Are these proteins completely novel? If not, you may proceed through homology searches. Alternatively, take a look at the use of phylogenetic profiles, co-occurrence profiles, or the so-called rosetta stone method. In brief, starting from a set of known genes, you can collect genes that tend to co-occur with those. This is the way they identified for instance genes involved in gliding motility in Myxococcus.

Thanks for your answer. This is a very unique protein. When a BLAST search is done on ncbi, the protein does not match any proteins known to assemble into pili in any other pathogens. The protein was characterised by Alteri 2006 upon purification of the pilin subunits by mass spec and was established as curli pili by biochemical characteriastics and appearance of the pili on electron micrographs. What are the steps taken to uncover a secretion and assembly pathways when the genes are unknown?