Links:

Primery Databases
Secondary Databases
CMR - Comprehensive Microbial Resource
CBS Genome Atlas Database
Special Databases
RDP - The Ribosomal Database Project
RFAM - RNA families (multiple sequence alignments, consensus secondary structures and covariance models)
GtRNAdb - Genomic tRNA Database (tRNAscan-SE analysis of complete genomes)
Protein Databases
ExPASy Proteomics Server
UniProt
PIR - Protein Information Resource
PEDANT - a Protein Extraction, Description and ANalysis Tool
ProDom
Prosite (Database of protein domains, families and functional sites)