▣ DNA Sequence Databases

DDBJ - DNA Data Bank of Japan (National Institute of Genetics)
GSDB - Genome Sequence Database (National Center for Genome Resources)
International Nucleotide Sequence Database Collaboration
NCBI - National Center for Biotechnology Information
NDB - Nucleic Acid Database Project
Tree of Life - phylogeny and biodiversity

▣ Protein Sequence and Structure Databases

▣ Integrated Genome Databases

ACEDB - Caenorhabditis elegans database (documentation)
ACEMBLY - an ACEDB program for sequence display & editing
DBGET/LinkDB - search 19 DNA, protein and gene databases
GenoBase - search EMBL, SwissPro, Prosite and Enzyme databanks
Heterogeneous Database Management Systems
IGD - Integrated Genome Database

▣ Metabolic Pathways

EMP Compound and EMP Pathways - Selkov Enzyme and Metabolic Pathway Database
SoyBase Metabolic Database
KEGG - Kyoto Encyclopedia of Genes and Genomes

▣ Enzymes

E.C. Enzyme Database
ENZYME - enzyme nomenclature database
Enzyme Structures Database - structures of enzymes deposited in the PDB
ReBase - restriction enzyme database

▣ Mutations

Breast Cancer Mutation Database (BIC)
Cystic Fibrosis Mutation Database
PAHDB - PAH Mutation Database
TBASE - transgenic/targeted mutation database
von Willebrand Factor (vWF) Database

▣ Transcription Factors

TRANSFAC - transcription factor database
TFFACTOR and TFSITE - transcription factor data
TRRD - Transcription Regulatory Regions Database

▣ Vectors

Vector-DB

▣ Organelles

MitoDat - Mendelian inheritance and the mitochondrion
GOBASE - organelle genome database

▣ Miscellaneous Databases

▣ EST Data: Public-Domain Sites

▣ Genomic Sequencing Projects

▣ Gene Mapping

▣ Human Chromosome-Specific

▣ Model Organisms

▣ Microbial Genomics

Bugs 'n Stuff
EcoCyc - encyclopedia of E. coli genes and metabolism
Glossary of Microbiology
GeneQuiz
TIGR Microbial Database