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4067  structures 9317  species 0  interactions 210855  sequences 1521  architectures

Clan: S5 (CL0329)


Ribosomal protein S5 domain 2-like superfamily Add an annotation

This superfamily contains a wide range of families that possess a structure similar to the second domain of ribosomal S5 protein.

This clan contains 18 families and the total number of domains in the clan is 210855. The clan was built by A Bateman.

Literature references

  1. Ishii R, Nureki O, Yokoyama S;, J Biol Chem. 2003;278:32397-32404.: Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus. PUBMED:12746447 EPMC:12746447


This clan contains the following 18 member families:

ChlI DNA_gyraseB DNA_mis_repair EFG_IV Fae GalKase_gal_bdg GHMP_kinases_N IGPD Lon_C LpxC Morc6_S5 Ribonuclease_P Ribosomal_S5_C Ribosomal_S9 RNase_PH Topo-VIb_trans UPF0029 Xol-1_N

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
RNase_PH (PF01138) 33449 (15.9%) View
GHMP_kinases_N (PF00288) 29307 (13.9%) View
EFG_IV (PF03764) 21771 (10.3%) View
DNA_gyraseB (PF00204) 18233 (8.6%) View
Lon_C (PF05362) 17660 (8.4%) View
ChlI (PF13541) 13165 (6.2%) View
Ribosomal_S5_C (PF03719) 12932 (6.1%) View
Ribosomal_S9 (PF00380) 12364 (5.9%) View
DNA_mis_repair (PF01119) 11775 (5.6%) View
IGPD (PF00475) 8422 (4.0%) View
UPF0029 (PF01205) 7903 (3.7%) View
Ribonuclease_P (PF00825) 7475 (3.5%) View
GalKase_gal_bdg (PF10509) 7191 (3.4%) View
LpxC (PF03331) 4671 (2.2%) View
Morc6_S5 (PF17942) 3117 (1.5%) View
Fae (PF08714) 753 (0.4%) View
Topo-VIb_trans (PF09239) 649 (0.3%) View
Xol-1_N (PF09108) 18 (0.0%) View
Total: 18 Total: 210855 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...



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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