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Ng FA109Q Nl DSM4691 Ns LMG5290

Fig. 11.3 Comparison of the cps locus of pathogenic and apathogenic Neisseria species. Regions with identical functions are depicted in the same colors. The following sequence data were used to compare the cps loci: NmB B1940: assembled from the GenBank sequences L09188, L09189, M57677, M95053, and Z13995; NmB MC58: AE002098; NmA Z2491: AL157959; NmC FAM18: NC_003221, homologous genes according to BLASTX[75] searches against the annotated neisserial genomes; Ng FA1090: AE004969; Nl DSM4691 and

Ns LMG5290: H. Claus and U. Vogel, unpublished data. The gene assignment of the meningococcal sequences was done following the annotation ofthe MC58 genome. Ng, N. gonorrhoeae; Nl, N. lactamica; Nm, N. meningitidis; Ns, N. sicca; DSM, German type culture collection (Deutsche Sammlung von Mikroorganismen), Braunschweig, Germany; LMG, Belgian collection ofmicro-organisms (Laboratorium voor Microbiologie, University of Gent), Gent, Belgium. (This figure also appears on page 243.)

Fig. 15.2 Alignment ofthe complete genome sequences, but inverted. 1, Disruption of the

sequences of L. pneumophila strains Paris, Lens, and Philadelphia 1, using the ACT (Artemis comparison tool) software (http:// www.sanger.ac.uk/Software/ACT/). Color code: Red blocks represent homologous sequences; blue blocks, homologous synteny by a 260-kbp inversion in strain Lens; 2, cluster encoding several efflux pumps missing in strain Lens; 3, Ivh type IV secretion system; 4, 65-kbp pathogenicity island of strain Philadelphia 1. (This figure also appears on page 329)

Fig. 16.1 Circular genome maps of L. monocytogenes EGD-e and L. innocua CLIP 11262, showing the position and orientation of genes. From the outside: Circles 1 and 2, L. innocua and L. monocytogenes genes on the + and-strands, respectively. Color coding: green, L. innocua genes; red, L. monocytogenes genes; black, genes specific to L. monocytogenes or L. innocua, respectively; orange, rRNA

Fig. 16.1 Circular genome maps of L. monocytogenes EGD-e and L. innocua CLIP 11262, showing the position and orientation of genes. From the outside: Circles 1 and 2, L. innocua and L. monocytogenes genes on the + and-strands, respectively. Color coding: green, L. innocua genes; red, L. monocytogenes genes; black, genes specific to L. monocytogenes or L. innocua, respectively; orange, rRNA

operons; purple, prophages. Circle 3, G+C content of L. monocytogenes (< 32.5% G+C in light yellow, 32.5-43.5% G+C in yellow, and >43.5% G+C in dark yellow). The scale in megabasepairs is indicated on the outside of the genome circles, with the origin of replication at position 0. Reprinted with permission from Ref. [2]. (This figure also appears on page 347.)

Fig. 16.2 The virulence gene cluster locus in the six species of the genus Listeria. The cluster is flanked by the housekeeping genes (black boxes) prs, vclB (lmo0209), and ldh in all six species. Genes controlled by PrfA are shown as boxes with black arrowheads. vclA (lmo0208) is present in all species except L. grayi. vclP is present in L. welshimeri, L. seeli-geri, and L. ivanovii. vclZ (lmo0207) is present

Fig. 16.2 The virulence gene cluster locus in the six species of the genus Listeria. The cluster is flanked by the housekeeping genes (black boxes) prs, vclB (lmo0209), and ldh in all six species. Genes controlled by PrfA are shown as boxes with black arrowheads. vclA (lmo0208) is present in all species except L. grayi. vclP is present in L. welshimeri, L. seeli-geri, and L. ivanovii. vclZ (lmo0207) is present in L. monocytogenes and L. innocua. vclYand vclX are inverted in L.seeligeri. Species-specific genes (medium gray) not under PrfA control include vclJ, vclF1, vclG1, vclG2, vclF2 of L. grayi, and vclCof L. seeligeri. Homologous genes are represented by boxes ofthe same color. Reprinted with permission from Refs. [73, 75]. (This figure also appears on page 350.)

Fig. 19.2 Domain architectures for select surface proteins from the pathogenic protozoa, demonstrating the almost exclusive nonover-lap in the catalogs ofextracellular proteins. Red stars indicate proteins composed of domain(s) invented in a lineage- or clade-specific fashion (e.g., a molecule found in

Fig. 19.2 Domain architectures for select surface proteins from the pathogenic protozoa, demonstrating the almost exclusive nonover-lap in the catalogs ofextracellular proteins. Red stars indicate proteins composed of domain(s) invented in a lineage- or clade-specific fashion (e.g., a molecule found in

Plasmodium but not in the apicomplexan Cryptosporidium or in kinetoplastids). The remaining domains originated either via vertical inheritance (followed by gene loss in widespread lineages) or by lateral transfer from a bacterial or metazoan source. (This figure also appears on page 425.)

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