Oh, E. coli, I've missed you! Since I left my happy little microbiology department at Virginia Tech and stumbled around the field of human proteomics the world has gotten so much more complex for me. Not to say there isn't complexity in microbiology! But I sure do prefer thinking about organisms with one big circular piece of DNA rather than exomes and introns and whatever. Lets just do: this is a gene and it makes a protein under this condition. I see a TATA box!
Obviously, though, E.coli hasn't give up all its secrets just yet. StepDB is a project that takes a swing at solving a few. This project aims to reveal the sub-cellular localization of proteins in our favorite model organism. How'd they do it? Through an intensive bioinformatics analysis that involves a lot of predictions and previously existing data from proteomic and genomic studies. Using this they are able to break E.coli proteins into 13 subcellular categories.
A lazy person would probably just do K12, but StepDB has information on the K12 and BL21strains and even has a tab down at the bottom where you can compare the two. This'll give you a rough measurement of the consistency of these predictions for when you check the homology of the protein from you organism of interest.
You can read more about StepDB here (currently in press at MCP)
You can actually visit it here.
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