Systematic fold recognition analysis of the sequences encoded by the genome of Mycoplasma pneumoniae

A robust tool for fold recognition was applied to the systematic analysisof the sequences below 200 residues encoded by the genome of Mycoplasmapneumoniae. The goal was to determine the additional information gainachievable in genome analysis by fold recognition, beyond the intrinsiclimits of homology studies. A list of 124 sequences encoding for solubleproteins or domains not homologous to each other, or to proteins with knownthree-dimensional structure, was analyzed, resulting in significant Zscores for the energy of the structural models in 12 of these cases. Thisresult indicates that systematic application of fold recognition techniquesto the analysis of structurally unassigned soluble proteins can lead tohigh-confidence structural predictions with an efficiency of about 10%, arelevant contribution besides the complementary approach of homologyanalysis. Four of the predictions presented include mapping of the putativeactive site of the target sequence and lead to the detection of probablecatalytic and binding residues. The data are discussed with reference tothe functional implications of the structural models and to the resultsreported for the homologous genome of Mycoplasma genitalium.