fold of a highly conserved and essential phage protein. In this case a simple mutation in the protein will not suffice for the phage to escape detection. In such cases, an alternative approach can be used that does not rely on isolation of escape mutants. An overexpression library of all phage genes can be co-expressed with the defense system of interest, and then assayed for immune activation. This approach was successfully applied for identification phage components that trigger diverse Avs systems2.
The main method used to pinpoint phage components that trigger a specific defense system of interest has been through a simple classic genetics approach, whereby mutant phages that overcome the defense system are examined. Such mutants often occur spontaneously and can thus be selected for by simply picking phage plaques that are able to form on a lawn of bacteria expressing the defense system :ref{doi=10.1016/j.cell.2023.02.029,10.1016/j.mib.2023.102325}. The hypothesis is that the phage mutant escapes bacterial immunity due to a mutation in the component sensed by the system. Thus, sequencing these phage mutants and identification of the mutated locus is the first required step. To validate that the mutated phage component is indeed the actual trigger of the defense system, follow up experiments are required. For example, in some cases expression of this phage component without any other phage genes is sufficient to elicit the activity of bacterial immune system. This approach was used to identify Borvo activation by expression of the phage DNA polymerase, Dazbog activation by expression of a phage DNA methylase, retron activation by either phage SSB proteins :ref{doi=10.1016/j.cell.2023.02.029} or by proteins that inhibit the host RecBCD3, CapRel triggering by the phage Capsid protein :ref{doi=10.1038/s41586-022-05444-z} and many more :ref{doi=10.1016/j.mib.2023.102325}. Additional biochemical pulldown assays can be used to assess binding of the defense system to the suspected phage trigger.
One major caveat in the above approach is that in some cases mutant phages that escape the immune system cannot be isolated. This can occur for example if the defense system senses a general fold of a highly conserved and essential phage protein. In this case a simple mutation in the protein will not suffice for the phage to escape detection. In such cases, an alternative approach can be used that does not rely on isolation of escape mutants. An overexpression library of all phage genes can be co-expressed with the defense system of interest, and then assayed for immune activation. This approach was successfully applied for identification phage components that trigger diverse Avs systems :ref{doi=10.1126/science.abm4096}.
## General concepts:
Although much is still unknown regarding how bacterial immune systems sense phage infection, by combining the data observed so far, several general concepts in immune sensing are beginning to come to light. First, mechanistically diverse immune systems appear to have converged to sense common conserved phage components4. These include the phage core replication machinery, host takeover machinery and structural components. Second, several studies have found cases in which defense occurs in a multi-layered fashion, whereby a second system is activated when the first one fails3,7,8. Research in upcoming years is expected to reveal additional guiding principles in the ways bacteria detect phages.
## References:
1. Banh D V, Roberts C G, Amador A M, Brady S F, & Marraffini L A. (2023) Bacterial cGAS senses a viral RNA to initiate immunity. bioRxiv 2023.03.07.531596 doi:10.1101/2023.03.07.531596.
2. Gao L A, Wilkinson M E, Strecker J, Makarova K S, Macrae R K, Koonin E V, & Zhang F. (2022) Prokaryotic innate immunity through pattern recognition of conserved viral proteins. Science 377: eabm4096.
3. Millman A, Bernheim A, Stokar-Avihail A, Fedorenko T, Voichek M, Leavitt A, Oppenheimer-Shaanan Y, & Sorek R. (2020) Bacterial Retrons Function In Anti-Phage Defense. Cell 183: 1551–1561.
4. Stokar-Avihail A, Fedorenko T, Hör J, Garb J, Leavitt A, Millman A, Shulman G, Wojtania N, Melamed S, Amitai G, & Sorek R. (2023) Discovery of phage determinants that confer sensitivity to bacterial immune systems. Cell 186: 1863-1876.e16.
5. Huiting E & Bondy-Denomy J. (2023) Defining the expanding mechanisms of phage-mediated activation of bacterial immunity. Curr. Opin. Microbiol. 74: 102325.
6. Zhang T, Tamman H, Coppieters ’t Wallant K, Kurata T, LeRoux M, Srikant S, Brodiazhenko T, Cepauskas A, Talavera A, Martens C, Atkinson G C, Hauryliuk V, Garcia-Pino A, & Laub M T. (2022) Direct activation of a bacterial innate immune system by a viral capsid protein. Nature 612: 132–140.
7. Rousset F, Depardieu F, Miele S, Dowding J, Laval A-L, Lieberman E, Garry D, Rocha E P C, Bernheim A, & Bikard D. (2022) Phages and their satellites encode hotspots of antiviral systems. Cell Host Microbe 30: 740–753.
8. Penner M, Morad I, Snyder L, & Kaufmann G. (1995) Phage T4-coded Stp: Double-edged effector of coupled DNA and tRNA-restriction systems. J. Mol. Biol. 249: 857–68.
Although much is still unknown regarding how bacterial immune systems sense phage infection, by combining the data observed so far, several general concepts in immune sensing are beginning to come to light. First, mechanistically diverse immune systems appear to have converged to sense common conserved phage components4. These include the phage core replication machinery, host takeover machinery and structural components. Second, several studies have found cases in which defense occurs in a multi-layered fashion, whereby a second system is activated when the first one fails :ref{doi=10.1016/j.cell.2020.09.065,10.1016/j.chom.2022.02.018,10.1006/jmbi.1995.0343}. Research in upcoming years is expected to reveal additional guiding principles in the ways bacteria detect phages.
content/3.defense-systems/abi2.md
View file @ 49298b16
......@@ -16,22 +16,24 @@ relevantAbstracts:
# Abi2
The Abi2 system is composed of one protein: Abi_2.
Here is an example found in the RefSeq database:
## Example of genomic structure
The Abi2 is composed of 1 protein: Abi_2.
Here is an example found in the RefSeq database:
![abi2](/abi2/Abi2.svg)
![abi2](/abi2/Abi2.svg){max-width=750px}
Abi2 system in the genome of *Clostridium butyricum* (GCF_014131795.1) is composed of 1 protein: Abi_2 (WP_035763709.1).
The Abi2 system in *Veillonella parvula* (GCF_002005185.1, NZ_CP019721) is composed of 1 protein: Abi_2 (WP_077707938.1)
## Distribution of the system among prokaryotes
The Abi2 system is present in a total of 176 different species.
Among the 22,803 complete genomes of RefSeq, the Abi2 is detected in 1231 genomes (5.4 %).
Among the 22k complete genomes of RefSeq, this system is present in 1210 genomes (5.3 %).
The system was detected in 202 different species.
![abi2](/abi2/Distribution_Abi2.svg)
![abi2](/abi2/Distribution_Abi2.svg){max-width=750px}
*Proportion of genome encoding the Abi2 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
Proportion of genome encoding the Abi2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
content/3.defense-systems/abia.md
View file @ 49298b16
......@@ -19,29 +19,30 @@ relevantAbstracts:
# AbiA
The AbiA system have been describe in a total of 2 subsystems.
## Example of genomic structure
Here is some example found in the RefSeq database:
A total of 2 subsystems have been described for the AbiA system.
![abia](/abia/AbiA_large.svg){max-width=750px}
Here is some examples found in the RefSeq database:
AbiA_large subsystem in the genome of *Lactobacillus amylovorus* (GCF_002706375.1) is composed of 1 protein: AbiA_large (WP_056940268.1).
![abia_large](/abia/AbiA_large.svg){max-width=750px}
![abia](/abia/AbiA_small.svg){max-width=750px}
The AbiA_large system in *Staphylococcus nepalensis* (GCF_002442935.1, NZ_CP017466) is composed of 1 protein: AbiA_large (WP_096808013.1)
AbiA_small subsystem in the genome of *Mesobacillus foraminis* (GCF_003667765.1) is composed of 2 proteins: AbiA_small (WP_121614402.1)and, AbiA_SLATT (WP_121614403.1).
![abia_small](/abia/AbiA_small.svg){max-width=750px}
## Distribution of the system among prokaryotes
The AbiA_small system in *Alicyclobacillus sp. SO9* (GCF_016406125.1, NZ_CP066339) is composed of 2 proteins AbiA_small (WP_198850075.1) AbiA_SLATT (WP_198850076.1)
The AbiA system is present in a total of 35 different species.
## Distribution of the system among prokaryotes
Among the 22,803 complete genomes of RefSeq, the AbiA is detected in 50 genomes (0.22 %).
Among the 22k complete genomes of RefSeq, this system is present in 50 genomes (0.2 %).
The system was detected in 35 different species.
![abia](/abia/Distribution_AbiA.svg){max-width=750px}
*Proportion of genome encoding the AbiA 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 AbiA system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
......
content/3.defense-systems/abib.md
View file @ 49298b16
......@@ -27,23 +27,25 @@ AbiB is a single-protein abortive infection defense system from *Lactococcus* th
AbiB system is still poorly understood. It is a single-protein system that was described as an abortive infection system. Upon phage infection, AbiB activation leads to a strong degradation of mRNAs :ref{doi=10.1046/j.1365-2958.1996.371896.x} that is expected to be the mechanism of phage inhibition. AbiB expression is constitutive and does increase during phage infection. It is only activated during phage infection, most likely through the recognition of an early phage protein. Which protein, and whether this activation is direct or indirect remains to be elucidated.
## Example of genomic structure
The AbiB system is composed of one protein: AbiB.
Here is an example found in the RefSeq database:
The AbiB is composed of 1 protein: AbiB.
Here is an example found in the RefSeq database:
![abib](/abib/AbiB.svg){max-width=750px}
AbiB system in the genome of *Lactococcus lactis* (GCF_020221755.1) is composed of 1 protein: AbiB (WP_047687114.1).
The AbiB system in *Lactococcus cremoris* (GCF_000312685.1, NC_019430) is composed of 1 protein: AbiB (WP_144019851.1)
## Distribution of the system among prokaryotes
The AbiB system is present in a total of 5 different species.
Among the 22,803 complete genomes of RefSeq, the AbiB is detected in 11 genomes (0.05 %).
Among the 22k complete genomes of RefSeq, this system is present in 13 genomes (0.1 %).
The system was detected in 5 different species.
![abib](/abib/Distribution_AbiB.svg){max-width=750px}
*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
......
content/3.defense-systems/abic.md
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......@@ -13,23 +13,27 @@ tableColumns:
---
# AbiC
The AbiC system is composed of one protein: AbiC.
Here is an example found in the RefSeq database:
## Example of genomic structure
The AbiC is composed of 1 protein: AbiC.
Here is an example found in the RefSeq database:
![abic](/abic/AbiC.svg){max-width=750px}
AbiC system in the genome of *Enterococcus faecium* (GCF_012933295.2) is composed of 1 protein: AbiC (WP_098388098.1).
The AbiC system in *Cupriavidus pauculus* (GCF_008693385.1, NZ_CP044066) is composed of 1 protein: AbiC (WP_150373977.1)
## Distribution of the system among prokaryotes
The AbiC system is present in a total of 110 different species.
Among the 22,803 complete genomes of RefSeq, the AbiC is detected in 91 genomes (0.4 %).
The system was detected in 57 different species.
Among the 22k complete genomes of RefSeq, this system is present in 196 genomes (0.9 %).
![abic](/abic/Distribution_AbiC.svg){max-width=750px}
![abic](/abic/Distribution_AbiC.svg){max-width="750"}
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
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content/3.defense-systems/abid.md
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---
# AbiD
The AbiD system is composed of one protein: AbiD.
Here is an example found in the RefSeq database:
## Example of genomic structure
![abid](/abid/AbiD.svg){max-width="750"}
The AbiD is composed of 1 protein: AbiD.
AbiD system in the genome of *Lachnospira eligens* (GCF_020735745.1) is composed of 1 protein: AbiD (WP_041688924.1).
Here is an example found in the RefSeq database:
![abid](/abid/AbiD.svg){max-width=750px}
The AbiD system in *Idiomarina sp. OT37-5b* (GCF_002968395.1, NZ_CP027188) is composed of 1 protein: AbiD (WP_105307479.1)
## Distribution of the system among prokaryotes
The AbiD system is present in a total of 874 different species.
Among the 22,803 complete genomes of RefSeq, the AbiD is detected in 2713 genomes (11.9 %).
The system was detected in 964 different species.
Among the 22k complete genomes of RefSeq, this system is present in 2748 genomes (12.1 %).
![abid](/abid/Distribution_AbiD.svg){max-width=750px}
![abid](/abid/Distribution_AbiD.svg){max-width="750"}
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
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content/3.defense-systems/abie.md
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## Example of genomic structure
The AbiE system is composed of 2 proteins: AbiEi_1 and, AbiEii.
The AbiE is composed of 2 proteins: AbiEii and AbiEi.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![abie](/abie/AbiE.svg){max-width=750px}
AbiE system in the genome of *Desulfuromonas versatilis* (GCF_019704135.1) is composed of 2 proteins: AbiEi_1 (WP_221251730.1)and, AbiEii (WP_221251731.1).
The AbiE system in *Halomonas piezotolerans* (GCF_012427705.1, NZ_CP048602) is composed of 2 proteins AbiEi_3 (WP_231125510.1) AbiEii (WP_231125511.1)
## Distribution of the system among prokaryotes
The AbiE system is present in a total of 962 different species.
Among the 22,803 complete genomes of RefSeq, the AbiE is detected in 3708 genomes (16.26 %).
Among the 22k complete genomes of RefSeq, this system is present in 3742 genomes (16.4 %).
The system was detected in 1107 different species.
![abie](/abie/Distribution_AbiE.svg){max-width=750px}
*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
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# AbiG
The AbiG system is composed of 2 proteins: AbiGi and, AbiGii.
Here is an example found in the RefSeq database:
## Example of genomic structure
The AbiG is composed of 2 proteins: AbiGi and AbiGii.
Here is an example found in the RefSeq database:
![abig](/abig/AbiG.svg){max-width=750px}
AbiG system in the genome of *Streptococcus mutans* (GCF_009738105.1) is composed of 2 proteins: AbiGi (WP_002266883.1)and, AbiGii (WP_002266884.1).
The AbiG system in *Staphylococcus simulans* (GCF_900474685.1, NZ_LS483313) is composed of 2 proteins AbiGi (WP_103364194.1) AbiGii (WP_070462993.1)
## Distribution of the system among prokaryotes
The AbiG system is present in a total of 23 different species.
Among the 22,803 complete genomes of RefSeq, the AbiG is detected in 32 genomes (0.14 %).
Among the 22k complete genomes of RefSeq, this system is present in 33 genomes (0.1 %).
The system was detected in 22 different species.
![abig](/abig/Distribution_AbiG.svg){max-width=750px}
*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
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# AbiH
## Example of genomic structure
The AbiH system is composed of one protein: AbiH.
The AbiH is composed of 1 protein: AbiH.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![abih](/abih/AbiH.svg){max-width=750px}
AbiH system in the genome of *Agrobacterium tumefaciens* (GCF_005221405.1) is composed of 1 protein: AbiH (WP_045021548.1).
The AbiH system in *Bacteroides faecium* (GCF_012113595.1, NZ_CP050831) is composed of 1 protein: AbiH (WP_167962074.1)
## Distribution of the system among prokaryotes
The AbiH system is present in a total of 408 different species.
Among the 22,803 complete genomes of RefSeq, the AbiH is detected in 1225 genomes (5.37 %).
Among the 22k complete genomes of RefSeq, this system is present in 1277 genomes (5.6 %).
The system was detected in 439 different species.
![abih](/abih/Distribution_AbiH.svg){max-width=750px}
*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
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# AbiI
## Example of genomic structure
The AbiI system is composed of one protein: AbiI.
The AbiI is composed of 1 protein: AbiI.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![abii](/abii/AbiI.svg){max-width=750px}
AbiI system in the genome of *Enterococcus faecalis* (GCF_002814115.1) is composed of 1 protein: AbiI (WP_002367720.1).
The AbiI system in *Macrococcus brunensis* (GCF_022343725.1, NZ_CP092179) is composed of 1 protein: AbiI (WP_239034930.1)
## Distribution of the system among prokaryotes
The AbiI system is present in a total of 8 different species.
Among the 22,803 complete genomes of RefSeq, the AbiI is detected in 6 genomes (0.03 %).
Among the 22k complete genomes of RefSeq, this system is present in 8 genomes (0.0 %).
The system was detected in 6 different species.
![abii](/abii/Distribution_AbiI.svg){max-width=750px}
*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
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# AbiJ
## Example of genomic structure
The AbiJ system is composed of one protein: AbiJ.
The AbiJ is composed of 1 protein: AbiJ.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![abij](/abij/AbiJ.svg){max-width=750px}
AbiJ system in the genome of *Loigolactobacillus backii* (GCF_001663735.1) is composed of 1 protein: AbiJ (WP_068377534.1).
The AbiJ system in *Marinobacter sp. LQ44* (GCF_001447155.2, NZ_CP014754) is composed of 1 protein: AbiJ (WP_058091398.1)
## Distribution of the system among prokaryotes
The AbiJ system is present in a total of 321 different species.
Among the 22,803 complete genomes of RefSeq, the AbiJ is detected in 686 genomes (3.01 %).
Among the 22k complete genomes of RefSeq, this system is present in 807 genomes (3.5 %).
The system was detected in 261 different species.
![abij](/abij/Distribution_AbiJ.svg){max-width=750px}
*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
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# AbiK
## Example of genomic structure
The AbiK system is composed of one protein: AbiK.
The AbiK is composed of 1 protein: AbiK.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![abik](/abik/AbiK.svg){max-width=750px}
AbiK system in the genome of *Lactococcus lactis* (GCF_002078995.2) is composed of 1 protein: AbiK (WP_081199340.1).
The AbiK system in *Lactobacillus ultunensis* (GCF_016647595.1, NZ_CP059829) is composed of 1 protein: AbiK (WP_007126124.1)
## Distribution of the system among prokaryotes
The AbiK system is present in a total of 32 different species.
Among the 22,803 complete genomes of RefSeq, the AbiK is detected in 107 genomes (0.47 %).
Among the 22k complete genomes of RefSeq, this system is present in 107 genomes (0.5 %).
The system was detected in 32 different species.
![abik](/abik/Distribution_AbiK.svg){max-width=750px}
*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
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## Example of genomic structure
The AbiL system is composed of 2 proteins: AbiLii2 and, AbiLi2.
The AbiL is composed of 2 proteins: AbiLi and AbiLii.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![abil](/abil/AbiL.svg){max-width=750px}
AbiL system in the genome of *Fusobacterium nucleatum* (GCF_003019785.1) is composed of 2 proteins: AbiLii2 (WP_005903821.1)and, AbiLi2 (WP_005903823.1).
The AbiL system in *Sulfurimonas sp. SWIR-19* (GCF_020410885.1, NZ_CP084578) is composed of 2 proteins AbiLi2 (WP_226066409.1) AbiLii2 (WP_226066410.1)
## Distribution of the system among prokaryotes
The AbiL system is present in a total of 456 different species.
Among the 22,803 complete genomes of RefSeq, the AbiL is detected in 188 genomes (0.82 %).
Among the 22k complete genomes of RefSeq, this system is present in 783 genomes (3.4 %).
The system was detected in 126 different species.
![abil](/abil/Distribution_AbiL.svg){max-width=750px}
*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
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# AbiN
## Example of genomic structure
The AbiN system is composed of one protein: AbiN.
The AbiN is composed of 1 protein: AbiN.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![abin](/abin/AbiN.svg){max-width=750px}
AbiN system in the genome of *Enterococcus faecalis* (GCF_016743895.1) is composed of 1 protein: AbiN (WP_002384355.1).
The AbiN system in *Listeria innocua* (GCF_023078395.1, NZ_CP095723) is composed of 1 protein: AbiN (WP_238929053.1)
## Distribution of the system among prokaryotes
The AbiN system is present in a total of 51 different species.
Among the 22,803 complete genomes of RefSeq, the AbiN is detected in 165 genomes (0.72 %).
Among the 22k complete genomes of RefSeq, this system is present in 167 genomes (0.7 %).
The system was detected in 52 different species.
![abin](/abin/Distribution_AbiN.svg){max-width=750px}
*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
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# AbiO
## Example of genomic structure
The AbiO system is composed of one protein: AbiO.
The AbiO is composed of 1 protein: AbiO.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![abio](/abio/AbiO.svg){max-width=750px}
AbiO system in the genome of *Pasteurella multocida* (GCF_016313205.1) is composed of 1 protein: AbiO (WP_005752771.1).
The AbiO system in *Pantoea agglomerans* (GCF_004117135.1, NZ_CP034477) is composed of 1 protein: AbiO (WP_129063585.1)
## Distribution of the system among prokaryotes
The AbiO system is present in a total of 67 different species.
Among the 22,803 complete genomes of RefSeq, the AbiO is detected in 100 genomes (0.44 %).
Among the 22k complete genomes of RefSeq, this system is present in 109 genomes (0.5 %).
The system was detected in 61 different species.
![abio](/abio/Distribution_AbiO.svg){max-width=750px}
*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
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# AbiP2
## Example of genomic structure
The AbiP2 system is composed of one protein: AbiP2.
The AbiP2 is composed of 1 protein: AbiP2.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![abip2](/abip2/AbiP2.svg){max-width=750px}
AbiP2 system in the genome of *Casimicrobium huifangae* (GCF_009746125.1) is composed of 1 protein: AbiP2 (WP_156862066.1).
The AbiP2 system in *Halomonas alkaliphila* (GCF_003612795.1, NZ_CP024811) is composed of 1 protein: AbiP2 (WP_120386816.1)
## Distribution of the system among prokaryotes
The AbiP2 system is present in a total of 98 different species.
Among the 22,803 complete genomes of RefSeq, the AbiP2 is detected in 299 genomes (1.31 %).
Among the 22k complete genomes of RefSeq, this system is present in 299 genomes (1.3 %).
The system was detected in 96 different species.
![abip2](/abip2/Distribution_AbiP2.svg){max-width=750px}
*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
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# AbiQ
## Example of genomic structure
The AbiQ system is composed of one protein: AbiQ.
The AbiQ is composed of 1 protein: AbiQ.
Here is an example found in the RefSeq database:
Here is an example found in the RefSeq database:
![abiq](/abiq/AbiQ.svg){max-width=750px}
AbiQ system in the genome of *Enterococcus sp.* (GCF_003812305.1) is composed of 1 protein: AbiQ (WP_123866849.1).
The AbiQ system in *Planococcus faecalis* (GCF_002009235.1, NZ_CP019401) is composed of 1 protein: AbiQ (WP_078080483.1)
## Distribution of the system among prokaryotes
The AbiQ system is present in a total of 110 different species.
Among the 22,803 complete genomes of RefSeq, the AbiQ is detected in 258 genomes (1.13 %).
Among the 22k complete genomes of RefSeq, this system is present in 262 genomes (1.1 %).
The system was detected in 111 different species.
![abiq](/abiq/Distribution_AbiQ.svg){max-width=750px}
*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
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