Fig. 1.

Systems that use Xer. (A) Scheme depicting the sequential integration of IMEXs. Triangles represent attP and dif sites, pointing from the XerD binding site to the XerC binding site. Chromosomal DNA (black), TLCϕ DNA (blue), and CTXϕ DNA (magenta) are indicated. Dotted triangles represent nonfunctional CTXϕ sites. (B) Sequence alignment of dif1, attP^CTX, attP^VGJ, attP^TLC, difA, and dif2. Bases differing from dif1 are indicated in color. Bases that do not fit the XerD binding site consensus are indicated in lowercase. XerC (●) and XerD (○) cleavage points are indicated. (C) Xer recombination pathways. XerC (light gray circles), XerD (dark gray circles), dif sites (red and black lines), and attP^CTX and attP^VGJ (magenta and green lines) are indicated. XerC and XerD catalysis-suitable conformations are depicted as horizontal and vertical synapses, respectively. Cleavage points are indicated as in B.