Unique Evolution of Symbiobacterium thermophilum Suggested from Gene Content and Orthologous Protein Sequence Comparisons
Figure 2
Phylogenetic relationships on the basis of 112 orthologous protein sequence comparisons among 54 Clostridia and B. subtilis. The 112 proteins were extracted as orthologous proteins from the 55 bacteria by a previously described method [15]. We constructed the 112 multiple alignments by using Clustal W [16]. Then, a concatenated multiple alignment of the 112 multiple alignments was generated. The complete multiple alignment had 52,204 amino acid sites, including 19,818 gap/insertion sites. Hence, phylogenetic analyses were performed on the basis of 32,386 amino acid sites without the gap/insertion sites. The neighbor-joining tree was reconstructed using MEGA software version 4 [14]. The bootstrap was performed with 1000 replicates. The rate variation among sites was assumed to have a gamma distributed rate (). No other default parameters were changed. The bar indicates a 10% difference.
