Summary: Helix-hairpin-helix domain
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Helix-hairpin-helix domain Provide feedback
No Pfam abstract.
Sawaya MR, Pelletier H, Kumar A, Wilson SH, Kraut J;, Science. 1994;264:1930-1935.: Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism. PUBMED:7516581 EPMC:7516581
Internal database links
|Similarity to PfamA using HHSearch:||HHH HHH_5|
External database links
This tab holds annotation information from the InterPro database.
No InterPro data for this Pfam family.
- 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 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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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Number in seed:||264|
|Number in full:||8280|
|Average length of the domain:||67.60 aa|
|Average identity of full alignment:||47 %|
|Average coverage of the sequence by the domain:||13.47 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||2|
|Download:||download the raw HMM for this family|
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The tree shows the occurrence of this domain across different species. More...
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There are 7 interactions for this family. 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 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_8 domain has been found. There are 327 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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