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Aminoacyl-tRNA synthetase sequences
ABC transporters
A database of the AraC/XylS protein family of positive regulators in bacteria.
Artificial Selected Proteins/Peptides Database
Cold shock domain-containing proteins
Annotated coding sequences from Arabidopsis
DEAD-box, DEAH-box, and DExH-box proteins
Database of Interacting Proteins
Endogenous GPCR List
G protein-coupled receptors; expression in cell lines
Esterases and alpha/beta hydrolase enzymes and relatives
Proteins with experimentally-verified function
Low-complexity or compositionally-biased protein sequences
Escherichia coli K-12 genome, gene products, and homologs
G protein-coupled receptors
Histone and histone fold sequences and structures
HIV epitopes
HIV reverse transcriptase and protease sequences
Information relevant to homeobox proteins, classification, and evolution
Homeodomain sequences, structures, and related genetic and genomic information
Large (>50 kDa) human proteins and cDNA sequences
Olfactory receptor genes and proteins
Immunoglobulin, T cell receptor, and MHC sequences from human and other vertebrates
Polymorphic sequences of human MHC and related genes
Major histocompatibility complex sequences
All known inteins (protein splicing elements): properties, sequences, bibliography
Protein families and domains
Sequences of proteins of immunological interest
Ligand-gated ion channel subunit sequences
Integrated information on sequence, structure, and function of lipases and esterases
Proteolytic enzymes (proteases/peptidases)
Integrated protein family information
  Metalloprotein Database and Browser 
Metal-binding sites in metalloproteins
MHC-binding peptides
Nuclear Protein Database (NPD) 
Proteins localized in the nucleus
Nuclear Receptor Resource 
Nuclear receptor superfamily
Nuclear hormone receptors
Sequences for lfactory receptor-like molecules
Transcription factors and gene expression
Peptaibol (antibiotic peptide) sequences
Protein phosphorylation sites
Non-redundant reference database with comprehensive protein sequences
Protein kinase sequences, enzymology, genetics, and molecular and structural properties.
Plant protease inhibitors
Functional geomics databases focusing on protein involved in plant phosphorylation and membrane transport, respectively
Protein Mutant database
Arabidopsis plasma membrane protein sequence and expression data
Protein Motif fingerprint database
Protein domain db (Automatically generated)
Protein-Protein interaction database
 An automatic hierarchical classification of Swiss-Prot proteins
Proteases and natural and synthetic protease inhibitors
Prosthetic centers and metal ions in protein active sites
PROSITE dictionary of protein sites and patterns
Comprehensive, annotated, non-redundant protein sequence databases
RNase P sequences, alignments, and structures
Nuclear scaffold/matrix attached regions
 SBASE domain db
Sequences, structures, and IgE epitopes of allergenic proteins
Sensory signal transduction proteins
7-transmembrane helix receptors
Curated protein sequences
Functional identification of proteins
trEST and trGEN are two databases of hypothetical protein sequences. Hits is a pre-compiled list of domains/signatures predicted on them.
Wnt proteins and phenotypes

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