Some important URL's for the databases

Protein Sequence (Primary)
SWISS-PROT a curated protein sequence database which strives to provide a high level of annotation, a minimal level of redundancy and high level of integration with other databases.
The ExPASy ( Ex pert P rotein A nalysis Sy stem) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE
PIR Protein Information resource:
The Entrez protein database
International Protein Index (IPI) proteomes of higher eukaryotic organisms.
MIPS Munich Information Center for protein Sequences
PEDANT - Protein Extraction, Description and ANalysis Tool
PROSITE Database of protein families and domains
Pfam common protein domains and families

Protein sequence (Composite)
OWL
NRDB

Protein sequence (Secondary)
PROSITE
Motif
Motif
PRINTS
Pfam

Macromolecular structures
Protein Data Bank (PDB)
Nucleic Acids Database (NDB)
HIV Protease Database
ReLiBase
PDBsum
CATH
SCOP
FSSP

Nucleotide sequences
Genbank
EMBL
DDBJ

Genome Sequences
Entrez Genomes
Complete Microbial Genomes Entrez Microbial Genome Database
TIGR The Institute for Genomic Research
COGs Cluster of Orthologous Groups
KEGG Kyoto Encyclopedia of Genes and Genomes
SGD Saccharomyces Genome Database
Database resources of Sanger
IRGSP The International Rice Genome Sequencing Project
ENSEMBL Eukaryotic Genomes
FLYBASE A Database of the Drosophila Genome
Maize Genetics/Genomics Database project
UK Cropnet Database Collection of crop and other databases
The Gramene Genome Browser is a web-based tool for viewing annotations mapped to plant (in particular cereal) genomes and physical maps.
Beauv Brachypodium distachyon (L.)
GrainGenes collection Wheat Genome database
LIS The Legume Information System
The SOL Genomics Network for species in the Euasterid clade, including the families Solanaceae
CyanoBase The genome databse for Cyanobacteria
SubtiList : dedicated to the genome of Bacillus subtilis 168, supplemented with observations made at the Institut Pasteur
Colibri : dedicated to the genome of Escherichia coli K-12, with revised feature annotations from EcoGene provided by Kenn Rudd
PyloriGene : dedicated to the genomes of Helicobacter pylori 26695 and J99, supplemented with observations made at the Institut Pasteur
MypuList : dedicated to the genome of Mycoplasma pulmonis UAB CTIP
Leproma : dedicated to the genome of Mycobacterium leprae .
BoviList : dedicated to the genome of Mycobacterium bovis .
TubercuList Analysis of the genomes of the tubercle bacilli
MGI Mouse Genome Informatics
ZFIN The Zebrafish Information Network
WormBase Worms database
GermOnline Germ cell growth and differentiation knowledgebase
ChromDB The Plant Chromatin Database
PlantsP Functional Genomics of Plant phosphorylation
BDGP Berkeley Drosophila Genome Project
Pseudomonas genome project Pseudomonas aeruginosa genome database
CYGD Comprehensive yeast genome database
Rat Genome Database Rat Genome Sequencing Consortium
Histone Sequence Database A comprehensive resource for histones and histone fold-containing proteins
Candida Genome Database a resource for genomic sequence data and gene and protein information for Candida albicans
Calcivirus Sequence Database Information on Calcivirus
HGVbase (the Human Genome Variation Database) Comprehensive catalog of normal human gene and genome variation
Ape Genome Sequence Silver Project database
HIV Sequence database
Genomes Online Database (GOLD) comprehensive access to information regarding complete and ongoing genome projects around the world.
VirGen A Comprehensive Viral Genome Resource
ISD The Influenza Sequence Database

Integrated Databases
InterPro
Sequence retrieval system (SRS)
Entrez
Integrated rice science database

Microarray-databases
ArrayExpress (European Bioinformatic Institute)
Gene Expression Omnibus (National Center for Biotechnology Information)
maxd (Univ. of Manchester)
SMD (Univ. of Stanford)
GPX (Scottish Centre for Genomic Technology and Informatics)

Protein Interactions
The General Repository for Interaction Datasets (The GRID) (Samuel Lunenfeld Research Institute) for protein-protein interaction
DIP : For protein – protein interaction
Transfac : For protein – DNA interaction

Pathway Databases
Metacyc : Reaction pathways for organisms other than E.coli
Ecocyc : Encyclopedia of E. coli Genes and Metabolism
BRENDA : For enzymatic catalysis
EMP : Enzyme and Metabolic Pathway
WIT : Pathway construction
MGDB : Microbial Genome Database
KEGG : Kyoto Encyclopedia of Genes and Genomes: Metabolic Pathways
LIGAND : Chemical Database for Enzyme Reactions
SPAD : Signaling Pathway Database
BRITE : Biomolecular Reaction pathways for Information Transfer and Expression