Sequence homologies identification

Elucidation of the Ras pathway in vertebrates was based on the identification of proteins having sequence homologies with those present in Drosophila and C. elegans. Expression or microinjection... 

As is the case with identifications based on protein molecular masses, it appears that the use of tryptic or other peptide masses as the basis for identification is extended with difficulty to mixtures of microorganisms. This reflects unpredictable suppression. Another limitation is redundancy of peptide masses across several microorganisms. For example, the most abundant proteins (SASPs), and thus the most abundant peptides, in spores of Bacillus anthracis and the closely related pesticide Bacillus thuringiensis have extensive sequence homology.25,82... 

W. T. Thylor. Identification of protein sequence homology by consensus template alignment./. MoL Biol. 755 233-258 (1986). 

Bacteria produce a wide variety of proteins with toxic effects, and it is possible to detect the potential for such biological activities by sequence homology to known molecules, or by the identification of specific amino acid motifs that are diagnostic for a particular activity (e.g., proteolysis or membranolysis). In these cases, it is often possible to introduce specific mutations by genetic engineering to render the protein nontoxic. Careful selection of the mutations, especially if done in the context of available structural information, such as an atomic-resolution model of the antigen, can produce a fully detoxified molecule that retains the antigenic properties that make it attractive as a vaccine candidate. 

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