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Uptake sequences are abundant sequence motifs, often located downstream of ORFs, that are used to facilitate the within-species horizontal transfer of DNA. A frequent word analysis of the complete genome sequence of Helicobacter pylori strain 26685 was performed to search for and determine the identity of an uptake sequence in this species. The results demonstrated that Hel. pylori does not possess an uptake sequence. This is the first naturally transformable Gram-negative species shown to lack such a transformation-targeting system.

The transposon Tn916 was evaluated as a tool for generalized mutagenesis of the genome of Haemophilus influenzae. This was achieved in silico by searching the genome sequence of H. influenzae Rd for the published Tn916 target site consensus sequence 5' TT/ATTTT(N)6AAAAAA/TA. This search identified 16 putative target sites. In subsequent experiments, integration of Tn916 did not occur at any of these sites. Using the nucleotide sequences of these observed integration sites, a new consensus sequence, 5' TTTTT(N)xAAAAA (4 < or = x < or = 7), was derived. This sequence reflects the curve-twist-curve DNA topology which is a feature common to all Tn916 integration sites. A search of the H. influenzae Rd genome using the new consensus sequence identified 167 potential target sites, representing approximately 1% of the total genome. Only 80 of these sites were located within ORFs. The presence of such a limited number of target sites places severe constraints on the use of Tn916 as a tool for generalized mutagenesis of the genome of H. influenzae.