I have a protein sequence containing a HTH motif. So I want to know is there any particular length or conserve sequence of DNA where it binds? Is there any tools or software available to predict the binding of that particular HTH sequence within the whole genome?
The HTH motif often acts only locally. The TFs block their own transcription, once a substrate if present the TF is released from the HTH motif and the operon gets transcripted into mRNA.
The TFs are not ment to act on the whole genome, they can interfer of course when there is more protein of it present. The motif is highly distinct for the particular TF found close to it.
Look at the programs MEME and MAST. MEME detects putative motifs and MAST allows to search for a pre-defined motif in a whole genome.
http://meme.nbcr.net/meme/doc/mast.html
Look at this website.
There are lot of tools available online as i can see your protein sequence containing HTM motif so you may use the meme program. It uses a statistical expectation maximization technique to find different fixed-width motifs. The BioProspector program uses a Gibbs sampling strategy to detect sequence motifs, and the motifs can be allowed to have variable widths.
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