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141  structures 5328  species 8  interactions 22334  sequences 462  architectures

Clan: His-Me_finger (CL0263)


His-Me finger endonuclease superfamily Add an annotation

This superfamily defined originally by SCOP contains a diverse range of endonucleases. Later Grishin identified the MH1 domain as belonging to the superfamily [1].

This clan contains 19 families and the total number of domains in the clan is 22334. The clan was built by A Bateman.

Literature references

  1. Grishin NV; , J Mol Biol. 2001;307:31-37.: Mh1 domain of Smad is a degraded homing endonuclease. PUBMED:11243801 EPMC:11243801


This clan contains the following 19 member families:

AHH Colicin-DNase DUF1524 Endonuclea_NS_2 Endonuclease_1 Endonuclease_7 Endonuclease_NS GH-E HNH HNH_2 HNH_3 HNH_4 HNH_5 ICEA LHH MH1 NinG WHH zf-His_Me_endon

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
HNH (PF01844) 7400 (33.1%) View
DUF1524 (PF07510) 2469 (11.1%) View
Endonuclease_NS (PF01223) 2367 (10.6%) View
HNH_2 (PF13391) 1540 (6.9%) View
Endonuclease_1 (PF04231) 1440 (6.4%) View
HNH_3 (PF13392) 1385 (6.2%) View
MH1 (PF03165) 1320 (5.9%) View
Endonuclea_NS_2 (PF13930) 1121 (5.0%) View
HNH_4 (PF13395) 798 (3.6%) View
NinG (PF05766) 590 (2.6%) View
Colicin-DNase (PF12639) 525 (2.4%) View
AHH (PF14412) 340 (1.5%) View
Endonuclease_7 (PF02945) 283 (1.3%) View
WHH (PF14414) 277 (1.2%) View
HNH_5 (PF14279) 136 (0.6%) View
LHH (PF14411) 102 (0.5%) View
GH-E (PF14410) 101 (0.5%) View
zf-His_Me_endon (PF05551) 70 (0.3%) View
ICEA (PF05315) 70 (0.3%) View
Total: 19 Total: 22334 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 8 interactions for this clan. More...

Interacting families
Endonuclease_1 Endonuclease_1
Endonuclease_7 Endonuclease_7
Endonuclease_NS Endonuclease_NS
HNH Colicin_Pyocin


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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