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212  structures 13758  species 21  interactions 115830  sequences 128  architectures

Clan: Met_repress (CL0057)

Summary

MetJ/Arc repressor, antitoxin of TA systems superfamily Add an annotation

This superfamily contains many antitoxin families, all of which carry a ribbon-helix-helix DNA-binding motif with the beta-ribbon located in and recognising the major groove of operator DNA [1].

This clan contains 26 families and the total number of domains in the clan is 115830. The clan was built by A Bateman.

Literature references

  1. Murayama K, Orth P, de la Hoz AB, Alonso JC, Saenger W; , J Mol Biol 2001;314:789-796.: Crystal structure of omega transcriptional repressor encoded by Streptococcus pyogenes plasmid pSM19035 at 1.5 A resolution. PUBMED:11733997 EPMC:11733997
  2. Gerdes K, Maisonneuve E;, Annu Rev Microbiol. 2012;66:103-123.: Bacterial persistence and toxin-antitoxin Loci. PUBMED:22994490 EPMC:22994490

Members

This clan contains the following 26 member families:

Arc BrnA_antitoxin CcdA CopG_antitoxin DUF1778 DUF2610 HicB HicB-like_2 HicB_lk_antitox MetJ Omega_Repress ParD ParD_antitoxin ParD_like ParG PSK_trans_fac REGB_T4 RelB RepB-RCR_reg RHH_1 RHH_3 RHH_4 RHH_5 RHH_7 TraY VapB_antitoxin

External database links

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

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Alignments

The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
RHH_1 (PF01402) 33433 (28.9%) View
VapB_antitoxin (PF09957) 12562 (10.8%) View
DUF1778 (PF08681) 9269 (8.0%) View
RelB (PF04221) 9147 (7.9%) View
PSK_trans_fac (PF07704) 8364 (7.2%) View
HicB_lk_antitox (PF15919) 6480 (5.6%) View
ParD_antitoxin (PF03693) 5379 (4.6%) View
CcdA (PF07362) 4960 (4.3%) View
Arc (PF03869) 3937 (3.4%) View
MetJ (PF01340) 3803 (3.3%) View
HicB (PF05534) 3494 (3.0%) View
ParD_like (PF11903) 2979 (2.6%) View
BrnA_antitoxin (PF14384) 2947 (2.5%) View
RepB-RCR_reg (PF10723) 2077 (1.8%) View
continued
Pfam family Num. domains Alignment
RHH_4 (PF13467) 2013 (1.7%) View
TraY (PF05509) 1409 (1.2%) View
RHH_3 (PF12651) 1053 (0.9%) View
Omega_Repress (PF07764) 521 (0.4%) View
RHH_7 (PF16777) 514 (0.4%) View
CopG_antitoxin (PF12441) 396 (0.3%) View
RHH_5 (PF07878) 326 (0.3%) View
HicB-like_2 (PF15970) 272 (0.2%) View
ParG (PF09274) 243 (0.2%) View
DUF2610 (PF11020) 97 (0.1%) View
ParD (PF09386) 87 (0.1%) View
REGB_T4 (PF10715) 68 (0.1%) View
Total: 26 Total: 115830 Clan alignment
 

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Family relationships

This diagram shows the relationships between members of this clan. More...

Species distribution

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This tree shows the occurrence of the domains in this clan across different species. More...

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Interactions

There are 21 interactions for this clan. More...

Interacting families
A B
Arc Arc
Repressor_Mnt
CcdA CcdA
CcdB CcdA
DUF1778 DUF1778
MetJ MetJ
NikR_C RHH_1
Omega_Repress Omega_Repress
ParD ParD
ParD_antitoxin ParD_antitoxin
ParE_toxin ParD_antitoxin
RelB
ParG ParG
PIN RHH_1
RelB ParE_toxin
RelB
RepB-RCR_reg RepB-RCR_reg
Repressor_Mnt Arc
RHH_1 NikR_C
RHH_1
RHH_4 RHH_4

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

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