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258  structures 6903  species 23  interactions 32875  sequences 202  architectures

Clan: Met_repress (CL0057)


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 37 families and the total number of domains in the clan is 32875. 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


This clan contains the following 37 member families:

Arc BrnA_antitoxin CcdA CopG_antitoxin DndE DUF1778 DUF1902 DUF2540 DUF2610 HicB HicB-like_2 HicB_lk_antitox MatP_C MetJ Omega_Repress ParB_C ParD ParD_antitoxin ParD_like ParG Plasmid_stab_B PSK_trans_fac RelB RepB-RCR_reg Repressor_Mnt RHH_1 RHH_3 RHH_4 RHH_5 RHH_6 RHH_7 RHH_8 SeqA_N TraY VAPB_antitox 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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The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
RHH_1 (PF01402) 6771 (20.6%) View
HicB_lk_antitox (PF15919) 4175 (12.7%) View
RelB (PF04221) 2807 (8.5%) View
ParD_antitoxin (PF03693) 2455 (7.5%) View
HicB (PF05534) 1902 (5.8%) View
BrnA_antitoxin (PF14384) 1752 (5.3%) View
RHH_4 (PF13467) 1718 (5.2%) View
DUF1778 (PF08681) 1509 (4.6%) View
VapB_antitoxin (PF09957) 1404 (4.3%) View
Arc (PF03869) 1097 (3.3%) View
ParD_like (PF11903) 918 (2.8%) View
CopG_antitoxin (PF12441) 836 (2.5%) View
CcdA (PF07362) 807 (2.5%) View
PSK_trans_fac (PF07704) 668 (2.0%) View
VAPB_antitox (PF02697) 416 (1.3%) View
RHH_5 (PF07878) 413 (1.3%) View
MetJ (PF01340) 391 (1.2%) View
SeqA_N (PF17206) 372 (1.1%) View
RHH_8 (PF17723) 364 (1.1%) View
Pfam family Num. domains Alignment
RHH_3 (PF12651) 349 (1.1%) View
DndE (PF08870) 334 (1.0%) View
MatP_C (PF17414) 276 (0.8%) View
DUF1902 (PF08972) 212 (0.6%) View
TraY (PF05509) 164 (0.5%) View
ParG (PF09274) 148 (0.5%) View
ParD (PF09386) 133 (0.4%) View
ParB_C (PF18064) 101 (0.3%) View
RHH_6 (PF16762) 82 (0.2%) View
HicB-like_2 (PF15970) 80 (0.2%) View
RepB-RCR_reg (PF10723) 59 (0.2%) View
DUF2610 (PF11020) 49 (0.1%) View
Plasmid_stab_B (PF10784) 47 (0.1%) View
Omega_Repress (PF07764) 23 (0.1%) View
VirC2 (PF07181) 16 (0.0%) View
RHH_7 (PF16777) 14 (0.0%) View
Repressor_Mnt (PF11423) 8 (0.0%) View
DUF2540 (PF10802) 5 (0.0%) View
Total: 37 Total: 32875 Clan alignment

Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.

Family relationships

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

Species distribution

Tree controls


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



There are 23 interactions for this clan. More...

Interacting families
Arc Arc
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
ParG ParG
Plasmid_stab_B Plasmid_stab_B
RelB ParE_toxin
RepB-RCR_reg RepB-RCR_reg
Repressor_Mnt Arc
RHH_1 NikR_C


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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