| The cystic fibrosis transmembrane conductance regulator (CFTR) consisting of ATP binding and transmembrane domains, and a unique regulatory (R) domain not found in other ATP binding cassette proteins. This R domain can be phosphorylated at different sites by PKA and PKC influencing the chloride channel function of CFTR. Similarity searches did not provide any information of R domain structure or function, even more, R domains from different species show low sequence similarity. Since the only significant similarity in the R domains is the location of the phosphorylation sites, we generated different R domain patterns masking amino acids between the phosphorylation sites. Because of the high number of the generated patterns we expected high number of matches in the UniProt database, therefore a relational database management system (RDBMS) was set up for handling the results. During the software development our system grow to a general package called mBioSQL that has higher performance compared to other solutions, and presents a generalized concept that the storage of analysis results in RDBMS allows further analysis in a convenient way. Using our system mostly nuclear proteins were indicated to have phosphorylation patterns similar to the R domain. |