The FtsK-XerCD/dif and FtsK-XerS/difSL systems. (A) Left: diagram of the XerC, XerD, XerS and Cre proteins, with their length and domain organization (in amino acid). The conserved residues involved in catalysis are indicated. Right: difSL and dif sites of representative bacteria with the recombinase binding sites, separated by the central region (CR) indicated. In difSL sites, upper case bases are part of the previously defined minimal site (28) and bases shown in bold typeface are inverted repeats within this minimal site. The left-half site is indicated by the pale grey bar and the right-half site by the dark grey bar. This convention is used throughout the paper. In dif sites, the two half sites recognized by XerC and XerD, respectively, are indicated. Lla, L. lactis; Spn, Streptococcus pneumoniae; Spy, S. pyogenes; Sag, S. agalactiae; Eco, E. coli; Hin, H. influenzae; Vch, V. cholerae; Ngo, Neisseria gonorrhoeae; Bsub, B. subtilis. (B) A diagram of the mechanism of recombination by Y-recombinase based on the data obtained for the Cre/loxP system. Y indicates the catalytic tyrosine residue. OH is the 5′ hydroxyl group created by DNA cleavages.