From 99407ee9a1679280abdb10e702ae561662219d06 Mon Sep 17 00:00:00 2001
From: ftesson <florian.tesson@pasteur.fr>
Date: Fri, 29 Sep 2023 15:18:39 +0200
Subject: [PATCH] add pfam columns in frontmatter
---
content/2.defense-systems/abi2.md | 5 +++++
content/2.defense-systems/abia.md | 2 ++
content/2.defense-systems/abic.md | 2 ++
content/2.defense-systems/abid.md | 2 ++
content/2.defense-systems/abie.md | 2 ++
content/2.defense-systems/abig.md | 2 ++
content/2.defense-systems/abih.md | 2 ++
content/2.defense-systems/abij.md | 2 ++
content/2.defense-systems/abik.md | 2 ++
content/2.defense-systems/abil.md | 2 ++
content/2.defense-systems/abio.md | 2 ++
content/2.defense-systems/abip2.md | 2 ++
content/2.defense-systems/abiq.md | 2 ++
content/2.defense-systems/abir.md | 2 ++
content/2.defense-systems/abit.md | 2 ++
content/2.defense-systems/abiu.md | 2 ++
content/2.defense-systems/abiv.md | 2 ++
content/2.defense-systems/aditi.md | 2 ++
content/2.defense-systems/avs.md | 2 ++
content/2.defense-systems/azaca.md | 2 ++
content/2.defense-systems/borvo.md | 2 ++
content/2.defense-systems/brex.md | 2 ++
content/2.defense-systems/caprel.md | 2 ++
content/2.defense-systems/card_nlr.md | 2 ++
content/2.defense-systems/cbass.md | 2 ++
content/2.defense-systems/dartg.md | 2 ++
content/2.defense-systems/dctpdeaminase.md | 2 ++
content/2.defense-systems/detocs.md | 2 ++
content/2.defense-systems/dgtpase.md | 2 ++
content/2.defense-systems/disarm.md | 2 ++
content/2.defense-systems/dnd.md | 2 ++
content/2.defense-systems/dodola.md | 2 ++
content/2.defense-systems/dpd.md | 2 ++
content/2.defense-systems/drt.md | 2 ++
content/2.defense-systems/druantia.md | 2 ++
content/2.defense-systems/dsr.md | 2 ++
content/2.defense-systems/eleos.md | 2 ++
content/2.defense-systems/fs_hp_sdh_sah.md | 2 ++
content/2.defense-systems/fs_sma.md | 2 ++
content/2.defense-systems/gabija.md | 2 ++
content/2.defense-systems/gao_her.md | 2 ++
content/2.defense-systems/gao_hhe.md | 2 ++
content/2.defense-systems/gao_iet.md | 2 ++
content/2.defense-systems/gao_mza.md | 2 ++
content/2.defense-systems/gao_qat.md | 2 ++
content/2.defense-systems/gao_rl.md | 2 ++
content/2.defense-systems/gaps2.md | 2 ++
content/2.defense-systems/hachiman.md | 2 ++
content/2.defense-systems/hna.md | 2 ++
content/2.defense-systems/jukab.md | 2 ++
content/2.defense-systems/kiwa.md | 2 ++
content/2.defense-systems/lamassu-fam.md | 2 ++
content/2.defense-systems/lit.md | 2 ++
content/2.defense-systems/mads.md | 2 ++
content/2.defense-systems/mazef.md | 2 ++
content/2.defense-systems/menshen.md | 2 ++
content/2.defense-systems/mok_hok_sok.md | 2 ++
content/2.defense-systems/mokosh.md | 2 ++
content/2.defense-systems/nhi.md | 2 ++
content/2.defense-systems/nlr.md | 2 ++
content/2.defense-systems/old_exonuclease.md | 2 ++
content/2.defense-systems/pago.md | 2 ++
content/2.defense-systems/panchino_gp28.md | 2 ++
content/2.defense-systems/pd-lambda-1.md | 2 ++
content/2.defense-systems/pd-lambda-2.md | 2 ++
content/2.defense-systems/pd-lambda-3.md | 2 ++
content/2.defense-systems/pd-lambda-5.md | 2 ++
content/2.defense-systems/pd-t4-1.md | 2 ++
content/2.defense-systems/pd-t4-2.md | 2 ++
content/2.defense-systems/pd-t4-4.md | 2 ++
content/2.defense-systems/pd-t4-5.md | 2 ++
content/2.defense-systems/pd-t4-6.md | 2 ++
content/2.defense-systems/pd-t4-8.md | 2 ++
content/2.defense-systems/pd-t4-9.md | 2 ++
content/2.defense-systems/pd-t7-2.md | 2 ++
content/2.defense-systems/pd-t7-4.md | 2 ++
content/2.defense-systems/pfiat.md | 2 ++
content/2.defense-systems/phrann_gp29_gp30.md | 2 ++
content/2.defense-systems/pif.md | 2 ++
content/2.defense-systems/prrc.md | 2 ++
content/2.defense-systems/psyrta.md | 2 ++
content/2.defense-systems/pycsar.md | 2 ++
content/2.defense-systems/retron.md | 2 ++
content/2.defense-systems/rexab.md | 2 ++
content/2.defense-systems/rloc.md | 2 ++
content/2.defense-systems/rm.md | 2 ++
content/2.defense-systems/rnlab.md | 2 ++
content/2.defense-systems/rosmerta.md | 2 ++
content/2.defense-systems/rst_2tm_1tm_tir.md | 2 ++
content/2.defense-systems/rst_duf4238.md | 2 ++
content/2.defense-systems/rst_gop_beta_cll.md | 2 ++
content/2.defense-systems/rst_helicaseduf2290.md | 2 ++
content/2.defense-systems/rst_hydrolase-3tm.md | 2 ++
content/2.defense-systems/rst_rt-nitrilase-tm.md | 2 ++
content/2.defense-systems/rst_tir-nlr.md | 2 ++
content/2.defense-systems/sanata.md | 2 ++
content/2.defense-systems/sefir.md | 2 ++
content/2.defense-systems/septu.md | 2 ++
content/2.defense-systems/shango.md | 2 ++
content/2.defense-systems/shedu.md | 2 ++
content/2.defense-systems/shosta.md | 2 ++
content/2.defense-systems/sofic.md | 2 ++
content/2.defense-systems/spbk.md | 2 ++
content/2.defense-systems/sspbcde.md | 2 ++
content/2.defense-systems/stk2.md | 2 ++
content/2.defense-systems/thoeris.md | 2 ++
content/2.defense-systems/tiamat.md | 2 ++
content/2.defense-systems/viperin.md | 2 ++
content/2.defense-systems/wadjet.md | 2 ++
content/2.defense-systems/zorya.md | 2 ++
110 files changed, 223 insertions(+)
diff --git a/content/2.defense-systems/abi2.md b/content/2.defense-systems/abi2.md
index d3c02731..6f8549ec 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 a7055ea9..dfc59ca9 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 cc1dd91b..aa9f9f39 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 0ae3b82f..41f5e4b6 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 23d85dda..b6b5fac0 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 7a013fbd..56d3ffb4 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 333517d5..c03615df 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 83dfbe0e..b2e9663d 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 6923486b..e8646b5d 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 3dee3534..dedac392 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 d89e1c5c..c445c3c4 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 1156872d..d3882bf2 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 f9438c7c..c1a35984 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 996b6ac5..f6192898 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 b1865fe5..745ffd70 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 96aba147..aab3cac1 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 eefbabd3..9264f4ba 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 f458596b..7cf40394 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 5b66512b..badac00d 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 c106da47..68d72594 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 4f2b3b35..204dda16 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 e9cb8dd0..00a9a263 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 1ad55442..0af2ca37 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 8cc15bd7..10d7c959 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 8a16ae01..0283bb78 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 ebe19f6d..43360126 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 563e14d0..76e0ef11 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 4fa1a737..f85fdc51 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 8226a1a3..0002507c 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 0ad07b78..fd21a80e 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 79d1ed31..bb5b8f40 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 367f760d..546c3eb7 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 ff62362f..eb479e92 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 8430ad29..d880cdf3 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 88068ad1..7eaab9cf 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 b4b959f9..165b5832 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 9c114b95..f1738f4d 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 8e64de23..7db0ba9c 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 de46a350..502da111 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 97410e3c..5de114e4 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 1d848a7e..771a2e63 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 9df0702d..77d1201a 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 8b7957a0..d618744e 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 87a59887..546f21f6 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 aa56459f..ad110e33 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 7f4ec5d5..76346a1d 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 4b63ea07..5dda7086 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 71b90a84..ef66cd4e 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 1717a49b..1933e3ce 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 e4c71ee1..55295693 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 044f267b..517226cb 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 628f2f7b..436fcca0 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 63950ee2..fd7f1c62 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 77782681..ef5756d1 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 1ee0682e..a9401491 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 ec508e9f..06f45bc2 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 33a83651..4ba47b49 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 d455ce34..a49346b2 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 0f2ce747..675aa49a 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 d8a572cf..47795fc9 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 069b112f..f87ae962 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 bf67ee06..b0c6c6cb 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 b1d1891b..7af6b020 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 7eda7e6d..2d28cf71 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 44c4f60e..15f2f182 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 70004319..751423dd 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 eef05860..32604e77 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 7d9cdb30..02a95e9c 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 2dd4523e..ccf93b28 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 d0b68a43..68953b39 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 856b8818..d64a4933 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 b47fb45a..59f76420 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 34c7eccf..d0af03b2 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 23424c29..e490e094 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 e2890ee3..08b19589 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 c7693137..a9e79b6b 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 7638ef7d..c12e0eaa 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 3149e458..a9a676db 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 58444a2c..35f6104d 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 317ff23b..2149d38b 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 616000fa..57f20a11 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 7888ee67..14cf0141 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 ab9d432b..88699293 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 46cff76a..23efd871 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 a413fe3a..5b7db799 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 60dd9da7..aa420662 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 0f9acc42..19f5afb7 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 d9ffb12f..8cb81a2e 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 761b4a4f..533f30ce 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 262546f1..95ba0b60 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 22080679..3d11950e 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 d935ef2d..ed03b133 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 00edbe61..de568982 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 a4453e14..fe87e58f 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 c7e52d93..d07a33c7 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 d3867a55..d032f257 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 b6b84790..5d3f6d7a 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 17e4a741..5f7a8218 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 0ce65b43..fd02239b 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 6b939d87..0c365cb3 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 f4b0e62d..02640091 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 b8d6f66d..a8d3ab59 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 221db9e4..f43df459 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 38618b53..c79f2d34 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 0cd7d51e..e9e59a5d 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 8ccf5b66..be35be5d 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 0959ef39..bafd49c3 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 46a2fdf9..4ac98994 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 8fa050f0..a6e65810 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 6cb8efbe..007f41ab 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:
---
::
+
--
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