Comparative sequence analysis of IS50 transposase-related protein sequences in conjunction with known structural, biochemical, and genetic data was used to determine domains and residues that play key roles in IS50 transposase function. BLAST and ClustalW analyses have been used to find and analyze six complete protein sequences that are related to the IS50 transposase. The protein sequence identity of these six homologs ranged from 25 to 55% in comparison to the IS50 transposase. Homologous motifs were found associated with each of the three catalytic residues. Residues that play roles in transposase-DNA binding, protein autoregulation, and DNA hairpin formation were also found to be conserved in addition to other residues of unknown function. On the other hand, some homologous sequences did not appear to be competent to encode the inhibitor regulatory protein. The results were also used to compare the IS50 transposase with the more distantly related transposase encoded by IS10.Transposable elements have played an important role in generating genetic diversity through their ability to cause insertions, deletions, inversions, and chromosome fusions. These elements are ubiquitous, and in some cases transposable elements and their inactive descendants can constitute the majority of a genome (12). The presence of a transposable element in a given genome is the product of lateral gene transfer. In bacteria, for instance, transposable elements may be introduced by means of DNA transformation, plasmid transfer, or phage infection. If an element was acquired recently by a given genome, it may well be absent from the genomes of close relatives.One class of transposable element ("cut and paste" transposons) moves from one DNA molecule to another (or from site to site within a DNA molecule) by a process that involves excision of the transposon DNA from the original site and integration of the transposon DNA into the second site. These DNA excision and integration processes are catalyzed by a transposon-specific protein called a transposase (26). Understanding how transposases function is of general importance because many transposases are members of a superfamily of proteins that includes human immunodeficiency virus type 1 integrase and possibly the RAG-1 protein responsible for the DNA cleavage events in the immune system V(D)J joining process. That is, this family of proteins share overall architectural properties, detailed active-site structures, and catalytic mechanisms (13,16,26,33).IS50 is a component of the composite transposon Tn5. IS50 transposase (also called Tn5 transposase) is an excellent model system because both biochemical and genetic data and detailed structural information are available (32, 33). As a result, the overall mechanism of IS50 transposition is well understood (see Fig. 1) and the roles of many protein residues in this process have been determined. However, structure-function studies of IS50 transposase are far from complete. For instance, the residues that participate in intramolecular regul...