Here are some databases of interest from the NAR summary issue on databases and Bioinformatics tools.
url: http://nar.oxfordjournals.org/content/vol35/suppl_1/index.shtml?etoc


SGDB: a database of synthetic genes re-designed for optimizing protein
over-expression
Gang Wu, Yuanpu Zheng, Imran Qureshi, Htar Thant Zin, Tyler Beck, Blazej Bulka, and Stephen J. Freeland
Nucl. Acids Res. 2007 35: D76-D79.
http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D76?etoc


VISTA Enhancer Browser--a database of tissue-specific human enhancers
Axel Visel, Simon Minovitsky, Inna Dubchak, and Len A. Pennacchio
Nucl. Acids Res. 2007 35: D88-D92.
http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D88?etoc



The ASAP II database: analysis and comparative genomics of alternative
splicing in 15 animal species
Namshin Kim, Alexander V. Alekseyenko, Meenakshi Roy, and Christopher Lee
Nucl. Acids Res. 2007 35: D93-D98.
http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D93?etoc




The Universal Protein Resource (UniProt)
The UniProt Consortium
Nucl. Acids Res. 2007 35: D193-D197.
http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D193?etoc



FireDB--a database of functionally important residues from proteins of
known structure
Gonzalo Lopez, A. Valencia, and M. Tress
Nucl. Acids Res. 2007 35: D219-D223.
http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D219?etoc



Phospho3D: a database of three-dimensional structures of protein
phosphorylation sites
Andreas Zanzoni, Gabriele Ausiello, Allegra Via, Pier Federico Gherardini, and Manuela Helmer-Citterich
Nucl. Acids Res. 2007 35: D229-D231.
http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D229?etoc



There are many more: check out http://nar.oxfordjournals.org/content/vol35/suppl_1/index.shtml?etoc