Figure 3-1: Left: Location and relative size (in kb) of prophages and prophage remnants R (in red) on the Streptococcus pyogenes strain SF370 genome map. The linked arrows indicate a possible site for homologous recombination between closely related prophage DNA segments. Right: The genome maps of three SF370 prophages and a prophage from S. pyogenes strain NIH1 are aligned with the attachment sites at the left and right ends. Prophage NIH1.1 has been identified as a genetic marker for recently emerged clinical isolates of S. pyogenes in Japan. The phage modules are color-coded (red: lysogeny, orange: DNA replication, yellow: transcriptional regulation?, green: DNA packaging and head, brown: head-to-tail, blue: tail, mauve: tail fiber, dark pink: lysis, black: superantigen/ mitogenic factor genes). Likely prophage inactivating mutations are indicated by large vertical arrows (replisome organizer, portal protein), an asterisk marks phage genes that potentially contribute to the virulence of the lysogenic host; the phage hyaluronidase is labeled by a triangle. Regions of DNA sequence similarity between the prophages are connected by blue shading (for details see 13).