Horizontal Gene Transfer

A prophage is easily seen in the genome of Escherichia coli K12 MG1655 by its different in gene structure and "red" colored coding sequence representing a high AT content it the wobble position.

A cryptic prophage is easily visualized in the genome of Escherichia coli K12 substrain MG1655 by adding the visualization layer for coloring coding sequence by the percent GC in their wobble positions. While the majority of coding sequence in K12 have a yellow-green color (showing a GC content slightly greater than 50%), the phage's coding sequence is heavily biased towards a high AT content in the wobble position. This results in its coding sequence being colored red. This is further seen by turning on the "Other Feature" visualization layer where a misc_feature that annotates the prophage is shown by a large orange block. This view can be recreated at: http://synteny.cnr.berkeley.edu/CoGe/GenomeView.pl?z=5&x=570000&dsgid=4242&chr=1&dsid=36725&gstid=1