What are MIPs?

The Major Intrinsic Protein (MIPs) belong to the superfamily of proteins which transport water as well as other neutral molecules across the cell membrane. Functionaly they are devided in two broad groups:

Aquaporin: Pure water channels and

Aquaglyceroporin: They can transport other neutral molecules also like glycerol.

What are the organisms for which MIPs have been identified?

The Major Intrinsic Proteins (MIPs) in MIPModDB belong to those species for which genome sequencing has been completed. The aquaporins were idetified from their genome sequence in NCBI itself using a protocol and were modelled by similar method as discussed in references given.

Do they represent the complete sets of MIPs for these organisms?

The identification of MIPs has been carried out from the available completed genome sequences which have been annotated. The correctness nad completeness of genome annotations are thus dependent on database itself. The unannotated might be the one missing in the identification process carried.

What is selectivity filter?

Selectivity filter is the narrowest region inside the channel. It is present nearly 8 A above the central pore in pure water transporting channel. It is mainly formed by four residues which line the channel. Two of these residues are contributed by loopE while other two residues come from helix2 and helix5.

What is meant by variations in NPA motif?

The NPA motif, contributed by two half helices of loopB and loopE are found to be highly conserved in MIPs. The, asparagine also forms hydrogen bonds with the water molecules crossing the channel. However, as the knowledge in MIPs increase, several exceptions to this conserved motif were observed. In present database, the MIPs can be identified with those variations (exceptions). They can be searched for variation in loopB motif and in loopE motif.


Naming scheme for the database
MIPModDB provides a unique identifier for each of its members. The naming scheme utilizes a unique combination of alphabets derived from the first two letters of the genus and the species, respectively. Following this is the 4 letter serial number which is independent of the organism or other sorting parameters. In case there is any ambiguity between two entries such that their first four letters are the same then the second entry uses the last two alphabets of the species, instead of the first two.

Creating a phylogenetic tree

In order to create a phylogenetic tree, at least three different MIP sequences are required. The server uses PHYLIP as a backend and provides three different methods for creating phylogenetic trees - Neighbour Joining (NJ), Maximum Parsimony (MP) and Maximum Likelihood (ML).

To make a phylogenetic tree, simply select the desired entries from the "Search Results" page and click on the "Get Phylogenetic Tree" button at the bottom of the page. This will take you to the phylogenetic tree creation page where you can select one of the three available tree creation methods (NJ,MP,ML).

The tree will be shown on the screen and can also be saved as a .dnd file. An option for viewing and downloading the bootstrap tree is also available for each method on the same page.

Obtaining FASTA sequences
FASTA sequences for the selected proteins can be obtained from the search results page by clicking on the "Get FASTA sequence" button.

Results page
The result page for individual members of the database provides more information including the hole-profile, gene structure, sequence-based information, structure-based information, aligment (in PIR and PAP format), modeled structure in PDB format, the structure superimposed with known members of the MIP family.

MIPDB http://genoweb.univ-rennes1.fr/Prot/
HOLE http://hole.biop.ox.ac.uk/hole
SCWRL3 http://dunbrack.fccc.edu/SCWRL3.php
MODELLER http://salilab.org/modeller
UNIPROT http://www.ebi.uniprot.org/
INTERPRO http://www.ebi.ac.uk/interpro/
NCBI http://www.ncbi.nlm.nih.gov
PDB http://www.pdb.org/
GROMACS http://www.gromacs.org/
PROCHECK http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html
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Bioinformatics and Biomolecular Simulation Laboratory, Department of Biological Sciences and Bioengineering,
Indian Institute of Technology, Kanpur, INDIA-208016
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