Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements

The parasitic bacterium Mycoplasma genitalium has a small, reduced genome w ith close to a basic set of genes. As a first step toward determining the f amilies of protein domains that form the products of these genes, we have u sed the multiple sequence programs PSI-BLAST and GEANFAMMER to match the se quences of the 467 gene products of M. genitalium to the sequences of the d omains that form proteins of known structure [Protein Data Bank (PDB) seque nces]. PDB sequences (274) match all of 106 M. genitalium sequences and som e parts of another 85; thus, 41% of its total sequences are matched in all or part. The evolutionary relationships of the PDB domains that match M. ge nitalium are described in the structural classification of proteins (SCOP) database. Using this information, we show that the domains in the matched M . genitalium sequences come from 114 superfamilies and that 58% of them hav e arisen by gene duplication. This level of duplication is more than twice that found by using pairwise sequence comparisons. The PDB domain matches a lso describe the domain structure of the matched sequences: just over a qua rter contain one domain and the rest have combinations of two or more domai ns.