How do you knockout an E. coli gene without disrupting the rest of the gene cluster?
Let's say that we have gene A, followed by gene B so that they overlap with 100 bases. If you want to knock out only gene A, you can do the following:


PCR gene A and clone it into a vector
PCR gene B and clone it into another vector
Insert a antibiotic resistance marker at the overlapping region of gene A and B

now you don't have functional gene A and gene B

Transform your cells only with the vector that contains gene B


Now you have disrupted only gene A but you have a functional gene B.