Table 5.
Prediction of PhoP-regulated genes in Sf301.
| Gene | Location | Predicted PhoP binding sites | Description or predicted function |
|---|---|---|---|
| phoP | Chromosome | tGGTTTAtttaaTGTTTAc | DNA-binding transcriptional regulator PhoP |
| yoaE | Chromosome | aTGTTTAactccCGTTTAa | Transporter |
| SF1755 | Chromosome | cCGTTTAaaattCGTTTAg | Porin |
| yrbL | Chromosome | tTGTTTAggtttTGTTTAa | Hypothetical protein |
| mgtA | Chromosome | tGGTTTAtcgttGGTTTAg | Magnesium-transporting ATPase MgtA |
| manX | Chromosome | tTAAACGggagtTAAACAt | PTS system mannose-specific transporter subunits IIAB |
| insA | Chromosome | cTAAACGaatttTAAACGg | Insertion element IS1 protein InsA |
| treR | Chromosome | cTAAACCaacgaTAAACCa | Trehalose repressor |
| mdoB | Chromosome | tTAAACGttggcTAAACGg | Phosphoglycerol transferase I |
| uspF | Chromosome | cGcTTTAggtctGGTTTAt | Stress-induced protein |
| SF1625 | Chromosome | aGGaTTAaaattGGTTTAa | Hypothetical protein |
| sbcD | Chromosome | aGaTTTAtgacaGaTTTAt | Exonuclease SbcD |
| icsA | pCP301 | tGGTTgAggcttTGTTTAa | Hypothetical protein |
| yffB | Chromosome | tGaTTTAattctGGTTaAa | Reductase |
| ygaU | Chromosome | tGaTTTAattctGGTTaAa | LysM domain/BON superfamily protein |
| ygaC | Chromosome | aGGTTcAtcgcgGcTTTAt | Hypothetical protein |
| SF2987 | Chromosome | gTGTTTAcctctGcTTTAt | Hypothetical protein |
| rpsL | Chromosome | cGtTTTAttacgTGTTTAc | 30S ribosomal protein S12 |
| malP | Chromosome | tGGTTTgcactaGcTTTAa | Maltodextrin phosphorylase |
| SF4150 | Chromosome | aGGaTTAtctgcGGTTTtt | Hypothetical protein |
| ubiC | Chromosome | aGGTTcAacagcGtTTTAc | Chorismate pyruvate lyase |
| SF1773 | Chromosome | gaGTTTAatggcGGTTaAg | Acetyltransferase |
| yjjM | Chromosome | tGtTTTAaatcgGGTTTta | Hypothetical protein |
| lpdA | Chromosome | tTGTTTAaaaatTGTTaAc | Dihydrolipoamide dehydrogenase |
| cbpA | Chromosome | cTGTTTAaaataTGTTcAg | Curved DNA-binding protein CbpA |
| yajG | Chromosome | aGGTTTcgtcctGGTTTtt | Polymerase/proteinase |
| ycbK | Chromosome | tGcTTTAcgggcGGTTaAg | Hypothetical protein |
| ycjY | Chromosome | aGGTcTAatcatGaTTTAg | Hypothetical protein |
| sdaA | Chromosome | cGGTTTttgattaGTTTAa | L-serine deaminase |
| SF1507.1 | Chromosome | tGaTTTAttagaGcTTTAt | Transmembrane anchor protein |
| slyB | Chromosome | ttGTTTAtaattGGTTgAt | Hypothetical protein |
| ybiC | Chromosome | aTGgTTAactccTGTTTAt | Hypothetical protein |
| mipA | Chromosome | tTGTTTAaggaaTGaTTAa | structural protein MipA |
| shf | pCP301 | tTGTTTAtgaatTGTTgAt | Carbohydrate transport protein |
| dppA | Chromosome | tTtTTTAatcttTGTTTgt | Dipeptide transport protein |
| hdeA | Chromosome | cTGTaTAtgtcaTGTTgAt | Acid stress chaperone HdeA |
| yhiW | Chromosome | aTGTTTgggcgaTtTTTAt | Putative ARAC-type regulatory protein |
| ipaH7.8 | pCP301 | aTGTgTAtcgttTtTTTAc | Invasion plasmid antigen |
The genes with a putative PhoP-binding motif in Sf301 were searched based on the PhoP box pattern [5′-(T/G) GTTTA-N5-(T/G) GTTTA-3′]. The putative PhoP binding sites in the promoter region were restricted to 400 bp before the start codon with at most 2 nt not matching. The bold sequences represent the PhoP box pattern in the predicted PhoP binding sites.