(Rough) Model for DNA evolution in E. coli genes
Bacterial DNA evolution is like other evolution in the sense that the mutation rates are probably random and biased somewhat by the physical and chemical structure of DNA as well as the presence and activity of DNA repair enzymes.  The mutation protocols for preparing mutant libraries from UV or chemical mutagens are a good place to start I would think - like this reference. Most of this stuff is oriented towards protocols used in the lab, not in the wild.  Like how much UV does E coli get in your gut?  Not much.  Still it does happen and is a typical baseline factor in evolution. 

Bacteria also mediate their own adaptation via phage transfer as well as direct lateral gene transfer, chromosomal rearrangement.  The dynamics of this evolution is just as interesting I think as site mutation as the bacteria can use its repair mechanisms and even actively upregulate some adaptation itself, responding to environmental changes.  The fundamental differences between bacterial evolution and say evolution of animals and plants come from the fact that life is relatively cheap - a single well adapted survivor can repopulate very quickly and so that even radical genetic diversity has a benefit even if some of the population dies off every generation from being a bad adaptive experiment.  (BTW animals do this too, but in the short lived haploid gamete phase, not so much as diploid animals). 

Well anyway back to bacteria.  Eric Alm's lab at MIT started with his work with operon evolution.  Genes grouped together on a single mRNA leap from one cluster to another across evolution, allowing for coordination of biochemical processes in the cell.  Lately they have been looking more intensely at the evolution of bacterial species, and how the selective environment influences bacterial adaptation. 

Its hard to be more specific since I'm not completely clear on your focus and needs here, but this is what I know.