diff --git a/content/2.defense-systems/abi2.md b/content/2.defense-systems/abi2.md
index d3c027315111e4c784e246358006c63a009d0ef0..6f8549ec2378baf5dd358518c8fe643e1b09cf1e 100644
--- a/content/2.defense-systems/abi2.md
+++ b/content/2.defense-systems/abi2.md
@@ -5,6 +5,10 @@ tableColumns:
doi: 10.1016/j.mib.2005.06.006
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.
+ Sensor: ''
+ Activator: ''
+ Effector: ''
+ PFAM: PF07751
---
# Abi2
@@ -28,3 +32,4 @@ Among the 22k complete genomes of RefSeq, this system is present in 1210 genomes
## Relevant abstracts
+
diff --git a/content/2.defense-systems/abia.md b/content/2.defense-systems/abia.md
index a7055ea9aa38800a9799c85d06b8c87c5fcd96f5..dfc59ca9e0a56774c04b0d861df26f408a994ff5 100644
--- a/content/2.defense-systems/abia.md
+++ b/content/2.defense-systems/abia.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00078, PF18160, PF18732
---
# AbiA
@@ -50,3 +51,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abic.md b/content/2.defense-systems/abic.md
index cc1dd91ba157f8af529b4664d17099a62f998b45..aa9f9f3989d296e8510b974ef64da50ccc397831 100644
--- a/content/2.defense-systems/abic.md
+++ b/content/2.defense-systems/abic.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF16872
---
# AbiC
@@ -51,3 +52,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abid.md b/content/2.defense-systems/abid.md
index 0ae3b82f26788b7f5a97a73874a17617d8b3fc6f..41f5e4b64c25a1c057f2d36ef4aa23ed1b803695 100644
--- a/content/2.defense-systems/abid.md
+++ b/content/2.defense-systems/abid.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF07751
---
# AbiD
@@ -45,3 +46,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abie.md b/content/2.defense-systems/abie.md
index 23d85dda387ce193e3f5c53a1c5130013b9c9006..b6b5fac03abfb8be32c796de20db579a012d9ea3 100644
--- a/content/2.defense-systems/abie.md
+++ b/content/2.defense-systems/abie.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF08843, PF09407, PF09952, PF11459, PF13338, PF17194
---
# AbiE
@@ -58,3 +59,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abig.md b/content/2.defense-systems/abig.md
index 7a013fbdd847b28ff0544ade71147b31b6e1bd17..56d3ffb4370530c962717394ada45d7238f4ccc8 100644
--- a/content/2.defense-systems/abig.md
+++ b/content/2.defense-systems/abig.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF10899, PF16873
---
# AbiG
@@ -45,3 +46,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abih.md b/content/2.defense-systems/abih.md
index 333517d5042eb0f1ed8dce5fa6aa8b1082d10360..c03615dfae2e97a8500c5ebf87bef623d337968d 100644
--- a/content/2.defense-systems/abih.md
+++ b/content/2.defense-systems/abih.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF14253
---
# AbiH
@@ -48,3 +49,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abij.md b/content/2.defense-systems/abij.md
index 83dfbe0e8a65e525d974ca05d55cd5790dbd3481..b2e9663d83e5debd9233fe7cf08fefac56011434 100644
--- a/content/2.defense-systems/abij.md
+++ b/content/2.defense-systems/abij.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF14355
---
# AbiJ
@@ -47,3 +48,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abik.md b/content/2.defense-systems/abik.md
index 6923486b07b13395f5f6c452bd88fde67a4d05f3..e8646b5d79a21964895df036d223599d6601b128 100644
--- a/content/2.defense-systems/abik.md
+++ b/content/2.defense-systems/abik.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00078
---
# AbiK
@@ -48,3 +49,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abil.md b/content/2.defense-systems/abil.md
index 3dee3534c6b119a70b0af4783f457f9590ebd3d8..dedac3928dbd4e72daa1ba2e78b2a00c22323946 100644
--- a/content/2.defense-systems/abil.md
+++ b/content/2.defense-systems/abil.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF13175, PF13304, PF13707
---
# AbiL
@@ -47,3 +48,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abio.md b/content/2.defense-systems/abio.md
index d89e1c5c2784760aaec1f17f97bbc44cd0d1b202..c445c3c4e485909ae142bd4200e8f22ec231d7ae 100644
--- a/content/2.defense-systems/abio.md
+++ b/content/2.defense-systems/abio.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF01443, PF09848
---
# AbiO
@@ -47,3 +48,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abip2.md b/content/2.defense-systems/abip2.md
index 1156872dbf26d58e2e9f42d39c0a04aaf5da238b..d3882bf2ae5f0aca68a944add1795e46233a2440 100644
--- a/content/2.defense-systems/abip2.md
+++ b/content/2.defense-systems/abip2.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00078
---
# AbiP2
@@ -50,3 +51,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abiq.md b/content/2.defense-systems/abiq.md
index f9438c7c79b84d43fd1a31009c8b76e8c0a5e876..c1a359849799420dbff796ce8ee5c457bbfa0b70 100644
--- a/content/2.defense-systems/abiq.md
+++ b/content/2.defense-systems/abiq.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF13958
---
# AbiQ
@@ -48,3 +49,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abir.md b/content/2.defense-systems/abir.md
index 996b6ac528f089fc7aa74eaa31fd47d85858cf59..f61928982035e5504a08f08fb5bb2532a5e19826 100644
--- a/content/2.defense-systems/abir.md
+++ b/content/2.defense-systems/abir.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00176, PF00271, PF04545, PF04851, PF13091
---
# AbiR
@@ -47,3 +48,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abit.md b/content/2.defense-systems/abit.md
index b1865fe56fb285e6f9fa103db60070a4c81e7b85..745ffd703703817924ec544c16af1eeb086b20eb 100644
--- a/content/2.defense-systems/abit.md
+++ b/content/2.defense-systems/abit.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF18864
---
# AbiT
@@ -47,3 +48,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abiu.md b/content/2.defense-systems/abiu.md
index 96aba14787a8a1e601be81671779506e62c7bde9..aab3cac16d94b81e7cca26db96e83940d463a1f9 100644
--- a/content/2.defense-systems/abiu.md
+++ b/content/2.defense-systems/abiu.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF10592
---
# AbiU
@@ -47,3 +48,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/abiv.md b/content/2.defense-systems/abiv.md
index eefbabd38f3d4422d3b459e1590563bdb79df06a..9264f4ba1520f766ebccde291c3fc529bf9a9ee8 100644
--- a/content/2.defense-systems/abiv.md
+++ b/content/2.defense-systems/abiv.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF18728
---
# AbiV
@@ -47,3 +48,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/aditi.md b/content/2.defense-systems/aditi.md
index f458596ba7964950ee64c56a18a17686067d59da..7cf403946c1550dd53e5c9b0edc09e0f0aa37259 100644
--- a/content/2.defense-systems/aditi.md
+++ b/content/2.defense-systems/aditi.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF18928
---
# Aditi
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/avs.md b/content/2.defense-systems/avs.md
index 5b66512b9d8ded9d8c8bd572c68f201faf8e1c9e..badac00d1f937d420265e56439c1735dd5af2364 100644
--- a/content/2.defense-systems/avs.md
+++ b/content/2.defense-systems/avs.md
@@ -9,6 +9,7 @@ tableColumns:
Activator: Direct binding
Effector: Diverse effectors (Nucleic acid degrading, putative Nucleotide modifying, putative Membrane disrupting)
+ PFAM: PF00753, PF13289, PF13365
---
# Avs
@@ -108,3 +109,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/azaca.md b/content/2.defense-systems/azaca.md
index c106da473403bedbe39d5afeb62609e3ddb7dbb7..68d725948eafebb2029bdbe35b29d563e520cb04 100644
--- a/content/2.defense-systems/azaca.md
+++ b/content/2.defense-systems/azaca.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00271
---
# Azaca
@@ -48,3 +49,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/borvo.md b/content/2.defense-systems/borvo.md
index 4f2b3b35fc3fe75471632d497a8ebaf09bd9a1b9..204dda167d23077dc76df2b5f6fc35aab126b8c2 100644
--- a/content/2.defense-systems/borvo.md
+++ b/content/2.defense-systems/borvo.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF12770
---
# Borvo
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/brex.md b/content/2.defense-systems/brex.md
index e9cb8dd08afcf7da22e9d7d8aaec988cc90f5059..00a9a263d5c0c4b6af90c80cee3777d3a28f0356 100644
--- a/content/2.defense-systems/brex.md
+++ b/content/2.defense-systems/brex.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00069, PF00176, PF00270, PF00271, PF01507, PF01555, PF02384, PF04851, PF07669, PF07714, PF08378, PF08665, PF08747, PF08849, PF10923, PF13337, PF16565
---
# BREX
@@ -86,3 +87,4 @@ items:
**2. Nunes-Alves C. Bacterial physiology: putting the 'BREX' on phage replication. Nat Rev Microbiol. 2015 Mar;13(3):129. doi: 10.1038/nrmicro3437. Epub 2015 Feb 2. PMID: 25639679.**
**3. Sumby P, Smith MC. Phase variation in the phage growth limitation system of Streptomyces coelicolor A3(2). J Bacteriol. 2003;185(15):4558-4563. doi:10.1128/JB.185.15.4558-4563.2003**
+
diff --git a/content/2.defense-systems/caprel.md b/content/2.defense-systems/caprel.md
index 1ad554427596fd8dfaa6c18dbb6646d25ef76208..0af2ca37b32220765b3a5da7b0427e21a055523b 100644
--- a/content/2.defense-systems/caprel.md
+++ b/content/2.defense-systems/caprel.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Sensing of phage protein
Activator: Direct
Effector: Nucleic acid degrading (pyrophosphorylates tRNAs)
+ PFAM: PF04607
---
# CapRel
@@ -66,3 +67,4 @@ items:
## References
Zhang T, Tamman H, Coppieters 't Wallant K, Kurata T, LeRoux M, Srikant S, Brodiazhenko T, Cepauskas A, Talavera A, Martens C, Atkinson GC, Hauryliuk V, Garcia-Pino A, Laub MT. Direct activation of a bacterial innate immune system by a viral capsid protein. Nature. 2022 Dec;612(7938):132-140. doi: 10.1038/s41586-022-05444-z. Epub 2022 Nov 16. PMID: 36385533.
+
diff --git a/content/2.defense-systems/card_nlr.md b/content/2.defense-systems/card_nlr.md
index 8cc15bd768d3272b59b50fd50cb7e5feb3dc122b..10d7c9591a06cd3b7be26f48907ae14b62bb9807 100644
--- a/content/2.defense-systems/card_nlr.md
+++ b/content/2.defense-systems/card_nlr.md
@@ -5,6 +5,7 @@ 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.
+ PFAM: PF00082, PF00089, PF00614, PF01223, PF13091, PF13191, PF13365
---
# CARD_NLR
@@ -19,3 +20,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/cbass.md b/content/2.defense-systems/cbass.md
index 8a16ae01939a5a288b07b23689154c921dacc82b..0283bb78b55a2a9d92166e95d60f7965b0961696 100644
--- a/content/2.defense-systems/cbass.md
+++ b/content/2.defense-systems/cbass.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Signaling molecules
Effector: Divers (Nucleic acid degrading, Nucleotide modifying, Membrane disrupting)
+ PFAM: PF00004, PF00027, PF00899, PF01048, PF01734, PF06508, PF10137, PF14461, PF14464, PF18134, PF18138, PF18144, PF18145, PF18153, PF18159, PF18167, PF18173, PF18178, PF18179, PF18186, PF18303, PF18967
---
# CBASS
@@ -68,3 +69,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/dartg.md b/content/2.defense-systems/dartg.md
index ebe19f6df71ef743989b66528321bdaaa21a2305..433601261823f0fc8af508c5fdfd0f987a7f2b5e 100644
--- a/content/2.defense-systems/dartg.md
+++ b/content/2.defense-systems/dartg.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Nucleic acid degrading (ADP-ribosylation)
+ PFAM: PF01661, PF14487
---
# DarTG
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/dctpdeaminase.md b/content/2.defense-systems/dctpdeaminase.md
index 563e14d05c447dbd287abd0c33b39af16cfaf96b..76e0ef11d34b4047f45f4f1adb9b37d46382140c 100644
--- a/content/2.defense-systems/dctpdeaminase.md
+++ b/content/2.defense-systems/dctpdeaminase.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Monitoring of the host cell machinery integrity
Activator: Direct
Effector: Nucleotide modifying
+ PFAM: PF00383, PF14437
---
# dCTPdeaminase
@@ -63,3 +64,4 @@ items:
- doi: 10.1038/s41564-022-01162-4
---
::
+
diff --git a/content/2.defense-systems/detocs.md b/content/2.defense-systems/detocs.md
index 4fa1a73724b3cda0543109fb71fe807c0420f6c8..f85fdc513baee5ca8cc41674e05c65fcd083868e 100644
--- a/content/2.defense-systems/detocs.md
+++ b/content/2.defense-systems/detocs.md
@@ -5,6 +5,7 @@ tableColumns:
doi: 10.1016/j.cell.2023.07.020
abstract: |
During viral infection, cells can deploy immune strategies that deprive viruses of molecules essential for their replication. Here, we report a family of immune effectors in bacteria that, upon phage infection, degrade cellular adenosine triphosphate (ATP) and deoxyadenosine triphosphate (dATP) by cleaving the N-glycosidic bond between the adenine and sugar moieties. These ATP nucleosidase effectors are widely distributed within multiple bacterial defense systems, including cyclic oligonucleotide-based antiviral signaling systems (CBASS), prokaryotic argonautes, and nucleotide-binding leucine-rich repeat (NLR)-like proteins, and we show that ATP and dATP degradation during infection halts phage propagation. By analyzing homologs of the immune ATP nucleosidase domain, we discover and characterize Detocs, a family of bacterial defense systems with a two-component phosphotransfer-signaling architecture. The immune ATP nucleosidase domain is also encoded within diverse eukaryotic proteins with immune-like architectures, and we show biochemically that eukaryotic homologs preserve the ATP nucleosidase activity. Our findings suggest that ATP and dATP degradation is a cell-autonomous innate immune strategy conserved across the tree of life.
+ PFAM: PF01048, PF18742
---
# Detocs
@@ -19,3 +20,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/dgtpase.md b/content/2.defense-systems/dgtpase.md
index 8226a1a385d3f3d24ef4677a721c061f8d9cd91e..0002507cef49ae0063b9029b8dc1582bf6e69bc2 100644
--- a/content/2.defense-systems/dgtpase.md
+++ b/content/2.defense-systems/dgtpase.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Monitoring of the host cell machinery integrity
Activator: Direc
Effector: Nucleotide modifying
+ PFAM: PF01966, PF13286
---
# dGTPase
@@ -52,3 +53,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/disarm.md b/content/2.defense-systems/disarm.md
index 0ad07b78686b94f68e924f004d04cb6edaeba713..fd21a80e4a8460e3736ba9f6395ddbda683939c2 100644
--- a/content/2.defense-systems/disarm.md
+++ b/content/2.defense-systems/disarm.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00145, PF00176, PF00271, PF04851, PF09369, PF13091
---
# DISARM
@@ -71,3 +72,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/dnd.md b/content/2.defense-systems/dnd.md
index 79d1ed31087122466a7cea1ad2c3762949c7ac25..bb5b8f4071b74a37b625748135ba725bfa91e6b5 100644
--- a/content/2.defense-systems/dnd.md
+++ b/content/2.defense-systems/dnd.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Detecting invading nucleic acid
Activator: Unknown
Effector: Nucleic acid degrading
+ PFAM: PF00266, PF01507, PF01935, PF08870, PF13476, PF14072
---
# Dnd
@@ -51,3 +52,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/dodola.md b/content/2.defense-systems/dodola.md
index 367f760dbceba13869fcb0574ffead60ba018a2e..546c3eb7b153996ba268f80440c9ae4b1365dae6 100644
--- a/content/2.defense-systems/dodola.md
+++ b/content/2.defense-systems/dodola.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00004, PF07724, PF07728
---
# Dodola
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/dpd.md b/content/2.defense-systems/dpd.md
index ff62362fd14a5e73f89b9d8dc1d96970c44b3d9f..eb479e92349b842da5e8a76006fe53e10d1e1638 100644
--- a/content/2.defense-systems/dpd.md
+++ b/content/2.defense-systems/dpd.md
@@ -5,6 +5,7 @@ tableColumns:
doi: 10.1073/pnas.1518570113
abstract: |
The discovery of ?20-kb gene clusters containing a family of paralogs of tRNA guanosine transglycosylase genes, called tgtA5, alongside 7-cyano-7-deazaguanine (preQ0) synthesis and DNA metabolism genes, led to the hypothesis that 7-deazaguanine derivatives are inserted in DNA. This was established by detecting 2’-deoxy-preQ0 and 2’-deoxy-7-amido-7-deazaguanosine in enzymatic hydrolysates of DNA extracted from the pathogenic, Gram-negative bacteria Salmonella enterica serovar Montevideo. These modifications were absent in the closely related S. enterica serovar Typhimurium LT2 and from a mutant of S. Montevideo, each lacking the gene cluster. This led us to rename the genes of the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA. Similar gene clusters were analyzed in ?150 phylogenetically diverse bacteria, and the modifications were detected in DNA from other organisms containing these clusters, including Kineococcus radiotolerans, Comamonas testosteroni, and Sphingopyxis alaskensis. Comparative genomic analysis shows that, in Enterobacteriaceae, the cluster is a genomic island integrated at the leuX locus, and the phylogenetic analysis of the TgtA5 family is consistent with widespread horizontal gene transfer. Comparison of transformation efficiencies of modified or unmodified plasmids into isogenic S. Montevideo strains containing or lacking the cluster strongly suggests a restriction-modification role for the cluster in Enterobacteriaceae. Another preQ0 derivative, 2’-deoxy-7-formamidino-7-deazaguanosine, was found in the Escherichia coli bacteriophage 9g, as predicted from the presence of homologs of genes involved in the synthesis of the archaeosine tRNA modification. These results illustrate a deep and unexpected evolutionary connection between DNA and tRNA metabolism.
+ PFAM: PF00176, PF00270, PF00271, PF01227, PF01242, PF04055, PF04851, PF06508, PF13091, PF13353, PF13394, PF14072
---
# Dpd
@@ -37,3 +38,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/drt.md b/content/2.defense-systems/drt.md
index 8430ad290c2cf7e55d7daebb2d270738440e2f36..d880cdf39837394191a84b414d0da42f8899e922 100644
--- a/content/2.defense-systems/drt.md
+++ b/content/2.defense-systems/drt.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00078
---
# DRT
@@ -89,3 +90,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/druantia.md b/content/2.defense-systems/druantia.md
index 88068ad1fb51a5c40796e35651ca504c860ab97f..7eaab9cfe2217ce792085dc3e1f8f5da8dc3d8a7 100644
--- a/content/2.defense-systems/druantia.md
+++ b/content/2.defense-systems/druantia.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00145, PF00270, PF00271, PF04851, PF09369, PF14236
---
# Druantia
@@ -54,3 +55,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/dsr.md b/content/2.defense-systems/dsr.md
index b4b959f9b47fa43340c6d96afcaf6db480da7387..165b5832dc7c1de3fa5a1efd242c783c7a8e0dd4 100644
--- a/content/2.defense-systems/dsr.md
+++ b/content/2.defense-systems/dsr.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Sensing phage protein
Activator: Direct
Effector: Nucleotide modifying
+ PFAM: PF13289
---
# Dsr
@@ -57,3 +58,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/eleos.md b/content/2.defense-systems/eleos.md
index 9c114b958f23c5d8b1459a42651ebbb4b3ee9a8e..f1738f4dcee24eaee9334b00907d1ea79a8acc28 100644
--- a/content/2.defense-systems/eleos.md
+++ b/content/2.defense-systems/eleos.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00350, PF01926, PF18709
---
# Eleos
@@ -48,3 +49,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/fs_hp_sdh_sah.md b/content/2.defense-systems/fs_hp_sdh_sah.md
index 8e64de232827829c855be1ffa05435c9d8ecdcbe..7db0ba9c3a3c29092a24fd41816a25aee67cf4eb 100644
--- a/content/2.defense-systems/fs_hp_sdh_sah.md
+++ b/content/2.defense-systems/fs_hp_sdh_sah.md
@@ -5,6 +5,7 @@ tableColumns:
doi: 10.1016/j.cell.2022.07.014
abstract: |
Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+ PFAM: PF01972
---
# FS_HP_SDH_sah
@@ -19,3 +20,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/fs_sma.md b/content/2.defense-systems/fs_sma.md
index de46a35048268e3781e3824dbd2ecdcb1c1af331..502da1115688ede9959038841aacbd4f88d94be0 100644
--- a/content/2.defense-systems/fs_sma.md
+++ b/content/2.defense-systems/fs_sma.md
@@ -5,6 +5,7 @@ tableColumns:
doi: 10.1016/j.cell.2022.07.014
abstract: |
Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+ PFAM: PF02452
---
# FS_Sma
@@ -19,3 +20,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/gabija.md b/content/2.defense-systems/gabija.md
index 97410e3c8b2dab6ddbc71d9b63571e119f36bd6f..5de114e47860d3f65e52b6ef48ddd0fa200c9f79 100644
--- a/content/2.defense-systems/gabija.md
+++ b/content/2.defense-systems/gabija.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Direct
Effector: Degrading nucleic acids
+ PFAM: PF00580, PF11398, PF13175, PF13245, PF13304, PF13361, PF13476
---
# Gabija
@@ -61,3 +62,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/gao_her.md b/content/2.defense-systems/gao_her.md
index 1d848a7e5b750cbd0bb4fd61eacc481ba8309f69..771a2e63272dac957d0e911202200492b369fb89 100644
--- a/content/2.defense-systems/gao_her.md
+++ b/content/2.defense-systems/gao_her.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF01935, PF10412, PF13289
---
# Gao_Her
@@ -52,3 +53,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/gao_hhe.md b/content/2.defense-systems/gao_hhe.md
index 9df0702d41652f0ed0a856b53dde16db53805c78..77d1201ad3e96895fc117738bde3c28ae378480f 100644
--- a/content/2.defense-systems/gao_hhe.md
+++ b/content/2.defense-systems/gao_hhe.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF04480, PF13086, PF13087, PF13195, PF18741
---
# Gao_Hhe
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/gao_iet.md b/content/2.defense-systems/gao_iet.md
index 8b7957a0dade05f188086ee16bc50f9fd20b4429..d618744ebdecb04cc53234f959dab9f73428dff1 100644
--- a/content/2.defense-systems/gao_iet.md
+++ b/content/2.defense-systems/gao_iet.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00004, PF00082
---
# Gao_Iet
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/gao_mza.md b/content/2.defense-systems/gao_mza.md
index 87a59887b9d8c381a5117713bed30581c5236dbc..546f21f6a6a88cb622e59ec67d6812bb6eca5495 100644
--- a/content/2.defense-systems/gao_mza.md
+++ b/content/2.defense-systems/gao_mza.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00023, PF04542, PF04545, PF10592, PF10593, PF13589, PF13606, PF14390
---
# Gao_Mza
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/gao_qat.md b/content/2.defense-systems/gao_qat.md
index aa56459f5e5277cef78287dce016a87ccb4a5fa6..ad110e3354628b98a72f571010b332c890de1085 100644
--- a/content/2.defense-systems/gao_qat.md
+++ b/content/2.defense-systems/gao_qat.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF01026, PF07693
---
# Gao_Qat
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/gao_rl.md b/content/2.defense-systems/gao_rl.md
index 7f4ec5d51ca278182192528f5fb0e4e64511cf3e..76346a1d2025bcf25889ec19863e54720221ba64 100644
--- a/content/2.defense-systems/gao_rl.md
+++ b/content/2.defense-systems/gao_rl.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00176, PF00271, PF04465, PF04851, PF06634, PF12635, PF13091, PF13287, PF13290
---
# Gao_RL
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/gaps2.md b/content/2.defense-systems/gaps2.md
index 4b63ea07ff902f0b4d488315128deba3aed03443..5dda7086fe2efe28368be342e1fa17dfefb43abb 100644
--- a/content/2.defense-systems/gaps2.md
+++ b/content/2.defense-systems/gaps2.md
@@ -5,6 +5,7 @@ tableColumns:
doi: 10.1101/2023.03.28.534373
abstract: |
Bacteria are found in ongoing conflicts with rivals and predators, which lead to an evolutionary arms race and the development of innate and adaptive immune systems. Although diverse bacterial immunity mechanisms have been recently identified, many remain unknown, and their dissemination within bacterial populations is poorly understood. Here, we describe a widespread genetic element, defined by the Gamma-Mobile-Trio (GMT) proteins, that serves as a mobile bacterial weapons armory. We show that GMT islands have cargo comprising various combinations of secreted antibacterial toxins, anti-phage defense systems, and secreted anti-eukaryotic toxins. This finding led us to identify four new anti-phage defense systems encoded within GMT islands and reveal their active domains and mechanisms of action. We also find the phage protein that triggers the activation of one of these systems. Thus, we can identify novel toxins and defense systems by investigating proteins of unknown function encoded within GMT islands. Our findings imply that the concept of "defense islands" may be broadened to include other types of bacterial innate immunity mechanisms, such as antibacterial and anti-eukaryotic toxins that appear to stockpile with anti-phage defense systems within GMT weapon islands.
+ PFAM: PF00533, PF01653, PF03119, PF03120, PF12826, PF14520
---
# GAPS2
@@ -19,3 +20,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/hachiman.md b/content/2.defense-systems/hachiman.md
index 71b90a84b0360b8d0823de001b78c4937d4b4463..ef66cd4e3da2601bcbaf542faffc6003f6f6af44 100644
--- a/content/2.defense-systems/hachiman.md
+++ b/content/2.defense-systems/hachiman.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00270, PF00271, PF04851, PF08878, PF14130
---
# Hachiman
@@ -61,3 +62,4 @@ items:
1. Doron S, Melamed S, Ofir G, et al. Systematic discovery of antiphage defense systems in the microbial pangenome. *Science*. 2018;359(6379):eaar4120. doi:10.1126/science.aar4120
2. Payne LJ, Todeschini TC, Wu Y, Perry BJ, Ronson CW, Fineran PC, Nobrega FL, Jackson SA. Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. Nucleic Acids Res. 2021 Nov 8;49(19):10868-10878. doi: 10.1093/nar/gkab883. PMID: 34606606; PMCID: PMC8565338.
+
diff --git a/content/2.defense-systems/hna.md b/content/2.defense-systems/hna.md
index 1717a49b839fc5cb9f3008739c75574e1581dfb4..1933e3cef49c1d3597b78f11a326bf235e703005 100644
--- a/content/2.defense-systems/hna.md
+++ b/content/2.defense-systems/hna.md
@@ -5,6 +5,7 @@ tableColumns:
doi: 10.1016/j.chom.2023.01.010
abstract: |
There is strong selection for the evolution of systems that protect bacterial populations from viral attack. We report a single phage defense protein, Hna, that provides protection against diverse phages in Sinorhizobium meliloti, a nitrogen-fixing alpha-proteobacterium. Homologs of Hna are distributed widely across bacterial lineages, and a homologous protein from Escherichia coli also confers phage defense. Hna contains superfamily II helicase motifs at its N terminus and a nuclease motif at its C terminus, with mutagenesis of these motifs inactivating viral defense. Hna variably impacts phage DNA replication but consistently triggers an abortive infection response in which infected cells carrying the system die but do not release phage progeny. A similar host cell response is triggered in cells containing Hna upon expression of a phage-encoded single-stranded DNA binding protein (SSB), independent of phage infection. Thus, we conclude that Hna limits phage spread by initiating abortive infection in response to a phage protein.
+ PFAM: PF00270, PF04851, PF13307
---
# Hna
@@ -19,3 +20,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/jukab.md b/content/2.defense-systems/jukab.md
index e4c71ee11880e0f754cb714a48bbd5fdc472f91e..55295693981ca38468826f78a82c88b5c094d644 100644
--- a/content/2.defense-systems/jukab.md
+++ b/content/2.defense-systems/jukab.md
@@ -5,6 +5,7 @@ tableColumns:
doi: 10.1101/2022.09.17.508391
abstract: |
Jumbo bacteriophages of the ?KZ-like family are characterized by large genomes (>200 kb) and the remarkable ability to assemble a proteinaceous nucleus-like structure. The nucleus protects the phage genome from canonical DNA-targeting immune systems, such as CRISPR-Cas and restriction-modification. We hypothesized that the failure of common bacterial defenses creates selective pressure for immune systems that target the unique jumbo phage biology. Here, we identify the "jumbo phage killer"(Juk) immune system that is deployed by a clinical isolate of Pseudomonas aeruginosa to resist PhiKZ. Juk immunity rescues the cell by preventing early phage transcription, DNA replication, and nucleus assembly. Phage infection is first sensed by JukA (formerly YaaW), which localizes rapidly to the site of phage infection at the cell pole, triggered by ejected phage factors. The effector protein JukB is recruited by JukA, which is required to enable immunity and the subsequent degradation of the phage DNA. JukA homologs are found in several bacterial phyla and are associated with numerous other putative effectors, many of which provided specific antiPhiKZ activity when expressed in P. aeruginosa. Together, these data reveal a novel strategy for immunity whereby immune factors are recruited to the site of phage protein and DNA ejection to prevent phage progression and save the cell.
+ PFAM: PF13099
---
# JukAB
@@ -19,3 +20,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/kiwa.md b/content/2.defense-systems/kiwa.md
index 044f267bc40050700721dd9b2f078a2bcfe529f0..517226cb0141a297dceb079bdb99ab1806119091 100644
--- a/content/2.defense-systems/kiwa.md
+++ b/content/2.defense-systems/kiwa.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF16162
---
# Kiwa
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/lamassu-fam.md b/content/2.defense-systems/lamassu-fam.md
index 628f2f7b7771e798310561c22ebb52f168d3153f..436fcca0416284f3796ee031ff8c52d5a0ebef39 100644
--- a/content/2.defense-systems/lamassu-fam.md
+++ b/content/2.defense-systems/lamassu-fam.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Diverse (Nucleic acid degrading (?), Nucleotide modifying (?), Membrane disrupting (?))
+ PFAM: PF00753, PF02463, PF05057, PF12532, PF13175, PF13289, PF13476, PF14130
---
# Lamassu-Fam
@@ -126,3 +127,4 @@ items:
2. Payne LJ, Todeschini TC, Wu Y, et al. Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. *Nucleic Acids Res*. 2021;49(19):10868-10878. doi:10.1093/nar/gkab883
3. Millman, A., Melamed, S., Leavitt, A., Doron, S., Bernheim, A., Hör, J., Lopatina, A., Ofir, G., Hochhauser, D., Stokar-Avihail, A., Tal, N., Sharir, S., Voichek, M., Erez, Z., Ferrer, J.L.M., Dar, D., Kacen, A., Amitai, G., Sorek, R., 2022. An expanding arsenal of immune systems that protect bacteria from phages. bioRxiv. https://doi.org/10.1101/2022.05.11.491447
+
diff --git a/content/2.defense-systems/lit.md b/content/2.defense-systems/lit.md
index 63950ee2217dcb775df273e9bbebecba2fadb887..fd7f1c625464bad513593761bb1ef4b74378a4af 100644
--- a/content/2.defense-systems/lit.md
+++ b/content/2.defense-systems/lit.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Monitoring host integrity
Activator: Direct
Effector: Other (Cleaves an elongation factor, inhibiting cellular translation
+ PFAM: PF10463
---
# Lit
@@ -48,3 +49,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/mads.md b/content/2.defense-systems/mads.md
index 77782681ce6e6022db8157633d542e0c232e03c0..ef5756d148a1dbf98af858f8b71f18dc005d902d 100644
--- a/content/2.defense-systems/mads.md
+++ b/content/2.defense-systems/mads.md
@@ -5,6 +5,7 @@ tableColumns:
doi: 10.1101/2023.03.30.534895
abstract: |
The constant arms race between bacteria and their phages has resulted in a large diversity of bacterial defence systems1,2, with many bacteria carrying several systems3,4. In response, phages often carry counter-defence genes5-9. If and how bacterial defence mechanisms interact to protect against phages with counter-defence genes remains unclear. Here, we report the existence of a novel defence system, coined MADS (Methylation Associated Defence System), which is located in a strongly conserved genomic defence hotspot in Pseudomonas aeruginosa and distributed across Gram-positive and Gram-negative bacteria. We find that the natural co-existence of MADS and a Type IE CRISPR-Cas adaptive immune system in the genome of P. aeruginosa SMC4386 provides synergistic levels of protection against phage DMS3, which carries an anti-CRISPR (acr) gene. Previous work has demonstrated that Acr-phages need to cooperate to overcome CRISPR immunity, with a first sacrificial phage causing host immunosuppression to enable successful secondary phage infections10,11. Modelling and experiments show that the co-existence of MADS and CRISPR-Cas provides strong and durable protection against Acr-phages by disrupting their cooperation and limiting the spread of mutants that overcome MADS. These data reveal that combining bacterial defences can robustly neutralise phage with counter-defence genes, even if each defence on its own can be readily by-passed, which is key to understanding how selection acts on defence combinations and their coevolutionary consequences.
+ PFAM: PF00069, PF01170, PF02384, PF07714, PF08378, PF12728, PF13304, PF13588
---
# MADS
@@ -19,3 +20,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/mazef.md b/content/2.defense-systems/mazef.md
index 1ee0682eededf5b81ba98809b209f546f1e01144..a9401491f733619a3954371d61da3832493f6e12 100644
--- a/content/2.defense-systems/mazef.md
+++ b/content/2.defense-systems/mazef.md
@@ -5,6 +5,7 @@ tableColumns:
doi: 10.1007/s00438-004-1048-y
abstract: |
The Escherichia coli gene pair mazEF is a regulatable chromosomal toxin-antitoxin module: mazF encodes a stable toxin and mazE encodes for a labile antitoxin that overcomes the lethal effect of MazF. Because MazE is labile, inhibition of mazE expression results in cell death. We studied the effect of mazEF on the development of bacteriophage P1 upon thermoinduction of the prophage P1CM c1ts and upon infection with virulent phage particles (P1vir). In several E. coli strains, we showed that the ?mazEF derivative strains produced significantly more phages than did the parent strain. In addition, upon induction of K38(P1CM c1ts), nearly all of the ?mazEF mutant cells lysed; in contrast, very few of the parental mazEF + K38 cells underwent lysis. However, most of these cells did not remain viable. Thus, while the ?mazEF cells die as a result of the lytic action of the phage, most of the mazEF + cells are killed by a different mechanism, apparently through the action of the chromosomal mazEF system itself. Furthermore, the introduction of lysogens into a growing non-lysogenic culture is lethal to ?mazEF but not for mazEF + cultures. Thus, although mazEF action causes individual cells to die, upon phage growth this is generally beneficial to the bacterial culture because it causes P1 phage exclusion from the bacterial population. These results provide additional support for the view that bacterial cultures may share some of the characteristics of multicellular organisms.
+ PFAM: PF02452, PF04014
---
# MazEF
@@ -19,3 +20,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/menshen.md b/content/2.defense-systems/menshen.md
index ec508e9f4cd0201a85dd6c7f2cfa617375a68641..06f45bc2d5aa329a39f5fd9b90baeef449e6dbe4 100644
--- a/content/2.defense-systems/menshen.md
+++ b/content/2.defense-systems/menshen.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF03235, PF05973, PF12476, PF13175, PF13304, PF13476
---
# Menshen
@@ -48,3 +49,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/mok_hok_sok.md b/content/2.defense-systems/mok_hok_sok.md
index 33a83651774df7934c5bc901084870f5d7a1772e..4ba47b49bb490c2464f8584e33178db594fbaab9 100644
--- a/content/2.defense-systems/mok_hok_sok.md
+++ b/content/2.defense-systems/mok_hok_sok.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Monitoring of the host cell machinery (?)
Activator: Unknown
Effector: Unknown
+ PFAM: PF01848
---
# Mok_Hok_Sok
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/mokosh.md b/content/2.defense-systems/mokosh.md
index d455ce34bf0fc2eb22358dacf270560595ed476d..a49346b2d0359d0d3c01092848d6ff6011693b92 100644
--- a/content/2.defense-systems/mokosh.md
+++ b/content/2.defense-systems/mokosh.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00069, PF07714, PF08378, PF13086, PF13087, PF13091, PF13245, PF13604
---
# Mokosh
@@ -52,3 +53,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/nhi.md b/content/2.defense-systems/nhi.md
index 0f2ce7478a3b363eed5fed92892cf085c75c9adf..675aa49a87ea1bc19dc64fef05ae1a7b1cb3a008 100644
--- a/content/2.defense-systems/nhi.md
+++ b/content/2.defense-systems/nhi.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Nucleic acid degrading (?)
+ PFAM: PF01443, PF09848, PF13604
---
# Nhi
@@ -54,3 +55,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/nlr.md b/content/2.defense-systems/nlr.md
index d8a572cf49d374c532a128beef9079a98aaa9c41..47795fc96ff1eea2f88827fb8e786788cbe2ebb7 100644
--- a/content/2.defense-systems/nlr.md
+++ b/content/2.defense-systems/nlr.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF05729
---
# NLR
@@ -66,3 +67,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/old_exonuclease.md b/content/2.defense-systems/old_exonuclease.md
index 069b112f0e66ed7f173c18d52d62b7df798159d2..f87ae962eb4aa67371ae8f1c5aeccee8e03feed9 100644
--- a/content/2.defense-systems/old_exonuclease.md
+++ b/content/2.defense-systems/old_exonuclease.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF13175, PF13304
---
# Old_exonuclease
@@ -42,3 +43,4 @@ A system from *Enterobacteria phage P2* in *Escherichia coli* has an anti-phage
**Rousset, F. et al. Phages and their satellites encode hotspots of antiviral systems. Cell Host & Microbe 30, 740-753.e5 (2022).**
Bacteria carry diverse genetic systems to defend against viral infection, some of which are found within prophages where they inhibit competing viruses. Phage satellites pose additional pressures on phages by hijacking key viral elements to their own benefit. Here, we show that E. coli P2-like phages and their parasitic P4-like satellites carry hotspots of genetic variation containing reservoirs of anti-phage systems. We validate the activity of diverse systems and describe PARIS, an abortive infection system triggered by a phage-encoded anti-restriction protein. Antiviral hotspots participate in inter-viral competition and shape dynamics between the bacterial host, P2-like phages, and P4-like satellites. Notably, the anti-phage activity of satellites can benefit the helper phage during competition with virulent phages, turning a parasitic relationship into a mutualistic one. Anti-phage hotspots are present across distant species and constitute a substantial source of systems that participate in the competition between mobile genetic elements.
+
diff --git a/content/2.defense-systems/pago.md b/content/2.defense-systems/pago.md
index bf67ee0606e071464f9dcd53afc2bcf10f9c6488..b0c6c6cb4f12dc1adeaf9cd546d6643c7ecce4a7 100644
--- a/content/2.defense-systems/pago.md
+++ b/content/2.defense-systems/pago.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Detecting invading nucleic acid
Activator: Direct
Effector: Diverse (Nucleotide modifyingn, Membrane disrupting)
+ PFAM: PF02171, PF13289, PF13676, PF14280, PF18742
---
# pAgo
@@ -67,3 +68,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/panchino_gp28.md b/content/2.defense-systems/panchino_gp28.md
index b1d1891b8baf8e5b038e32c5430954435a0ebcbf..7af6b020d3d24d0512a11775590eabc16f13729e 100644
--- a/content/2.defense-systems/panchino_gp28.md
+++ b/content/2.defense-systems/panchino_gp28.md
@@ -5,6 +5,7 @@ tableColumns:
doi: 10.1038/nmicrobiol.2016.251
abstract: |
Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.
+ PFAM: PF01170, PF02384, PF13588
---
# Panchino_gp28
@@ -19,3 +20,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-lambda-1.md b/content/2.defense-systems/pd-lambda-1.md
index 7eda7e6d39b8336bddd0b4a302215472399f0a57..2d28cf7113d72403b706ea483d1dfd82284d9dee 100644
--- a/content/2.defense-systems/pd-lambda-1.md
+++ b/content/2.defense-systems/pd-lambda-1.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF10544, PF13250, PF13455
---
# PD-Lambda-1
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-lambda-2.md b/content/2.defense-systems/pd-lambda-2.md
index 44c4f60edd0aed20be918b9e9e3665df1e542215..15f2f18291b4349c32ac377f5c6ffafc4c367f9a 100644
--- a/content/2.defense-systems/pd-lambda-2.md
+++ b/content/2.defense-systems/pd-lambda-2.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF06114, PF09907, PF14350
---
# PD-Lambda-2
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-lambda-3.md b/content/2.defense-systems/pd-lambda-3.md
index 7000431905faf729922ffa8e3ca5eca2b17f65c1..751423dd7d828f9c0b3d4fce8a7b605c0dd9cfd9 100644
--- a/content/2.defense-systems/pd-lambda-3.md
+++ b/content/2.defense-systems/pd-lambda-3.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF09509
---
# PD-Lambda-3
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-lambda-5.md b/content/2.defense-systems/pd-lambda-5.md
index eef05860ef8ee1b7f1bfa5bfaedc13b5ce8e4890..32604e771b7ae3756653d4a77fe25aac35f5abe4 100644
--- a/content/2.defense-systems/pd-lambda-5.md
+++ b/content/2.defense-systems/pd-lambda-5.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF02086
---
# PD-Lambda-5
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-t4-1.md b/content/2.defense-systems/pd-t4-1.md
index 7d9cdb3052fbf4f139cb4d11a449c7dfe70d2508..02a95e9cc53d24d78c7a2ad2a90bd82f3ed281da 100644
--- a/content/2.defense-systems/pd-t4-1.md
+++ b/content/2.defense-systems/pd-t4-1.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF13020
---
# PD-T4-1
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-t4-2.md b/content/2.defense-systems/pd-t4-2.md
index 2dd4523eeb405689a70ddaf68b31018b0b196412..ccf93b285f65d4bd7e692220d1ffc3c9dbaf6c15 100644
--- a/content/2.defense-systems/pd-t4-2.md
+++ b/content/2.defense-systems/pd-t4-2.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF03235, PF18735
---
# PD-T4-2
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-t4-4.md b/content/2.defense-systems/pd-t4-4.md
index d0b68a43a46421c0d2b5e034ee50e9fdb5320365..68953b39261e9bad6c4fa9ed9df04b050bcd0100 100644
--- a/content/2.defense-systems/pd-t4-4.md
+++ b/content/2.defense-systems/pd-t4-4.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF13175, PF13304
---
# PD-T4-4
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-t4-5.md b/content/2.defense-systems/pd-t4-5.md
index 856b8818ba002994dd22af14b4cc9c3859e4908d..d64a49331ba86e6a98ddac354eeb8530c91a1ed7 100644
--- a/content/2.defense-systems/pd-t4-5.md
+++ b/content/2.defense-systems/pd-t4-5.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF07751
---
# PD-T4-5
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-t4-6.md b/content/2.defense-systems/pd-t4-6.md
index b47fb45ac31df2301509661aa4f664712dd6a03b..59f764206671fe3be317753e6024c327a80e844a 100644
--- a/content/2.defense-systems/pd-t4-6.md
+++ b/content/2.defense-systems/pd-t4-6.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00069, PF03793, PF07714
---
# PD-T4-6
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-t4-8.md b/content/2.defense-systems/pd-t4-8.md
index 34c7eccf97b4950ff6595c7a64cf2d8c7a5637f5..d0af03b235bd0189a63d3215b3a400a73b9e601e 100644
--- a/content/2.defense-systems/pd-t4-8.md
+++ b/content/2.defense-systems/pd-t4-8.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF14082
---
# PD-T4-8
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-t4-9.md b/content/2.defense-systems/pd-t4-9.md
index 23424c29bb2f6a50a7c0fa9f981e91be69f387d2..e490e0942a920576d55df1224e1fd0bdbd62691f 100644
--- a/content/2.defense-systems/pd-t4-9.md
+++ b/content/2.defense-systems/pd-t4-9.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF02556
---
# PD-T4-9
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-t7-2.md b/content/2.defense-systems/pd-t7-2.md
index e2890ee347f0045102928e94e929dbef5d8ed75c..08b19589cff5c570444dbb381aa70e062e42d359 100644
--- a/content/2.defense-systems/pd-t7-2.md
+++ b/content/2.defense-systems/pd-t7-2.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF01935, PF13289
---
# PD-T7-2
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pd-t7-4.md b/content/2.defense-systems/pd-t7-4.md
index c7693137a922e2d0f81ba2d3e3cd6d0eedc032d7..a9e79b6b0783e20d81b39659d252b2e393d6539d 100644
--- a/content/2.defense-systems/pd-t7-4.md
+++ b/content/2.defense-systems/pd-t7-4.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF13643
---
# PD-T7-4
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pfiat.md b/content/2.defense-systems/pfiat.md
index 7638ef7de124497dc41a5565385b06872277eb48..c12e0eaa0ae3fed604e0300bd8eb97912740c357 100644
--- a/content/2.defense-systems/pfiat.md
+++ b/content/2.defense-systems/pfiat.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF02604, PF05016
---
# PfiAT
@@ -40,3 +41,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/phrann_gp29_gp30.md b/content/2.defense-systems/phrann_gp29_gp30.md
index 3149e458b2c4c41282039053255b414a3c14e079..a9a676db5b349b0ced5dbc99d3421f813812da71 100644
--- a/content/2.defense-systems/phrann_gp29_gp30.md
+++ b/content/2.defense-systems/phrann_gp29_gp30.md
@@ -5,6 +5,7 @@ tableColumns:
doi: 10.1038/nmicrobiol.2016.251
abstract: |
Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.
+ PFAM: PF04607
---
# Phrann_gp29_gp30
@@ -38,3 +39,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pif.md b/content/2.defense-systems/pif.md
index 58444a2c4ad0d2b0cdd8beeb3335a991fc5fa827..35f6104de85a6eab8dc36b1686e3f07b13ce7e3e 100644
--- a/content/2.defense-systems/pif.md
+++ b/content/2.defense-systems/pif.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Sensing of phage protein
Activator: Unknown
Effector: Membrane disrupting (?)
+ PFAM: PF07693
---
# Pif
@@ -48,3 +49,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/prrc.md b/content/2.defense-systems/prrc.md
index 317ff23baa45d36a7b27312a8ee19e30c8933a18..2149d38b41670a31ea525d7ffbbec6f1d0dc3d1a 100644
--- a/content/2.defense-systems/prrc.md
+++ b/content/2.defense-systems/prrc.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Monitor the integrity of the bacterial cell machinery
Activator: Direct
Effector: Nucleic acid degrading
+ PFAM: PF00270, PF02384, PF04313, PF04851, PF12008, PF12161, PF13166, PF18766
---
# PrrC
@@ -47,3 +48,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/psyrta.md b/content/2.defense-systems/psyrta.md
index 616000fa4fa341d15b4c1436bca1106732365b5d..57f20a11716effef05b80b3d35d00411b3bbf564 100644
--- a/content/2.defense-systems/psyrta.md
+++ b/content/2.defense-systems/psyrta.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00270, PF00271, PF02481, PF04851, PF18306
---
# PsyrTA
@@ -47,3 +48,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/pycsar.md b/content/2.defense-systems/pycsar.md
index 7888ee671958969f5c981c1fb16268bdafcfd02f..14cf01416881ead3a83de41ae0bd5542112a9f0d 100644
--- a/content/2.defense-systems/pycsar.md
+++ b/content/2.defense-systems/pycsar.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Signaling molecules
Effector: Membrane disrupting, Nucleotides modifying
+ PFAM: PF00004, PF00027, PF00211, PF00899, PF01734, PF10137, PF14461, PF14464, PF18145, PF18153, PF18303, PF18967
---
# Pycsar
@@ -48,3 +49,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/retron.md b/content/2.defense-systems/retron.md
index ab9d432b8cff85aedbb13adedc8207d38137ebe3..886992931b235224a309ad23cbd024608b5e263f 100644
--- a/content/2.defense-systems/retron.md
+++ b/content/2.defense-systems/retron.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Monitor the integrity of the bacterial cell machinery
Activator: Unknown
Effector: Diverse
+ PFAM: PF00078, PF00089, PF01381, PF01582, PF12686, PF12844, PF13175, PF13304, PF13365, PF13476, PF13560, PF13676
---
# Retron
@@ -149,3 +150,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rexab.md b/content/2.defense-systems/rexab.md
index 46cff76a02f6f19ccc87c9bc87b77fd91cd1cccc..23efd871d3ad67eb8488a4ccd53b6f23e095926b 100644
--- a/content/2.defense-systems/rexab.md
+++ b/content/2.defense-systems/rexab.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Sensing of complex phage protein/DNA
Activator: Direct
Effector: Membrane disrupting
+ PFAM: PF15968, PF15969
---
# RexAB
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rloc.md b/content/2.defense-systems/rloc.md
index a413fe3a7c81adcdf703a7293b6b0b8c95f4a780..5b7db799e25557bd9f88e9cd7b3caeebf8d0fd3f 100644
--- a/content/2.defense-systems/rloc.md
+++ b/content/2.defense-systems/rloc.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Monitor the integrity of the bacterial cell machinery
Activator: Unknown
Effector: Nucleic acid degrading
+ PFAM: PF13166
---
# RloC
@@ -47,3 +48,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rm.md b/content/2.defense-systems/rm.md
index 60dd9da788929826ee041b84a6ec09f1f5417d1d..aa4206626acff18fc6f609599e1b9d751abd24ec 100644
--- a/content/2.defense-systems/rm.md
+++ b/content/2.defense-systems/rm.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Detecting invading nucleic acid
Activator: Direct
Effector: Nucleic acid degrading
+ PFAM: PF00270, PF02384, PF04313, PF04851, PF12008, PF12161, PF18766
---
# RM
@@ -56,3 +57,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rnlab.md b/content/2.defense-systems/rnlab.md
index 0f9acc42f4f8410981c2cd389339f002138a7df4..19f5afb7ab8d5b71e4e5d978deb9be6d4ac2aab5 100644
--- a/content/2.defense-systems/rnlab.md
+++ b/content/2.defense-systems/rnlab.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Monitor the integrity of the bacterial cell machinery
Activator: Direct
Effector: Nucleic acid degrading
+ PFAM: PF15933, PF15935, PF18869, PF19034
---
# RnlAB
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rosmerta.md b/content/2.defense-systems/rosmerta.md
index d9ffb12f10f0b7a9fbfe689b7d3cb95f420ce18a..8cb81a2e4d25a53c583bdb408b405cf538546b28 100644
--- a/content/2.defense-systems/rosmerta.md
+++ b/content/2.defense-systems/rosmerta.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF01381, PF06114, PF12844, PF13443, PF13560
---
# RosmerTA
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rst_2tm_1tm_tir.md b/content/2.defense-systems/rst_2tm_1tm_tir.md
index 761b4a4f64b1a7e4bf76a98e93ab265c5ce25ade..533f30ce5f9daa8a4e1a3184c312888f9c151ab9 100644
--- a/content/2.defense-systems/rst_2tm_1tm_tir.md
+++ b/content/2.defense-systems/rst_2tm_1tm_tir.md
@@ -5,6 +5,7 @@ tableColumns:
doi: 10.1016/j.chom.2022.02.018
abstract: |
Bacteria carry diverse genetic systems to defend against viral infection, some of which are found within prophages where they inhibit competing viruses. Phage satellites pose additional pressures on phages by hijacking key viral elements to their own benefit. Here, we show that E. coli P2-like phages and their parasitic P4-like satellites carry hotspots of genetic variation containing reservoirs of anti-phage systems. We validate the activity of diverse systems and describe PARIS, an abortive infection system triggered by a phage-encoded anti-restriction protein. Antiviral hotspots participate in inter-viral competition and shape dynamics between the bacterial host, P2-like phages, and P4-like satellites. Notably, the anti-phage activity of satellites can benefit the helper phage during competition with virulent phages, turning a parasitic relationship into a mutualistic one. Anti-phage hotspots are present across distant species and constitute a substantial source of systems that participate in the competition between mobile genetic elements.
+ PFAM: PF13676
---
# Rst_2TM_1TM_TIR
@@ -37,3 +38,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rst_duf4238.md b/content/2.defense-systems/rst_duf4238.md
index 262546f1f66aa8381f376027323710022bcdc9b7..95ba0b60c3652d537d73a6934eab4cbf3ab68a87 100644
--- a/content/2.defense-systems/rst_duf4238.md
+++ b/content/2.defense-systems/rst_duf4238.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF14022
---
# Rst_DUF4238
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rst_gop_beta_cll.md b/content/2.defense-systems/rst_gop_beta_cll.md
index 220806795da0e6cc4faea652e88de1855d8279a2..3d11950e030ca830dee981e9c091ac44e8bf9536 100644
--- a/content/2.defense-systems/rst_gop_beta_cll.md
+++ b/content/2.defense-systems/rst_gop_beta_cll.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF14350
---
# Rst_gop_beta_cll
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rst_helicaseduf2290.md b/content/2.defense-systems/rst_helicaseduf2290.md
index d935ef2d8a120c5408fcdce2d064216b34b35860..ed03b13384a1f7f2d6e609ba471329f4c57034fe 100644
--- a/content/2.defense-systems/rst_helicaseduf2290.md
+++ b/content/2.defense-systems/rst_helicaseduf2290.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF10053, PF13538
---
# Rst_HelicaseDUF2290
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rst_hydrolase-3tm.md b/content/2.defense-systems/rst_hydrolase-3tm.md
index 00edbe611de878ae1d141cabe0759504882a1c8a..de56898245dc84222ed34071c22461072e1a42d7 100644
--- a/content/2.defense-systems/rst_hydrolase-3tm.md
+++ b/content/2.defense-systems/rst_hydrolase-3tm.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF13242, PF13419
---
# Rst_Hydrolase-3Tm
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rst_rt-nitrilase-tm.md b/content/2.defense-systems/rst_rt-nitrilase-tm.md
index a4453e14c587f23d62db4acfa1a500b56896a652..fe87e58fa6a488bb14b7787302bdbad81bfa1d8f 100644
--- a/content/2.defense-systems/rst_rt-nitrilase-tm.md
+++ b/content/2.defense-systems/rst_rt-nitrilase-tm.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00078
---
# Rst_RT-nitrilase-Tm
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/rst_tir-nlr.md b/content/2.defense-systems/rst_tir-nlr.md
index c7e52d931a81317937f80433b0df3024463a31c7..d07a33c7d8f9cc73986260029b99ab42d7184930 100644
--- a/content/2.defense-systems/rst_tir-nlr.md
+++ b/content/2.defense-systems/rst_tir-nlr.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF13676
---
# Rst_TIR-NLR
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/sanata.md b/content/2.defense-systems/sanata.md
index d3867a55115b17a154a8b8be5f27188ba34f00b2..d032f25771fdc50fd4a7f09edf691535a7b8b123 100644
--- a/content/2.defense-systems/sanata.md
+++ b/content/2.defense-systems/sanata.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF08843
---
# SanaTA
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/sefir.md b/content/2.defense-systems/sefir.md
index b6b8479006094309d74236b780d94e40520d10c1..5d3f6d7a0839184aa8d36d12e3877a6519eb8145 100644
--- a/content/2.defense-systems/sefir.md
+++ b/content/2.defense-systems/sefir.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF08357, PF13676
---
# SEFIR
@@ -59,3 +60,4 @@ items:
## References
[1] Millman, A. et al. An expanded arsenal of immune systems that protect bacteria from phages. Cell Host Microbe 30, 1556-1569.e5 (2022).
[2] Novatchkova, M., Leibbrandt, A., Werzowa, J., Neubüser, A., & Eisenhaber, F. (2003). The STIR-domain superfamily in signal transduction, development and immunity. _Trends in biochemical sciences_, _28_(5), 226-229.
+
diff --git a/content/2.defense-systems/septu.md b/content/2.defense-systems/septu.md
index 17e4a741116f99d3bea3d3bb72a08f939abc4a37..5f7a8218325c7b8a634c137d0f479ea4f965e84f 100644
--- a/content/2.defense-systems/septu.md
+++ b/content/2.defense-systems/septu.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF13175, PF13304, PF13476
---
# Septu
@@ -50,3 +51,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/shango.md b/content/2.defense-systems/shango.md
index 0ce65b4317aa6635842ecdaa5a782dcdf2a0b9e5..fd02239b88b9fc19a435ec159a8ba44200cd108f 100644
--- a/content/2.defense-systems/shango.md
+++ b/content/2.defense-systems/shango.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00270, PF00271, PF05099, PF10923, PF13208, PF15615
---
# Shango
@@ -67,3 +68,4 @@ Shango was discovered in parallel by Adi Millman (Sorek group) and the team of J
[2] Johnson, Matthew, Laderman, Eric, Huiting, Erin, Zhang, Charles, Davidson, Alan, & Bondy-Denomy, Joseph. (2022). _Core Defense Hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems_. [https://doi.org/10.5281/ZENODO.7254690](https://doi.org/10.5281/ZENODO.7254690)
[3] Alekhina, O., Valkovicova, L., & Turna, J. (2011). Study of membrane attachment and in vivo co-localization of TerB protein from uropathogenic Escherichia coli KL53. _General physiology and biophysics_, _30_(3), 286-292.
+
diff --git a/content/2.defense-systems/shedu.md b/content/2.defense-systems/shedu.md
index 6b939d8718a6b71c9c58c7274e976ae90f5e70d8..0c365cb36820c98c8af4944e59634e13d98a46ff 100644
--- a/content/2.defense-systems/shedu.md
+++ b/content/2.defense-systems/shedu.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF14082
---
# Shedu
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/shosta.md b/content/2.defense-systems/shosta.md
index f4b0e62d836031ba0386c4c514b7b323d8eb87da..02640091e6ac4900782e51a9c2681394ccbb8a7a 100644
--- a/content/2.defense-systems/shosta.md
+++ b/content/2.defense-systems/shosta.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF02481
---
# ShosTA
@@ -50,3 +51,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/sofic.md b/content/2.defense-systems/sofic.md
index b8d6f66dd993693cf05d68558fb11782daee647a..a8d3ab5928e4a47dc5946072455a158bd2a6cf7c 100644
--- a/content/2.defense-systems/sofic.md
+++ b/content/2.defense-systems/sofic.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF02661, PF13784
---
# SoFIC
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/spbk.md b/content/2.defense-systems/spbk.md
index 221db9e4040a62b7b72934d3023cc6a05e70444d..f43df459e39cd982537eca3f1a996263f59525c4 100644
--- a/content/2.defense-systems/spbk.md
+++ b/content/2.defense-systems/spbk.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF13676
---
# SpbK
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/sspbcde.md b/content/2.defense-systems/sspbcde.md
index 38618b531f256479107329630e1447db90d1e574..c79f2d34ea9dadce2320ca05b3c06573716877bc 100644
--- a/content/2.defense-systems/sspbcde.md
+++ b/content/2.defense-systems/sspbcde.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Detecting invading nucleic acid
Activator: Direct
Effector: Nucleic acid degrading
+ PFAM: PF01507, PF01580, PF03235, PF07510, PF13182
---
# SspBCDE
@@ -53,3 +54,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/stk2.md b/content/2.defense-systems/stk2.md
index 0cd7d51e1aa4520a137ab36e052635783c3ddb68..e9e59a5d8b184f7f7e522cfb0c40f70f403d2375 100644
--- a/content/2.defense-systems/stk2.md
+++ b/content/2.defense-systems/stk2.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Sensing of phage protein
Activator: Direct
Effector: Other (protein modifying)
+ PFAM: PF00069, PF07714
---
# Stk2
@@ -57,3 +58,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/thoeris.md b/content/2.defense-systems/thoeris.md
index 8ccf5b662570c39e4e6966335a9664bef49f4a3f..be35be5d0868ea4667c5aa7602e85053e1bd687e 100644
--- a/content/2.defense-systems/thoeris.md
+++ b/content/2.defense-systems/thoeris.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Signaling
Effector: Nucleotide modifying
+ PFAM: PF08937, PF13289, PF18185
---
# Thoeris
@@ -55,3 +56,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/tiamat.md b/content/2.defense-systems/tiamat.md
index 0959ef39d2d762428cb66b959ef1d886f39e9290..bafd49c353b1c7f0afc5544b3d1d615d8eb41e3e 100644
--- a/content/2.defense-systems/tiamat.md
+++ b/content/2.defense-systems/tiamat.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00656, PF13020
---
# Tiamat
@@ -46,3 +47,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/viperin.md b/content/2.defense-systems/viperin.md
index 46a2fdf95f29332e2a2b18f7216d38fabf50bc69..4ac98994c8401a9e1197d0626ed9241e1ea70bff 100644
--- a/content/2.defense-systems/viperin.md
+++ b/content/2.defense-systems/viperin.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Direct
Effector: Nucleotide modifying
+ PFAM: PF04055, PF13353
---
# Viperin
@@ -97,3 +98,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/wadjet.md b/content/2.defense-systems/wadjet.md
index 8fa050f0e5294c211ec6d8ab5d6d46b029896870..a6e658107a60b14d8204f55638241b57e6aeaa5d 100644
--- a/content/2.defense-systems/wadjet.md
+++ b/content/2.defense-systems/wadjet.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Detecting invading nucleic acid
Activator: Direct
Effector: Nucleic acid degrading
+ PFAM: PF09660, PF09661, PF09664, PF09983, PF11795, PF11796, PF11855, PF13555, PF13558, PF13835
---
# Wadjet
@@ -48,3 +49,4 @@ items:
---
::
+
diff --git a/content/2.defense-systems/zorya.md b/content/2.defense-systems/zorya.md
index 6cb8efbec5d72455f183d7b2538566e834523e53..007f41ab14429154ad26324aae03f988dd5ec4f2 100644
--- a/content/2.defense-systems/zorya.md
+++ b/content/2.defense-systems/zorya.md
@@ -8,6 +8,7 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: PF00176, PF00271, PF00691, PF04851, PF15611
---
# Zorya
@@ -55,3 +56,4 @@ items:
---
::
+