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134  structures 1598  species 0  interactions 52547  sequences 787  architectures

Clan: HMG-box (CL0114)


HMG-box like superfamily Add an annotation

This clan includes the DNA-binding HMG-box proteins as well as the YABBY-like transcription factors.

This clan contains 8 families and the total number of domains in the clan is 52547. The clan was built by A Bateman.


This clan contains the following 8 member families:

Ccdc124 CHDNT HMG_box HMG_box_2 HMG_box_5 MATalpha_HMGbox Protamine_like YABBY

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
HMG_box (PF00505) 40204 (76.5%) View
HMG_box_2 (PF09011) 5019 (9.6%) View
CHDNT (PF08073) 2414 (4.6%) View
YABBY (PF04690) 2062 (3.9%) View
Ccdc124 (PF06244) 1628 (3.1%) View
HMG_box_5 (PF14887) 807 (1.5%) View
MATalpha_HMGbox (PF04769) 265 (0.5%) View
Protamine_like (PF06382) 148 (0.3%) View
Total: 8 Total: 52547 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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