The homology sequence of Saccharomyces cerevisiae mitochondrial protein import machinery subunits in the genomes and proteomes of 27 species in different evolution levels were searched, and further analysis the relationship between sequence similarity of the subunits and their mitochondria location. The result reveals that modules in the same position of mitochondria show a similar sequence similarity curve. In the same module, sequence similarity curve always have its own peaks and troughs. On the whole, the sequence similarity rise from the outer membrane to matrix of the mitochondria. Furthermore, mitochondrial protein import machinery subunits also show sequence similarity with some function not associated proteins, and these subunits generally concentration on the outer and inner membrane of the mitochondria.
