Characterization of the hfq gene in H. influenzae . (A) CLUSTALW alignment between the Hfq of E. coli (Hfq_Ec) and H. influenzae. Amino acids denoted by asterisks (*) are identical, colons (:) strongly similar and dots (.) weakly similar. The secondary structure of the E. coli Hfq is indicated above the sequence and dashed-line boxes denote the Sm1 and Sm2 motifs. The shaded boxes are residues that are important in RNA binding by the Hfq of S. aureus and the two signature motifs of Hfq are underlined. This was modified from the figure of Nielson et al. . (B) Fluorescent intensities of primer extension products synthesized from H. influenzae RNA. (C) Sequence of the transcription start site (+1) and the proposed promoter region for the H. influenzae Hfq gene. The sequence complementary to the primer used for primer extension is boxed, the transcription start site is boldfaced, and the putative −10 and −35 promoter sequences are underlined.