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1504  structures 9237  species 0  interactions 170158  sequences 1341  architectures

Clan: HHH (CL0198)


Helix-hairpin-helix superfamily Add an annotation

This superfamily includes Helix-hairpin-helix DNA-binding domains.

This clan contains 23 families and the total number of domains in the clan is 170158. The clan was built by A Bateman.

Literature references

  1. Doherty AJ, Serpell LC, Ponting CP; , Nucleic Acids Res 1996;24:2488-2497.: The helix-hairpin-helix DNA-binding motif: a structural basis for non-sequence-specific recognition of DNA. PUBMED:8692686 EPMC:8692686
  2. Shao X, Grishin NV; , Nucleic Acids Res 2000;28:2643-2650.: Common fold in helix-hairpin-helix proteins. PUBMED:10908318 EPMC:10908318


This clan contains the following 23 member families:

Cdd1 DNA_pol_B_N DNA_pol_lambd_f DUF3173 DUF3701 DUF4332 DUF655 HHH HhH-GPD HHH_2 HHH_3 HHH_4 HHH_5 HHH_6 HHH_7 HHH_8 HHH_9 IMS_HHH PsbU RNA_pol_A_CTD T2SSK TfoX_C Transposase_20

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
HhH-GPD (PF00730) 29081 (17.1%) View
HHH_5 (PF14520) 27835 (16.4%) View
HHH_3 (PF12836) 16747 (9.8%) View
HHH (PF00633) 16414 (9.6%) View
HHH_6 (PF14579) 14234 (8.4%) View
Transposase_20 (PF02371) 12117 (7.1%) View
HHH_2 (PF12826) 10898 (6.4%) View
RNA_pol_A_CTD (PF03118) 8908 (5.2%) View
HHH_9 (PF17674) 7727 (4.5%) View
IMS_HHH (PF11798) 6389 (3.8%) View
HHH_8 (PF14716) 5824 (3.4%) View
HHH_4 (PF14490) 3275 (1.9%) View
Pfam family Num. domains Alignment
DNA_pol_lambd_f (PF10391) 3219 (1.9%) View
T2SSK (PF03934) 2124 (1.2%) View
HHH_7 (PF14635) 1953 (1.1%) View
TfoX_C (PF04994) 1108 (0.7%) View
DUF4332 (PF14229) 746 (0.4%) View
Cdd1 (PF11731) 394 (0.2%) View
DNA_pol_B_N (PF18094) 306 (0.2%) View
DUF655 (PF04919) 286 (0.2%) View
DUF3701 (PF12482) 234 (0.1%) View
PsbU (PF06514) 193 (0.1%) View
DUF3173 (PF11372) 146 (0.1%) View
Total: 23 Total: 170158 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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