Prodoric (http://www.prodoric.de/) is a good database for Prokaryotic gene regulation. It covers quite a few taxa including E. coli.

Try RegulonDB and/or EcoCyc.

You might find this reference interesting as general review of TF databases (inc. bacterial):

Charoensawan V, Wilson D, Teichmann SA. Genomic repertoires of DNA-binding transcription factors across the tree of life. Nucleic Acids Res. 2010 Nov 1;38(21):7364-77. PubMed PMID: 20675356

If you are working with Corynebacteria, E. coli, or Mycobacterium tubercolosis try CoryneRegNet

RhizoRegNet is a similar database for Rhizobia

One of the coolest features of the RegNets is the JavaApplet for rendering regulatory networks. Click the GraphVis button, after searching for a regulatory gene.

If you work with E. coli in particular, you can find a great amount of very useful data here: RegulonDB download page. Hope this helps.

DBTBS is a database of transcription factors for Bacillus subtilis.

Try CollecTF, a database of transcription factor binding sites (TFBS) in the Bacteria domain.

And here is a new algorithm for de-novo prediction of TFBS in prokaryotes. They also use some of the databases mentioned here before as sources for their validation.

Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes Shaoqiang Zhang, Shan Li, Phuc T Pham and Zhengchang Su

I have more or less the same problem. Nevertheless, I found the model organism of my bacteria and I can see the information on it. The big deal is I can just see the information and search the similar sequence manually but not compare my file including my genome and obtain the results automatically. That take very long time and is not possible of all do. Someone has a method to do this?

RegPrecise (http://regprecise.lbl.gov) is a web resource for collection, visualization and analysis of transcriptional regulons reconstructed by comparative genomics.

quite awesome!