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1719  structures 5545  species 58  interactions 174117  sequences 3468  architectures

Clan: RNase_H (CL0219)


Ribonuclease H-like superfamily Add an annotation

This clan includes a diverse set of nucleases that share a similar structure to Ribonuclease H.

This clan contains 52 families and the total number of domains in the clan is 174117. The clan was built by A Bateman.

Literature references

  1. Rice P, Craigie R, Davies DR; , Curr Opin Struct Biol. 1996;6:76-83.: Retroviral integrases and their cousins. PUBMED:8696976 EPMC:8696976


This clan contains the following 52 member families:

Arena_ncap_C CAF1 DDE_1 DDE_2 DDE_3 DDE_5 DDE_Tnp_1 DDE_Tnp_1_2 DDE_Tnp_1_3 DDE_Tnp_1_4 DDE_Tnp_1_5 DDE_Tnp_1_6 DDE_Tnp_1_7 DDE_Tnp_2 DDE_Tnp_4 DDE_Tnp_IS1 DDE_Tnp_IS1595 DDE_Tnp_IS240 DDE_Tnp_IS66 DDE_Tnp_ISAZ013 DDE_Tnp_ISL3 DNA_pol_A_exo1 DNA_pol_B_exo1 DNA_pol_B_exo2 DUF2779 DUF3882 DUF4152 DUF5051 Maelstrom MULE NurA OrfB_IS605 Piwi Plant_tran Pox_A22 RNase_H RNase_H_2 RNase_HII RNase_T RNaseH_like RuvC rve rve_2 rve_3 RVT_3 Taq-exonuc Terminase_3C Terminase_6C Transposase_1 Transposase_mut UPF0236 Ydc2-catalyt

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
rve (PF00665) 27128 (15.6%) View
RNase_T (PF00929) 17169 (9.9%) View
DDE_3 (PF13358) 9829 (5.6%) View
DDE_Tnp_1 (PF01609) 9422 (5.4%) View
DNA_pol_A_exo1 (PF01612) 9146 (5.3%) View
RNase_H (PF00075) 6832 (3.9%) View
DDE_Tnp_4 (PF13359) 6329 (3.6%) View
RVT_3 (PF13456) 5939 (3.4%) View
RNase_HII (PF01351) 5711 (3.3%) View
DDE_1 (PF03184) 5596 (3.2%) View
MULE (PF10551) 5511 (3.2%) View
Piwi (PF02171) 5084 (2.9%) View
OrfB_IS605 (PF01385) 5054 (2.9%) View
Transposase_mut (PF00872) 4726 (2.7%) View
DNA_pol_B_exo1 (PF03104) 4631 (2.7%) View
CAF1 (PF04857) 3640 (2.1%) View
DDE_Tnp_1_7 (PF13843) 3604 (2.1%) View
DDE_Tnp_ISL3 (PF01610) 3544 (2.0%) View
RuvC (PF02075) 3534 (2.0%) View
DDE_Tnp_IS66 (PF03050) 3057 (1.8%) View
DDE_Tnp_1_2 (PF13586) 2855 (1.6%) View
rve_3 (PF13683) 2791 (1.6%) View
DDE_Tnp_IS1595 (PF12762) 2682 (1.5%) View
Plant_tran (PF04827) 1945 (1.1%) View
DDE_Tnp_1_6 (PF13751) 1937 (1.1%) View
DDE_5 (PF13546) 1907 (1.1%) View
DDE_Tnp_IS240 (PF13610) 1738 (1.0%) View
Pfam family Num. domains Alignment
DDE_Tnp_1_4 (PF13701) 1676 (1.0%) View
RNase_H_2 (PF13482) 1416 (0.8%) View
Terminase_6C (PF17289) 1058 (0.6%) View
Transposase_1 (PF01359) 1049 (0.6%) View
DDE_Tnp_1_3 (PF13612) 1042 (0.6%) View
rve_2 (PF13333) 861 (0.5%) View
DDE_Tnp_IS1 (PF03400) 782 (0.4%) View
DDE_Tnp_ISAZ013 (PF07592) 720 (0.4%) View
DNA_pol_B_exo2 (PF10108) 605 (0.3%) View
DDE_Tnp_1_5 (PF13737) 591 (0.3%) View
NurA (PF09376) 522 (0.3%) View
UPF0236 (PF06782) 431 (0.2%) View
DUF5051 (PF16473) 412 (0.2%) View
RNaseH_like (PF04308) 336 (0.2%) View
DUF2779 (PF11074) 318 (0.2%) View
Terminase_3C (PF17288) 296 (0.2%) View
Ydc2-catalyt (PF09159) 243 (0.1%) View
Maelstrom (PF13017) 220 (0.1%) View
DDE_2 (PF02914) 92 (0.1%) View
DDE_Tnp_2 (PF04693) 48 (0.0%) View
Taq-exonuc (PF09281) 21 (0.0%) View
Pox_A22 (PF04848) 15 (0.0%) View
DUF4152 (PF13680) 13 (0.0%) View
DUF3882 (PF07066) 5 (0.0%) View
Arena_ncap_C (PF17290) 4 (0.0%) View
Total: 52 Total: 174117
No alignment ℹ

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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...



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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