DNA motif database / no TF - database of DNA motifs for binding of DNA replication proteins (Nov/14/2008 )

Hi everybody,
i have a nice set of genomic DNA sequences out of a genomic screen. I want to look for sequence motifs potentially "coding" for binding regions of proteins involved in DNA replication (e.g. DNA polymerases, PCNA etc. or Telomerase proteins). However, there are thousands of databases for transcription factor binding sites but I did not find a single one for other DNA binding proteins.
Does anybody know a databas for DNA sequence motifs for DNA proteins other than Transcription factors?

Thanks for any answer,

Axel

Axel[/quote]

Any protein that shows one of these motifs is a DNA binding protein.
1. helix-turn-helix motif
2. helix-loop-helix motif
3. leucine zipper motif
4. zinc finger motif

It is the specific transcription factors from these families that bind to specific DNA sequences, and then they recruit the co-factors, which do not require specific DNA motifs. They bind to the transcription factors primarily.
[/quote]


Hi,
thanks for your answer, but I do not want to look for motifs in proteins. I ask for initiation sites encoded by a specific DNA sequence motif for protzeins involved in DNA replication. For E.coli for example the Rep1-3 protein have some initiation sites. But to my knowledge there are no equivalent proteins in human. Searching the literature one can find lots of proteins involved in DNA replication like PCNA and others, but I did not find DNA sequnce motifs.
The question for me is: Do DNA sequences exist, that code for initiation sites for DNA binding proteins others than transcription factors and exist databases like that for the transcription factor binding sites.

thanks again for answers,

Axel