Here are some links to relevant web pages:

Personal Pages

Ian Paulsen's Lab Wiki
Milton Saier's Web Page

Relevant Sites

E. coli index
EcoCyc
NCBI
MIPS
Colibri
Subtilist
EBI

Databases

COG Database
PDB Protein Data Bank
PFam Protein Families
Prosite Protein Patterns
Blocks Protein Domains
ProDom Protein Domains

Genomes

TIGR
NCBI Genomes
Baylor College of Medicine
CalTech
Lawrence Berkeley National Laboratory
Sanger Center
University of Washington
Washington University