Summary: Helix-hairpin-helix motif
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Helix-hairpin-helix motif Provide feedback
No Pfam abstract.
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
McDonald SM, Close D, Xin H, Formosa T, Hill CP;, Mol Cell. 2010;40:725-735.: Structure and biological importance of the Spn1-Spt6 interaction, and its regulatory role in nucleosome binding. PUBMED:21094070 EPMC:21094070
Kiely CM, Marguerat S, Garcia JF, Madhani HD, Bahler J, Winston F;, Mol Cell Biol. 2011;31:4193-4204.: Spt6 is required for heterochromatic silencing in the fission yeast Schizosaccharomyces pombe. PUBMED:21844224 EPMC:21844224
Internal database links
|Similarity to PfamA using HHSearch:||HHH_3|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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This superfamily includes Helix-hairpin-helix DNA-binding domains.
The clan contains the following 20 members:Cdd1 DNA_pol_lambd_f DUF3173 DUF4332 DUF655 HHH HhH-GPD HHH_2 HHH_3 HHH_4 HHH_5 HHH_6 HHH_7 HHH_8 IMS_HHH PsbU RNA_pol_A_CTD T2SSK TfoX_C Transposase_20
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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Key: available, not generated, — not available.
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Curation and family details
|Seed source:||Pfam-B_9510 (release 26.0)|
|Author:||Wood V, Coggill P|
|Number in seed:||3|
|Number in full:||587|
|Average length of the domain:||104.70 aa|
|Average identity of full alignment:||41 %|
|Average coverage of the sequence by the domain:||6.97 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||4|
|Download:||download the raw HMM for this family|
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There are 3 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the HHH_7 domain has been found. There are 2 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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