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. 2012 Jan;40(Database issue):D362-9.
doi: 10.1093/nar/gkr914. Epub 2011 Nov 12.

MIPModDB: A Central Resource for the Superfamily of Major Intrinsic Proteins

Free PMC article

MIPModDB: A Central Resource for the Superfamily of Major Intrinsic Proteins

Anjali Bansal Gupta et al. Nucleic Acids Res. .
Free PMC article


The channel proteins belonging to the major intrinsic 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 neutral molecules and gases across the membrane. They have internal homology and possess conserved sequence motifs. By analyzing a large number of publicly available genome sequences, we have identified more than 1000 MIPs from diverse 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, sequence 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 evolutionary relationship. Sequences and structures of selected MIPs can be downloaded from MIPModDB database which is freely available at


Figure 1.
Figure 1.
Screenshot of a representative MIP protein, human aquaporin 1. Information about gene structure, substitutions in NPA motif, residues forming the ar/R selectivity filter, sequence similarity with the templates, RMSD calculated for the modeled structure with the three template structures are some of the features reported for a given MIP in the protein page.
Figure 2.
Figure 2.
(A) Superposition of the modeled MIP structure with 1J4N, the structure of bovine aquporin shown in two different orientations, namely, parallel (left) and perpendicular (right) to the channel axis. (B) The four residues of the ar/R selectivity filter superposed on that of 1J4N structure. (C) Comparison of HOLE radius profiles plotted for the water channel (green), glycerol facilitator (blue) and the modeled MIP structure (red). The ar/R selectivity filter is approximately located at −10 Å. (D) Phylogenetic tree calculated for all MIPs of a representative organism Phytophthora infestans using parsimony method.
Figure 3.
Figure 3.
Structure-based sequence alignment for a selected set of MIPs. This alignment is always produced with the six high-resolution MIP structures and their PDB IDs are also shown. This alignment is produced for the six transmembrane segments and the two functionally important loops B and E. The residues forming the ar/R selectivity filter are shown in the dark brown background. Seventeen positions previously identified to occur in the helix–helix interface (16) are highly group conserved when small and weakly polar residues are considered together as a group. They are displayed in cyan background.

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