FOLD AND FUNCTION PREDICTIONS FOR MYCOPLASMA-GENITALIUM PROTEINS

Background: Uncharacterized proteins from newly sequenced genomes prov ide perfect targets for fold and function prediction. Results: For 38% of the entire genome of Mycoplasma genitalium, sequence similarity to a protein with a known structure can be recognized using a new sequen ce alignment algorithm. When comparing genomes of IM. genitalium and E scherichia coli, > 80% of M. genitalium proteins have a significant se quence similarity to a protein in E. coli and there are > 40 examples that have not been recognized before. For all cases of proteins with s ignificant profile similarities, there are strong analogies in their f unctions, if the functions of both proteins are known. The results pre sented here and other recent results strongly support the argument tha t such proteins are actually homologous. Assuming this homology allows one to make tentative functional assignments for > 50 previously unch aracterized proteins, including such intriguing cases as the putative beta-lactam antibiotic resistance protein in M. genitalium. Conclusion s: Using a new profile-to-profile alignment algorithm, the three-dimen sional fold can be predicted for almost 40% of proteins from a genome of the small bacterium M. genitalium, and tentative function can be as signed to almost 80% of the entire genome. Some predictions lead to ne w insights about known functions or point to hitherto unexpected featu res of M. genitalium.