I guess this has been discussed before, but has anyone actually implemented this strategy outlined in this paper? Specifically for bacteria? It describes how to localize protein products subcellularly. I am wondering if there is a one-button solution for subcellular localization for bacteria.

http://www.nature.com/nprot/journal/v2/n4/abs/nprot.2007.131.html

Locating proteins in the cell using TargetP, SignalP and related tools

Olof Emanuelsson1, Søren Brunak2, Gunnar von Heijne3 & Henrik Nielsen2

Abstract Determining the subcellular localization of a protein is an important first step toward understanding its function. Here, we describe the properties of three well-known N-terminal sequence motifs directing proteins to the secretory pathway, mitochondria and chloroplasts, and sketch a brief history of methods to predict subcellular localization based on these sorting signals and other sequence properties. We then outline how to use a number of internet-accessible tools to arrive at a reliable subcellular localization prediction for eukaryotic and prokaryotic proteins. In particular, we provide detailed step-by-step instructions for the coupled use of the amino-acid sequence-based predictors TargetP, SignalP, ChloroP and TMHMM, which are all hosted at the Center for Biological Sequence Analysis, Technical University of Denmark. In addition, we describe and provide web references to other useful subcellular localization predictors. Finally, we discuss predictive performance measures in general and the performance of TargetP and SignalP in particular.