FIG. 4.
Similar deduced amino acid sequences of Acinetobacter PcaU and PobR. The aligned amino acid sequences are flanked by their encoding nucleotide sequences. Asterisks mark identical residues in the aligned amino acid sequences; nucleotide sequences extending both upstream and downstream from pcaU are shown. Two methionine codons, separated by nine nucleotide residues, are plausible start codons for pcaU translation; these codons are underlined. Because of uncertainty about the start codons, it is possible to conclude only that PcaU contains either 274 or 278 residues. The weight matrix comparison method of Dodd and Egan (12) assessed the likelihood of the shaded PcaU sequence being a helix-turn-helix DNA binding motif to be 100%, on the basis of a standard deviation score of 4.6; the corresponding value for the shaded PobR sequence is 5.2 (9). Restriction sites used in this investigation are labelled and marked by double overlining. Dashed arrows both upstream and downstream of pcaU indicate inverted repetitions that subsequent experiments demonstrated to be in sites where PcaU binds to DNA. Double overlining and underlining mark the EcoRI and XmnI sites bordering an upstream DNA fragment that was shown to bind PcaU. Double-dashed arrows indicate the positions of primers used to amplify a downstream DNA fragment that binds PcaU.