**3. Conclusions**

Previous physiological, ecological and biochemical studies [4] as well as genomic analyses [5], indicate that the anoxygenic phototroph bacterium *Cfl. aurantiacus* has many interesting and certain unique features in its metabolic pathways. The evolutionary links of *Cfl. aurantiacus* and other phototrophic bacteria suggested from this report are summarized in **Table 1.** It has been recognized that the type II RCs were transferred between the *Chloroflexi* species (or FAPs) and the anoxygenic phototrophic Proteobacteria. Sequence alignments and phylogenetic analyses illustrated in this report suggest: (i) Some *Cfl. aurantiacus* enzymes in essential metabolic pathways are more related to the anoxygenic phototrophic Proteobacteria than other phototrophic bacteria, whereas other enzymes are more related to other phototrophic bacteria than anoxygenic phototrophic Proteobacteria; and (ii) some *Cfl. aurantiacus* enzymes in essential carbon metabolic pathways are more related to nonphotosynthetic microbes than other phyla of phototrophic bacteria. Together, our studies support lateral/horizontal gene transfers among microbes, and suggest that photosynthesis is likely an adaption to the environments [9].


a The *Cfl. aurantiacus* complex I with clustered genes (**Fig. 2A**) b The *Cfl. aurantiacus* complex I without clustered genes (**Fig. 2B**) c The putative bchE genes in some cyanobacteria have been reported not to function as anaerobic cyclase.

Table 1. Evolutionary perspectives of selective proteins/enzymes/cellular complexes in *Cfl. aurantiacus* versus other phyla of phototrophic bacteria
