## 3 Results
### PhoR Gene and Amino Acid Sequences Differed between Serovars  
The predicted protein sequences of the _phoB_, _phoR_, _phoU_, _pstA_, _pstB_, _pstC_, _iraP_, _rposS_, and _rrsB_ genes among strains of the different servours were compared, and the lengths of the nucleic acid and predicted protein sequences were conserved. For the sequenced strains in this study (those with an asterisk (*) in Table 1), the predicted amino acid sequences of PhoU, PstB, PstC, IraP, RpoS, and RrsB were identical (Supplementary Figure S1). Five of these six genes had SNP differences between the eight strains and four servours (Supplementary Figure S2), but the changes resulted in the same predicted protein sequence. The DNA sequences for the _iraP_ gene were identical in all the strains (Supplementary Figure S2). Among these six genes, the largest number of SNP differences were in _phoU_, which ranged from 0-24 SNPs between the strains (Supplementary Figure S2). The remaining three genes involved in Pi metabolism (_phoB_, _phoR_, and _pstA_) had differences in the nucleic acid and in the predicted protein sequences between the eight strains and four servours (Figure 3; Supplementary Figures S1 and S2). The _phoB_ and _pstA_ genes were the same size, with _phoB_ at 690 bp, _phoR_ at 1296 bp, and _pstA_ at 891 bp. The ranges of SNP differences were 0-11 for _phoB_, 0-13 for _phoR_, and 0-24 for _pstA_. The predicted protein sequences of the transcription regulator PhoB were identical in seven of the eightstrains; the sole difference was \(S\). Kentucky RM17366, which had a Met73 Leu substitution. The predicted amino acid sequence of \(pstA\) varied only for the \(S\). Give strains RM18465 and RM20875, which each had an Ile120 Val substitution. This variant would result in a conserved substitution in this inner membrane protein responsible for Pi translocation across the membrane [46]. The gene with the most predicted amino acid substitutions was the histidine kinase \(phoR\) (Figure 3). There were four different PhoR protein sequences among the eight strains. The two \(S\). Typhimurium strains and one of the \(S\). Kentucky strains (RM17366) shared identical PhoR amino acid sequences. Both \(S\). Enteritidis strains had an Ala347 Val substitution of this sequence. The two \(S\). Give strains and \(S\). Kentucky strain RM19068 had a Val346 Ala substitution, and RM19068 had an additional Thr340 Lys substitution. The valine-alanine substitutions were conservative amino acid substitutions. Threonine-lysine resulted in R groups with a charge difference (neutral--basic, respectively). All of the amino acid changes in the predicted PhoR sequence were in the catalytic ATP-binding (CA) domain of the protein responsible for autophosphorylation of this sensor histidine kinase [47]. Figure 2: Heat map of 41 phenotype differences between the serovars. Strains were analyzed via phenotype microarray at least three times and background-subtracted, and the averages for strains were grouped into serovars. The numbers (OU range 0–500) are a measure of intensity of redox dye that reflects usage of the compound tested. The type of pre-configured microplates tested, the phenotype tested, and the chemical compound in the well are indicated. Cells are colored to indicate ranges of OU values (<20 OUs: lavelor; 20–100 OUs: yellow; >100 OUs: blue). To determine if these PhoR amino acid differences between serovars were present in additional _Salmonella_ genomes, additional PhoR sequences were compared from the genomes of serovars Enteritidis, Give, Kentucky, and Typhimurium. Including the 8 strains highlighted in Figure 3, the PhoR sequences from 10 Enteritidis strains, 10 Give strains, 15 Kentucky strains, and 11 Typhimurium strains were compared (Figure 4). All the \(S\). Typhimurium PhoR sequences were identical to each other. All the \(S\). Enteritidis had the same Ala347 Val substation indicated above (Figure 3), and 9 of the 10 were identical. \(S\). Enteritidis strain 1729765 contained a Leu22 Phe, which is a conserved substitution. Nine of the \(S\).