Figure 2

The Zur regulatory consensus in γ-Proteobacteria. (a) Original putative Zur binding sites were derived from Panina et al's study [29]. They were predicted from 13 genes in γ-Proteobacteria including E. coli, Klebsiella pneumoniae, Salmonella typhi, Y. pestis, and Vibrio cholerae, by the comparative genomics analysis [29]. Both coding and non-coding sequences of the above Zur sites were trimmed into 19 bp inverted repeat sequences and then aligned to generate a sequence-logo with a Zur box sequence (AATGTTATAW TATAACATT). (b) A position count matrix was generated as well from the alignment, where each row represented a position and each column a nucleotide. This matrix was subsequently used for the computational pattern matching analysis.