Figure 1

Phylogenetic tree, conserved gene context and multiple alignment of L36 ribosomal proteins. A maximum-likelihood unrooted tree was built using the MOLPHY program. The same program was used to compute bootstrap probabilities. Those branches that were supported by bootstrap probability greater than 70% are marked by small black circles. Gene names of organisms that have duplications of this protein are highlighted by different colors. The red-outlined arrowindicates a protein that probably has been subject to HGT (see text). Those branches whose alternative placements were assessed using the RELL method are indicated by circles with numbers (see Table 3). The scale bar (10) indicates the number of substitutions per 100 sites. Conserved genes in the neighborhood of the L36 gene are shown by colored arrows (center of figure). White arrows indicate adjacent genes that encode translation-system proteins but whose context is not conserved in genomes of distant species. Orthologous genes are shown in the same color. Genes are denoted by systematic names adopted for the respective genomes; a key is given in Table 2. Gene name abbreviations: IF-1, translation initiation factor IF-1; secY, preprotein translocase subunit SecY; L36, S13, S11, S3, S14, L31, L34, ribosomal proteins. A partial multiple alignment of L36 protein sequences is shown on the right (the complete multiple alignment used for the tree construction contained 41 positions); cysteines and histidines of the Zn-ribbon are shown in magenta. Remnants of this motif in sequences that do not have all four conserved residues of the Zn-ribbon are shown in green.