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Background  The alpha (α) proteobacteria, a very large and diverse group, are presently characterized solely on the basis of 16S rRNA trees, with no known molecular characteristic that is unique to this group. The genomes of three α-proteobacteria,  Rickettsia prowazekii  (RP),  Caulobacter crescentus  (CC) and  Bartonella quintana  (BQ), were analyzed in order to search for proteins that are unique to this group.    Results  Blast analyses of protein sequences from the above genomes have led to the identification of 61 proteins which are distinctive characteristics of α-proteobacteria and are generally not found in any other bacteria. These α-proteobacterial signature proteins are generally of hypothetical functions and they can be classified as follows: (i) Six proteins (CC2102, CC3292, CC3319, CC1887, CC1725 and CC1365) which are uniquely present in most sequenced α-proteobacterial genomes; (ii) Ten proteins (CC1211, CC1886, CC2245, CC3470, CC0520, CC0365, CC0366, CC1977, CC3010 and CC0100) which are present in all α-proteobacteria except the  Rickettsiales ; (iii) Five proteins (CC2345, CC3115, CC3401, CC3467 and CC1021) not found in the intracellular bacteria belonging to the order  Rickettsiales  and the  Bartonellaceae  family; (iv) Four proteins (CC1652, CC2247, CC3295 and CC1035) that are absent from various  Rickettsiales  as well as  Rhodobacterales ; (v) Three proteins (RP104, RP105 and RP106) that are unique to the order  Rickettsiales  and four proteins (RP766, RP192, RP030 and RP187) which are specific for the  Rickettsiaceae  family; (vi) Six proteins (BQ00140, BQ00720, BQ03880, BQ12030, BQ07670 and BQ11900) which are specific to the order  Rhizobiales ; (vii) Four proteins (BQ01660, BQ02450, BQ03770 and BQ13470) which are specific for the order  Rhizobiales  excluding the family  Bradyrhizobiaceae ; (viii) Nine proteins (BQ12190, BQ11460, BQ11450, BQ11430, BQ11380, BQ11160, BQ11120, BQ11100 and BQ11030 which are distinctive of the  Bartonellaceae  family;(ix) Six proteins (CC0189, CC0569, CC0331, CC0349, CC2323 and CC2637) which show sporadic distribution in α-proteobacteria, (x) Four proteins (CC2585, CC0226, CC2790 and RP382) in which lateral gene transfers are indicated to have occurred between α-proteobacteria and a limited number of other bacteria.    Conclusion  The identified proteins provide novel means for defining and identifying the α-proteobacteria and many of its subgroups in clear molecular terms and in understanding the evolution of this group of species. These signature proteins, together with the large number of α-proteobacteria specific indels that have recently been identified   , provide evidence that all species from this diverse group share many unifying and distinctive characteristics. Functional studies on these proteins should prove very helpful in the identification of such characteristics.

Signature proteins that are distinctive of alpha proteobacteria