MIPDB: a relational database dedicated to MIP family proteins.
BACKGROUND
The MIPs (major intrinsic proteins) constitute a large family of membrane proteins that facilitate the passive transport of water and small neutral solutes across cell membranes. Since water is the most abundant molecule in all living organisms, the discovery of selective water-transporting channels called AQPs (aquaporins) has led to new knowledge on both the physiological and molecular mechanisms of membrane permeability. The MIPs are identified in Archaea, Bacteria and Eukaryota, and the rapid accumulation of new sequences in the database provides an opportunity for large-scale analysis, to identify functional and/or structural signatures or to infer evolutionary relationships. To help perform such an analysis, we have developed MIPDB (database for MIP proteins), a relational database dedicated to members of the MIP family.


RESULTS
MIPDB is a motif-oriented database that integrates data on 785 MIP proteins from more than 200 organisms and contains 230 distinct sequence motifs. MIPDB proposes the classification of MIP proteins into three functional subgroups: AQPs, glycerol-uptake facilitators and aquaglyceroporins. Plant MIPs are classified into three specific subgroups according to their subcellular distribution in the plasma membrane, tonoplast or the symbiosome membrane. Some motifs of the database are highly selective and can be used to predict the transport function or subcellular localization of unknown MIP proteins.


CONCLUSIONS
MIPDB offers a user-friendly and intuitive interface for a rapid and easy access to MIP resources and to sequence analysis tools. MIPDB is a web application, publicly accessible at http://idefix.univ-rennes1.fr:8080/Prot/index.html.
El Karkouri
Khalid
K
UMR CNRS 6026 Interactions Cellulaires et Moléculaires, Université de Rennes 1, équipe SDM (Structure et Dynamique des Macromolécules), Campus de Beaulieu, Bât. 13, 35042 Rennes Cedex, France.
Gueuné
Hervé
H
Delamarche
Christian
C
D020816:Amino Acid Motifs; D020346:Aquaporins; D001105:Archaea; D001419:Bacteria; D019992:Databases as Topic; D005057:Eukaryotic Cells; D005136:Eye Proteins / Q000145:classification; D008562:Membrane Glycoproteins / Q000145:classification; D017386:Sequence Homology, Amino Acid
D020346:Aquaporins; D005136:Eye Proteins; D008562:Membrane Glycoproteins; C030328:aquaporin 0