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234  structures 1338  species 21  interactions 6188  sequences 83  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 29 families and the total number of domains in the clan is 6188. 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 29 member families:

Arc BrnA_antitoxin CcdA CopG_antitoxin DUF1778 DUF1902 DUF2540 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 VirC2

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) 1508 (24.4%) View
HicB_lk_antitox (PF15919) 951 (15.4%) View
RelB (PF04221) 666 (10.8%) View
HicB (PF05534) 391 (6.3%) View
ParD_antitoxin (PF03693) 376 (6.1%) View
DUF1778 (PF08681) 328 (5.3%) View
BrnA_antitoxin (PF14384) 292 (4.7%) View
VapB_antitoxin (PF09957) 250 (4.0%) View
RHH_4 (PF13467) 246 (4.0%) View
Arc (PF03869) 180 (2.9%) View
ParD_like (PF11903) 164 (2.7%) View
CcdA (PF07362) 139 (2.2%) View
RHH_5 (PF07878) 128 (2.1%) View
CopG_antitoxin (PF12441) 102 (1.6%) View
PSK_trans_fac (PF07704) 98 (1.6%) View
continued
Pfam family Num. domains Alignment
MetJ (PF01340) 97 (1.6%) View
RHH_3 (PF12651) 89 (1.4%) View
DUF1902 (PF08972) 43 (0.7%) View
TraY (PF05509) 35 (0.6%) View
ParG (PF09274) 28 (0.5%) View
HicB-like_2 (PF15970) 17 (0.3%) View
DUF2610 (PF11020) 15 (0.2%) View
RepB-RCR_reg (PF10723) 15 (0.2%) View
ParD (PF09386) 12 (0.2%) View
Omega_Repress (PF07764) 6 (0.1%) View
DUF2540 (PF10802) 5 (0.1%) View
VirC2 (PF07181) 3 (0.0%) View
RHH_7 (PF16777) 3 (0.0%) View
REGB_T4 (PF10715) 1 (0.0%) View
Total: 29 Total: 6188 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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