Partial sequence alignments of RNA polymerase β subunit (RpoB) showing a large insert (boxed) that is a distinctive characteristic of various species and not found in any other bacteria

<p><b>Copyright information:</b></p><p>Taken from "Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups"</p><p>http://www.biomedcentral.com/1471-2180/7/106</p><p>BMC Microbiology 2007;7():106-106.</p><p>Published online 28 Nov 2007</p><p>PMCID:PMC2241609.</p><p></p> There are two homologs of RpoB in and only one of these contains the insert. The dashes (-) denote identity with the amino acid on the top line

Character compatibility cliques showing the two largest cliques of mutually compatible characters based on the two states sites in the concatenated sequence alignment for 12 conserved proteins

<p><b>Copyright information:</b></p><p>Taken from "Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups"</p><p>http://www.biomedcentral.com/1471-2180/7/106</p><p>BMC Microbiology 2007;7():106-106.</p><p>Published online 28 Nov 2007</p><p>PMCID:PMC2241609.</p><p></p> The cliques consisted of 350 mutually compatible characters. The numbers of characters that distinguished different clades are indicated on the nodes. Rooting was done using the sequences for . *, as in Figure 1

A neighbour-joining distance tree based on concatenated sequences for 12 conserved proteins

<p><b>Copyright information:</b></p><p>Taken from "Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups"</p><p>http://www.biomedcentral.com/1471-2180/7/106</p><p>BMC Microbiology 2007;7():106-106.</p><p>Published online 28 Nov 2007</p><p>PMCID:PMC2241609.</p><p></p> The numbers on the nodes indicate bootstrap scores (out of 100) observed in the neighbour-joining (NJ), maximum parsimony (MP) and maximum-likelihood (ML) analyses (NJ/MP/ML). The species marked with * are presently not part of the order, but the results of phylogenetic and phylogenomic studies presented here suggest their placement in this group

Character compatibility tree (or the largest clique of mutually compatible characters) based on two states sites in the concatenated sequence alignment for the 12 proteins

<p><b>Copyright information:</b></p><p>Taken from "Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species"</p><p>http://www.biomedcentral.com/1471-2148/7/71</p><p>BMC Evolutionary Biology 2007;7():71-71.</p><p>Published online 8 May 2007</p><p>PMCID:PMC1887533.</p><p></p> The clique consisted of 410 mutually compatible characters. The numbers of characters that distinguished different clades are indicated on the nodes. Rooting was done using the sequences for species

Summary of the phylogenomic analyses showing the species distribution of various α-proteobacteria-specific proteins and the suggested evolutionary stages where the genes for these proteins have likely evolved

<p><b>Copyright information:</b></p><p>Taken from "Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups"</p><p>http://www.biomedcentral.com/1471-2180/7/106</p><p>BMC Microbiology 2007;7():106-106.</p><p>Published online 28 Nov 2007</p><p>PMCID:PMC2241609.</p><p></p> The genes IDs for some proteins described in earlier work are indicated [17]. The information for all other proteins can be found in the indicated Tables or Additional files. A large numbers of conserved indels that are specific for different groups or clades within α-proteobacteria shown here have also been identified in our earlier work [16] (not shown here). The branching order of α-proteobacteria relative to other bacteria has been established in earlier work [32,58]

A summary diagram showing the evolutionary stages where different signature proteins and conserved indels that are specific for the and species have likely evolved or originated

<p><b>Copyright information:</b></p><p>Taken from "Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species"</p><p>http://www.biomedcentral.com/1471-2148/7/71</p><p>BMC Evolutionary Biology 2007;7():71-71.</p><p>Published online 8 May 2007</p><p>PMCID:PMC1887533.</p><p></p> Some of the conserved inserts that are specific for these groups or indicate their branching position relative to other bacterial phyla have been described in earlier work [30,43,69]

Neighbour-joining tree based on concatenated sequences for 12 highly conserved proteins

<p><b>Copyright information:</b></p><p>Taken from "Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species"</p><p>http://www.biomedcentral.com/1471-2148/7/71</p><p>BMC Evolutionary Biology 2007;7():71-71.</p><p>Published online 8 May 2007</p><p>PMCID:PMC1887533.</p><p></p> The tree was rooted using sequences for species and numbers on the nodes indicate bootstrap scores in the NJ and maximum-likelihood analyses (NJ/MP). The branching position of , which became available after this analysis was completed, is not shown. However, our analysis of a smaller dataset indicates that it exhibits closest affinity for the flavobacteria (results not shown)

Partial sequence alignments of DNA Gyrase B showing a 4 aa insert that is mainly specific for the species

<p><b>Copyright information:</b></p><p>Taken from "Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups"</p><p>http://www.biomedcentral.com/1471-2180/7/106</p><p>BMC Microbiology 2007;7():106-106.</p><p>Published online 28 Nov 2007</p><p>PMCID:PMC2241609.</p><p></p> A 4–5 aa insert present in some other α-proteobacteria could be due to either LGTs or taxonomic anomalies. The dashes (-) denote identity with the amino acid on the top line. Sequence information for other groups of bacteria (which do not contain this insert) is not shown

Partial sequence alignments of alanyl-tRNA synthetase showing a conserved insert of about 12–14 aa that is a distinctive characteristic of homologs and not found in other bacteria

<p><b>Copyright information:</b></p><p>Taken from "Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species"</p><p>http://www.biomedcentral.com/1471-2148/7/71</p><p>BMC Evolutionary Biology 2007;7():71-71.</p><p>Published online 8 May 2007</p><p>PMCID:PMC1887533.</p><p></p> The dashes (-) denote identity with the amino acid on the top line. Additional abbreviations: