Table 1

List of the putative PmrAB targets in S. typhimurium

Name: name of the gene in the S. typhimurium genome (NC_003197). For genes that are divergently transcribed and have a shared intergenic region, the gene for which the motif is detected on the plus strand is indicated first and the gene for which the motif is on the minus strand is indicated after the slash. Description: annotation of the encoded proteins and genome location of the genes (derived from GenBank and Sanger annotation). Score: normalized score assigned to the respective motifs by MotifLocator. Site: instance of the motif as detected in the respective intergenic sequence. Distribution (COG): distribution of the protein as determined by our analysis. The distribution is indicated by a binary profile that indicates the presence 1 versus absence 0 of the protein in species (serovars) of, respectively, Salmonella, E. coli, Shigella and Yersinia (for example, 1111 indicates protein present in all four species; 1000: protein present in Salmonella species only). Distribution: distribution of the protein encoded by the corresponding gene in nine bacterial genomes as determined by McClelland et al. [38]. Proteins having close homologs in at least one Salmonella strain but not in E. coli or K. pneumoniae are indicated by 'some Salmonella only'. Genes that contain close homologs in all genomes are indicated by 'all nine genomes'. Other combinations are indicated by 'other distributions'. ? indicates that the authors were not certain about the statement. Differences between the distribution as determined by McClelland et al. and the one determined by our analysis is due to the difference in selection criteria used to identify close homologs (see Materials and methods). Alignment: indicates whether the intergenic regions in the dataset could be locally aligned (nd, no local alignment detected that contained the original sequence of S. typhimurium; m, local alignment detected. If the dataset only contained homologs from Salmonella species, local alignments were considered noninformative (indicated by /)). Footprint: denotes whether the PmrA motif is conserved in the close homologs. +, the retrieved putative PmrA motif is conserved; -, the intergenic sequences of the orthologs could be locally aligned but the PmrA motif was not part of the conserved regions. Most promising PmrAB targets that contained a PmrA motif matching the PmrA consensus (Figure 4) are in bold face. PmrA motifs that are experimentally validated in this study are indicated by an asterisk.

Marchal et al. Genome Biology 2004 5:R9   doi:10.1186/gb-2004-5-2-r9