from Sarath Chandra Janga and Gabriel Moreno-Hagelsieb writing in Bacterial Gene Regulation and Transcriptional Networks:
An average of 60% of prokaryotic genes are organized into operons-polycistronic transcription units, making them a very important feature of their genomic organization. Operons most commonly contain genes whose products have functional associations and are abundant because they constitute an easy means for coregulation and the associated genes can act as a functional unit with a higher success rate in horizontal gene transfer events than single genes. Operons are transcribed from a single promoter, thus rarely needing genomic features between their constituting genes, naturally resulting in shorter distances between genes in operons than between adjacent genes in different transcription units. Thus, operons can be predicted based on distances between adjacent genes in the same DNA strand. This feature, intergenic distance, is the most informative criterion for predicting operons. However, predictions based on conservation of gene order followed by phylogenetic profiles, provide cleaner predictions, albeit with much lower coverage. Transcriptional terminators and other sequence features might add quality to operon predictions, but the gain is minimal for most prokaryotes. Operon organization is not well conserved with evolutionary divergence. However, operons rearrange in a functionally coherent manner. Thus, the combination of operon predictions with operon rearrangements constitutes the most powerful source for the prediction of functional associations by genomic context in prokaryotes.
Further reading: Bacterial Gene Regulation and Transcriptional Networks