Abstract: Transmembrane transport is an essential component of the cell life.
Many genes encoding known or putative transport proteins are found in bacterial
genomes. In most cases their substrate specificity is not experimentally
determined and only approximately predicted by comparative genomic analysis.
Even less is known about the 3D structure of transporters. Nevertheless, the
published experimental data demonstrate that channel-forming residues
determine the substrate specificity of secondary transporters and analysis of
these residues would provide better understanding of the transport mechanism.
We developed a simple computational method for identification of
channel-forming residues in transporter sequences. It is based on the analysis
of amino acids frequencies in bacterial secondary transporters. We applied this
method to a variety of transmembrane proteins with resolved 3D structure. The
predictions are in sufficiently good agreement with the real protein
structure.
