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1809  structures 2160  species 82  interactions 43410  sequences 491  architectures

Clan: S5 (CL0329)

Summary

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 17 families and the total number of domains in the clan is 43410. 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

Members

This clan contains the following 17 member families:

ChlI DNA_gyraseB DNA_mis_repair EFG_IV Fae GalKase_gal_bdg GHMP_kinases_N IGPD Lon_C LpxC 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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Alignments

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

Pfam family Num. domains Alignment
RNase_PH (PF01138) 6879 (15.8%) View
GHMP_kinases_N (PF00288) 6351 (14.6%) View
EFG_IV (PF03764) 4718 (10.9%) View
Lon_C (PF05362) 3713 (8.6%) View
DNA_gyraseB (PF00204) 3524 (8.1%) View
Ribosomal_S5_C (PF03719) 2898 (6.7%) View
Ribosomal_S9 (PF00380) 2676 (6.2%) View
DNA_mis_repair (PF01119) 2493 (5.7%) View
ChlI (PF13541) 2468 (5.7%) View
UPF0029 (PF01205) 1789 (4.1%) View
IGPD (PF00475) 1637 (3.8%) View
GalKase_gal_bdg (PF10509) 1510 (3.5%) View
Ribonuclease_P (PF00825) 1500 (3.5%) View
LpxC (PF03331) 888 (2.0%) View
Topo-VIb_trans (PF09239) 177 (0.4%) View
Fae (PF08714) 177 (0.4%) View
Xol-1_N (PF09108) 12 (0.0%) View
Total: 17 Total: 43410 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

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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 82 interactions for this clan. More...

Interacting families
A B
AAA Lon_C
AAA_32 Lon_C
DNA_gyraseB DNA_gyraseB
HATPase_c
ECR1_N RNase_PH
EFG_II EFG_IV
EFG_IV EFG_C
Exotox-A_cataly
GTP_EFTU
HABP4_PAI-RBP1
Ribosomal_S7
Ribosomal_S7e
RS4NT
S4
Exotox-A_cataly EFG_IV
Fae Fae
FbpA Topo-VIb_trans
GalKase_gal_bdg GHMP_kinases_C
GHMP_kinases_N
GHMP_kinases_C GHMP_kinases_N
GHMP_kinases_N GHMP_kinases_C
GHMP_kinases_N
GTP_EFTU_D2 EFG_IV
HATPase_c DNA_gyraseB
DNA_mis_repair
Topo-VIb_trans
HATPase_c_3 DNA_mis_repair
IGPD IGPD
KH_1 RNase_PH
Lon_C Lon_C
LpxC LpxC
Mg_chelatase Lon_C
PDZ_2 Lon_C
PNPase RNase_PH
PNPase_C RNase_PH
Ribonuclease_P Ribonuclease_P
Ribosom_S12_S23 EFG_IV
Ribosomal_L5_C Ribosomal_S5_C
Ribosomal_L6 Ribosomal_S5_C
Ribosomal_S10 Ribosomal_S9
Ribosomal_S14 Ribosomal_S9
Ribosomal_S19e Ribosomal_S9
Ribosomal_S2 Ribosomal_S9
Ribosomal_S21e Ribosomal_S5_C
Ribosomal_S27 Ribosomal_S9
Ribosomal_S4 Ribosomal_S5_C
Ribosomal_S5 Ribosomal_S5_C
Ribosomal_S5_C Ribosomal_L6
Ribosomal_S21e
Ribosomal_S4
Ribosomal_S8
Ribosomal_S6e Ribosomal_S9
Ribosomal_S7 Ribosomal_S9
Ribosomal_S8 Ribosomal_S5_C
Ribosomal_S9 DUF258
Ribosomal_L11
Ribosomal_L11_N
Ribosomal_S10
Ribosomal_S14
Ribosomal_S19e
Ribosomal_S25
Ribosomal_S6e
Ribosomal_S7e
WD40
RNase_PH ECR1_N
EXOSC1
KH_1
PNPase
PNPase_C
RNase_PH
RNase_PH_C
RNB
S1
RNase_PH_C RNase_PH
RRF EFG_IV
S1 RNase_PH
Topo-VIb_trans HATPase_c
Topo-VIb_trans
TP6A_N Topo-VIb_trans
ubiquitin Ribosomal_S9
WD40 Ribosomal_S9
Xol-1_N Xol-1_GHMP-like

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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