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Background  The reliable identification of proteins containing 50 or fewer amino acids is difficult due to the limited information content in short sequences. The 37 amino acid CydX protein in  Escherichia coli  is a member of the cytochrome  bd  oxidase complex, an enzyme found throughout Eubacteria. To investigate the extent of CydX conservation and prevalence and evaluate different methods of small protein homologue identification, we surveyed 1095 Eubacteria species for the presence of the small protein.    Results  Over 300 homologues were identified, including 80 unannotated genes. The ability of both closely-related and divergent homologues to complement the  E. coli  Δ cydX  mutant supports our identification techniques, and suggests that CydX homologues retain similar function among divergent species. However, sequence analysis of these proteins shows a great degree of variability, with only a few highly-conserved residues. An analysis of the co-variation between CydX homologues and their corresponding  cydA  and  cydB  genes shows a close synteny of the small protein with the CydA long Q-loop. Phylogenetic analysis suggests that the  cydABX  operon has undergone horizontal gene transfer, although the  cydX  gene likely evolved in a progenitor of the Alpha, Beta, and Gammaproteobacteria. Further investigation of  cydAB  operons identified two additional conserved hypothetical small proteins: CydY encoded in CydA Qlong  operons that lack  cydX , and CydZ encoded in more than 150 CydA Qshort  operons.    Conclusions  This study provides a systematic analysis of bioinformatics techniques required for the unique challenges present in small protein identification and phylogenetic analyses. These results elucidate the prevalence of CydX throughout the Proteobacteria, provide insight into the selection pressure and sequence requirements for CydX function, and suggest a potential functional interaction between the small protein and the CydA Q-loop, an enigmatic domain of the cytochrome  bd  oxidase complex. Finally, these results identify other conserved small proteins encoded in cytochrome  bd  oxidase operons, suggesting that small protein subunits may be a more common component of these enzymes than previously thought.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-946) contains supplementary material, which is available to authorized users.

Conservation analysis of the CydX protein yields insights into small protein identification and evolution