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Background  Alpha proteobacteria are one of the largest and most extensively studied groups within bacteria. However, for these bacteria as a whole and for all of its major subgroups (viz.  Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales  and  Caulobacterales ), very few or no distinctive molecular or biochemical characteristics are known.    Results  We have carried out comprehensive phylogenomic analyses by means of Blastp and PSI-Blast searches on the open reading frames in the genomes of several α-proteobacteria (viz.  Bradyrhizobium japonicum ,  Brucella suis ,  Caulobacter crescentus ,  Gluconobacter oxydans ,  Mesorhizobium loti ,  Nitrobacter winogradskyi ,  Novosphingobium aromaticivorans ,  Rhodobacter sphaeroides  2.4.1,  Silicibacter sp . TM1040,  Rhodospirillum rubrum  and  Wolbachia  ( Drosophila ) endosymbiont). These studies have identified several proteins that are distinctive characteristics of all α-proteobacteria, as well as numerous proteins that are unique repertoires of all of its main orders (viz.  Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales  and  Caulobacterales ) and many families (viz.  Rickettsiaceae, Anaplasmataceae, Rhodospirillaceae, Acetobacteraceae, Bradyrhiozobiaceae, Brucellaceae  and  Bartonellaceae ). Many other proteins that are present at different phylogenetic depths in α-proteobacteria provide important information regarding their evolution. The evolutionary relationships among α-proteobacteria as deduced from these studies are in excellent agreement with their branching pattern in the phylogenetic trees and character compatibility cliques based on concatenated sequences for many conserved proteins. These studies provide evidence that the major groups within α-proteobacteria have diverged in the following order: ( Rickettsiales ( Rhodospirillales  ( Sphingomonadales  ( Rhodobacterales  ( Caulobacterales-Parvularculales  ( Rhizobiales . We also describe two conserved inserts in DNA Gyrase B and RNA polymerase beta subunit that are distinctive characteristics of the  Sphingomonadales  and  Rhodosprilllales  species, respectively. The results presented here also provide support for the grouping of  Hyphomonadacea e and  Parvularcula  species with the  Caulobacterales  and the placement of  Stappia aggregata  with the  Rhizobiaceae  group.    Conclusion  The α-proteobacteria-specific proteins and indels described here provide novel and powerful means for the taxonomic, biochemical and molecular biological studies on these bacteria. Their functional studies should prove helpful in identifying novel biochemical and physiological characteristics that are unique to these bacteria.

Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups