Genome alignment by the progressive MAUVE between A. actinomycetemcomitans strains. The program identifies stretches of nucleotide matches and selects locally collinear blocks (LCB) that meet a minimum weight criteria. Homologous LCBs between genomes are connected with a line and identified by the same color. Blocks that are inverted are placed under the center line of the genome. (a) Serotype b strain HK1651 (upper) and serotype c strain D11S-1 (lower). Nine LCB were identified. The predicted locations of Ori are indicated with red arrows. These two genomes are largely in synteny, which is also indicated by a relatively low reversal distance of 5 (see Table 1). The rearrangement between the genomes possibly involves an inversion along the Ori-Ter axis of the two LCBs flanking the Ori. (b) An optimal scenario of genome conversion between strain HK1651 and D11S-1 based on the GRIMM analysis. The LCBs are identified as numbered block arrows and also marked if they are involved in reversal in each step. The illustration merely gives an example and does not imply that the sequence of the inversions has to be the same as depicted. The result suggests that it is possible to convert one genome to the other by 5 steps of genome reversion. (c) Genome alignment of serotype b strain HK1651 (upper) and serotype a strain D7S-1 (lower). One hundred and two LCB were identified. These two genomes show little resemblance in their arrangements, which is also reflected by a relatively high reversal distance of 80 (see Table 1).