To explore the role of proteases in pathogenesis and as potential drug targets we need to elucidate their function and effect on biological networks. In this paper, we describe the application of Pathway Logic (PL) (http://pl.csl.sri.com/) to the symbolic modeling of the interaction networks of proteases of Gram-positive bacteria and the use of Pathway Logic Assistant tool to browse and query these models. Pathway Logic is a systems biology approach to biological processes as integrated systems rather than isolated parts based on formal methods and rewriting logic. These models are developed using Maude, a formal language and tool set based on rewriting logic. We show how this approach can be used to represent and analyze systems at multiple levels of details. The Pathway Logic Assistant tool (PLA) enables us to identify key proteases and regulatory molecules – ‘choke points’ by comparing different pathways or networks within and across species and to predict how these molecules, if inhibited or avoided would affect the pathway or network.