Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes

Three integrated genomic context methods were used to annotate uncharacterized proteins in 102 bacterial genomes. Of 7853 orthologous groups with unknown function containing 45 110 proteins, 1738 groups could be linked to functionally asso-ciated partners. In many cases, those partners are uncharacterized themselves (hinting at newly identi-fied modules) or have been described in general terms only. However, we were able to assign pathways, cellular processes or physical complexes for 273 groups (encompassing 3624 previously functionally uncharacterized proteins)