MIPModDB: a central resource for the superfamily of major intrinsic proteins

Abstract

The channel proteins belonging to the major intrin-sic proteins (MIP) superfamily are diverse and are found in all forms of life. Water-transporting aquaporin and glycerol-specific aquaglyceroporin are the prototype members of the MIP superfamily. MIPs have also been shown to transport other neu-tral molecules and gases across the membrane. They have internal homology and possess con-served sequence motifs. By analyzing a large num-ber of publicly available genome sequences, we have identified more than 1000 MIPs from di-verse organisms. We have developed a database MIPModDB which will be a unified resource for all MIPs. For each MIP entry, this database contains information about the source, gene structure, se-quence features, substitutions in the conserved NPA motifs, structural model, the residues forming the selectivity filter and channel radius profile. For selected set of MIPs, it is possible to derive structure-based sequence alignment and evolution-ary relationship. Sequences and structures of se-lected MIPs can be downloaded from MIPModDB database which is freely available a