Nucleotide sequence homologies in control regions of prokaryotic genomes

Functional recognition sites for several regulatory factors, including RNA polymerase, cyclic adenosine monophosphate receptor protein and ribosomes, do not always have strong consensus nucleotide sequence homology, yet they are capable of biological activity. Using the computer, other nucleotide sequences can be found that have equal or significantly greater consensus homology, but whose biological function has not been characterized. This analysis shows that no arbitrary 'cutoff score' can successfully distinguish active recognition sites from uncharacterized homologies, due to the great natural diversity in the strength and conservation of functional sites. It also predicts that the strong 'cryptic' homologies presented here are of two types: some might already have a biological function which has so far not been detected, whereas certain single-point mutations might be able to confer activity upon the others by correcting a key structural defect.