Figure 5. Model for the rearrangement of block 2.

Block 2 (green) is present between block 1 (yellow) and block 3 (light blue) in N. gonorrhoeae strains NCCP11945 (shown) and TCDC-NG08107. In our model, this region of DNA has been deleted from this location in strain FA1090, making blocks 1 and 3 adjacent (Figure 1). This is shown at the single base level through alignment of sequence to the left and right of the block 2 sequence in strain NCCP11945 (top) with the contiguous sequence of blocks 1 and 3 in strain FA1090 (bottom). The block 2 region of DNA is located elsewhere in the strain FA1090 genome in an inverted orientation (Figure 1). Excision appears to have been via flanking IS1106 elements (Table S3), followed by ISNgo2 element mediated integration using the native ISNgo2 element in block 2 (green arrow; Table S1).