Background The large number of sexually transmitted diseases cases caused globally each year by Chlamydia trachomatis has made this organism a World Health Organization priority for vaccine development. Even after a decade of availability of C. trachomatis genome sequence, no promising vaccine has seen the light of the day. This clearly indicates the challenges in discovering new vaccines against this organism but also suggests a gap in our current understanding of Chalmydial biology. We attempt to bridge this gap by carrying out extensive annotation of hypothetical proteins of C. trachomatis and further identification of candidate genes that might be involved during the immune response against this organism. In this study, we have shortlisted proteins secreted by the general export pathway of C. trachomatis from among the hypothetical proteins of this organism with an aim to identify novel vaccine candidate gene/s.

Methodology Characterization of the proteins was carried out using various Bioinformatic tools, Pfam, Tigrfam, Scanprosite, CDD, Signal P, SigPred, TMPred, TMHMM and Lipo P.

Results 336 hypothetical proteins were deduced from the C. trachomatis genome and were analysed with several software tools for functional annotation. Next we identified the hypothertical proteins are secreted via the general export pathway (GEP) using bioinformatics approach. We were able to classify the shortlisted proteins into three broad categories as outer membrane proteins, secretory proteins and lipoproteins. These shortlisted candidate proteins could possibly induce protective immunity or elicit immune responses of diagnostic value. Few of them can further turn out to be good vaccine candidate genes as well.

Conclusion The identification of novel secreted proteins of C. trachomatis opens the way to studies on their subcellular localization and to the immunological characterization of these proteins to define their potential for immunological diagnosis and/or vaccine design.