Table 1 List of the putative PmrAB targets in S. typhimurium
Name | Description | Score | Instance | Alignment | Footprint | Distribution (COG) | Distribution [38] |
Minus strand | Â | Â | Â | Â | Â | Â | Â |
STM1273 | Putative nitric oxide reductase | 0.848436 | CTTAATGTTTTCTTAAT | / | / | 1000 | All Salmonella only |
STM2132 | Pseudogene; frameshift; putative RBS for STM2133 | 0.814252 | TTTTAGATTCACTTAAT | / | / | 1000 | Some or all Salmonella only |
STM4596 | Paralog of E. coli ORF, hypothetical protein (AAC73478.1); BLAST hit to putative inner membrane protein | 0.806962 | TTTAATATTCACTTAAA | / | / | 1000 | Some Salmonella only |
STM3131 | Putative cytoplasmic protein; putative RBS for STM3130; putative first gene of operon with STM3130 (putative hypothetical protein) | 0.801641 | CTTAATTTTTACTTATT | / | / | 1000 | All Salmonella only |
STM1020 | Gifsy-2 prophage | 0.791616 | CTTATTGTTAAGTCAAT | / | / | 1000 | Other distributions |
stdA | STM3029; paralog of E. coli putative fimbrial-like protein (AAC73813.1); BLAST hit to putative fimbrial-like protein | 0.788548 | CAAAACATTAACTTAAT | / | / | 1000 | Subspecies 1 only? |
ugd | STM2080; S. typhimurium UDP-glucose 6-dehydrogenase | 0.781719 | CTCAGAATTAACTTAAT | m | + | 1100 | All nine genomes |
sinR | STM0304; S. typhimurium SINR protein. (SW:SINR_SALTY) transcriptional regulator | 0.780204 | CTTGATATCATCTTAAT | / | / | Â | Subspecies 1 only |
STM3131 | Putative cytoplasmic protein; putative RBS for STM3130; putative first gene of operon with STM3130; (putative hypothetical protein) | 0.772846 | CTTAATACTCACATTAT | / | / | 1000 | Other distributions |
STM4413 | Putative imidazolonepropionase and related amidohydrolases; putative RBS for STM4412; first gene of operon with STM4412 (D-galactonate transport) | 0.771153 | GTGAATGTTAAATTAAT | / | / | 1000 | Some or all Salmonella only |
ybdO | STM0606; ortholog of E. coli putative transcriptional regulator LYSR-type (AAC73704.1); BLAST hit to putative transcriptional regulator, LysR family | 0.769839 | CTTAATGTAGAGTTTAT | m | + | 1110 | All Salmonella only |
oraA | STM2828; ortholog of E. coli regulator, OraA protein (AAC75740.1); BLAST hit to regulator | 0.766748 | CTTGATGGTAATTTAAC | m | - | 1110 | All nine genomes |
sdhC | STM0732; Ortholog of E. coli succinate dehydrogenase, cytochrome b556 (AAC73815.1); Putative RBS for sdhD; first gene of putative operon encoding succinate dehydrogenase | 0.765950 | CTTATTATTCCCTTAAG | / | / | 1000 | All nine genomes |
ycaR | STM0987; Ortholog of E. coli ORF, hypothetical protein (AAC74003.1); BLAST hit to putative inner membrane protein; Putative RBS for kdsB; first gene of a putative operon with ksdB (CMP-3-deoxy-D-manno-octulosanate transferase) | 0.765889 | TTCAATATTAACATAAT | / | / | 1000 | All nine genomes |
lasT | STM4600; Ortholog of E. coli ORF, hypothetical protein (AAC77356.1); BLAST hit to putative tRNA*tRNA methyltransferase | 0.765754 | ATTTAGGATAATTTAAT | nd | / | 1110 | All nine genomes |
STM2137 | Putative cytoplasmic protein | 0.764036 | TTTAACCTTAATTTAAT | nd | / | 1100 | Some Salmonella only |
STM1672 | Putative cytoplasmic protein | 0.762904 | ATTAATAGTCACTTATT | / | / | 1000 | Subspecies 1 only? |
gcvA | STM2982; Ortholog of E. coli positive regulator of gcv operon (AAC75850.1); first gene of putative operon (gcvA, ygdD, ygdE containing a SAM-dependent methyltransferase) | 0.761166 | CTTAATGTCGAATGAAT | m | + | 1111 | All nine genomes |
ycgO | STM1801; Ortholog of E. coli ORF, hypothetical protein (AAC74275.1); BLAST hit to putative CPA1 family, Na:H transport protein | 0.760685 | TTTAACATTAACATAAT | m | + | 1110 | All nine genomes? |
STM2287 | Paralog of E. coli putative sulfatase* phosphatase (AAC75329.1); BLAST hit to putative cytoplasmic protein | 0.759519 | CTTATTATTCACATAAC | / | / | 1000 | Some or all Salmonella only? |
yebW | STM1852; Ortholog of E. coli ORF, hypothetical protein (AAC74907.1); BLAST hit to putative inner membrane lipoprotein | 0.754895 | CTCAATGTTAACTACTT | / | / | 1000 | All nine genomes? |
STM0897 | Hypothetical protein Fels-1 prophage | 0.754468 | CGTAAGGCTCTTTTAAT | / | / | 1000 | Some Salmonella only |
lpfA | STM3640; S. typhimurium long polar fimbrial protein A precursor; first gene of a putative fimbriae synthesis operon | 0.753228 | ATTAAGAATAAATTAAT | / | / | 1000 | Other distributions |
Plus strand | Â | Â | Â | Â | Â | Â | Â |
yjdB* | STM4293; S. typhimurium hypothetical 61.6 kDa protein in basS*pmrA-adiY intergenic region. (SW:YJDB_SALTY) putative integral membrane protein; Putative RBS for basR; first gene of the putative operon (yjdB basR basS) | 0.930146 | CTTAAGGTTCACTTAAT | m | + | 1111 | All nine genomes |
ugd | STM2080; S. typhimurium UDP-glucose 6-dehydrogenase | 0.913666 | CTTAATATTAACTTAAT | m | + | 1100 | All nine genomes |
yfbE/ais | STM2297; Ortholog of E. coli putative enzyme (AAC75313.1); first gene of the yfbE operon; shared intergenic with ais | 0.912660 | CTTAATGTTAATTTAAT | m | + | 1111 | All nine genomes? |
STM1269*/STM1268 | Putative chorismate mutase; intergenic shared with STM1268 | 0.888478 | CTTAATGTTATCTTAAT | / | / | 1000 | All Salmonella only |
STM0692 | Paralog of E. coli nitrogen assimilation control protein (AAC75050.1); putative transcriptional regulator, LysR family | 0.814773 | CTTGATGTTGATTTAAT | / | / | 1000 | All Salmonella only |
ybjG/mdfA* | STM0865; Ortholog of E. coli orf, hypothetical protein (AAC73928.1); putative permease; intergenic shared with mdfA (multidrug translocase) | 0.810981 | CTTTAAGGTTAATTTAA | m | + | 1111 | All nine genomes |
STM2901 | Hypothetical protein putative cytoplasmic protein; located downstream of pathogenicity island 1 | 0.803712 | CTTAATATCAATATAAT | / | / | 1000 | Other distributions |
yhjC/yhjB | STM3607; Ortholog of E. coli putative transcriptional regulator LysR-type (AAC76546.1); intergenic shared with yhjB (putative transcriptional regulator) | 0.796967 | TTGAATATTAATTTAAT | nd | / | 1110 | All nine genomes? |
yjbE/pgi | STM4222; Ortholog of E. coli orf, hypothetical protein (AAC76996.1); BLAST hit to putative outer membrane protein; first gene of the putative operon (yjbE, yjbF, yjbG, yjbH) consisting of putative outer membrane (lipo)proteins; intergenic shared with pgi (glucosephosphate isomerase) | 0.791181 | TTTAATTTTAACTTATT | / | / | 1000 | All nine genomes? |
yibD* | STM3707; Ortholog of E. coli putative regulator (AAC76639.1); BLAST hit to putative glycosyltransferase | 0.790879 | CTTAATAGTTTCTTAAT | m | + | 1100 | Other distributions |
STM1926/flhC | Putative cytoplasmic protein Putative RBS for STM1926; first gene of a putative operon with yecG (putative universal stres protein); shared intergenic with flhC en flhD (flagellar transcriptional activator) | 0.790699 | CCTAATGTTCACTTTTT | / | / | 1000 | Some or all Salmonella only |
STM0334/STM0335 | Putative cytoplasmic protein; shared intergenic with STM0335 | 0.789514 | TTTCATATTCATTTAAT | / | / | 1000 | Some Salmonella only |
ybdN | STM0605; Ortholog of E. coli orf, hypothetical protein (AAC73703.1); BLAST hit to putative 3-phosphoadenosine 5-phosphosulfate sulfotransferase (PAPS reductase)*FAD synthetase Putative RBS for ybdM; first gene of a putative operon with ybdM (hypothetical transcriptional regulator) | 0.788778 | ATTAATATAAATTTAAT | nd | / | 1100 | All nine genomes? |
glgB | STM3538; Ortholog of E. coli 1,4-alpha-glucan branching enzyme (AAC76457.1); BLAST hit to 1,4-alpha-glucan branching enzyme; Putative RBS for glgX; putative first gene of operon involved in glycogen synthesis | 0.779808 | TTTAAGGGTAGCTTAAT | m | - | 1111 | All nine genomes |
leuO | STM0115; S. typhimurium probable activator protein in leuabcd operon. (SW:LEUO_SALTY) putative transcriptional regulator (LysR family) | 0.776490 | ATTAATGTTAACTTTTT | m | - | 1111 | All nine genomes |
STM0343 | Paralog of E. coli orf, hypothetical protein (AAC75237.1); BLAST hit to AAC75237.1 identity in aa 10 - 512 putative Diguanylate cyclase*phosphodiesterase domain | 0.774271 | ATTAATGTTACTTTAGT | nd | / | 1100 | Subspecies 1 only |
orf242 | STM1390 S. typhimurium ORF242 (gi|4456866) putative regulatory proteins, merR family | 0.773644 | CTTAGTCTTCATTTGAT | / | / | 1000 | Other distributions |
STM1868A/mig-3 | Lytic enzyme; intergenic shared with mig-3 (phage assembly protein) | 0.773462 | CTTAATGATTATTTATT | / | / | 1000 | ? |
STM2763/STM2726 | Paralog of E. coli prophage CP4-57 integrase (AAC75670.1); BLAST hit to putative integrase; intergenic shared with STM2726 (putative inner membrane) | 0.772053 | ATTAATGTCCATTTAGT | / | / | 1000 | S. typhimurium only |
pntA | STM1479; Ortholog of E. coli pyridine nucleotide transhydrogenase, alpha subunit (AAC74675.1); Blast hit to AAC74675.1 pyridine nucleotide transhydrogenase (proton pump), alpha subunit; Putative RBS for pntB; first gene of the putative operon (pntA, pntB) | 0.770547 | TTTAATGTTAATTTCTT | m | - | 1111 | All nine genomes |
STM0057/cit2 | Putative citrate-sodium symport; intergenic shared with citC2 (citrate lyase synthetase) | 0.767968 | CTCATGGTTCATTGAAT | nd | / | 1110 | Other distributions |
yrbF | STM3313; Ortholog of E. coli putative ATP-binding component of a transport system (AAC76227.1); Blast hit to AAC76227.1 putative ABC superfamily (atp_bind) transport protein; Putative RBS for yrbE; RegulonDB:STMS1H003330; first gene of putative yrb operon (ABC transporter) | 0.766758 | CCTAATTTTGACTTTAT | m | + | 1111 | All nine genomes |
yejG | STM2220; Paralog of E. coli orf, hypothetical protein (AAC75242.1); Blast hit to putative cytoplasmic protein | 0.767099 | CTTTATGTTTATTTTAT | m | + | 1111 | All nine genomes |
slsA | STM3761; putative inner membrane protein | 0.765418 | CTTTATGTTATTTAAAT | nd | / | 1110 | Other distributions |
yhcN | STM3361; Ortholog of E. coli orf, hypothetical protein (AAC76270.1); Blast hit to putative outer membrane protein | 0.764452 | ATTAGTGTATACTTAAT | m | + | 1111 | All nine genomes? |
yceP | STM1161; Ortholog of E. coli orf, hypothetical protein (AAC74144.1); Blast hit to putative cytoplasmic protein | 0.764191 | TTTATTGTTCATATAAT | m | + | 1100 | All nine genomes |
STM4098 | putative arylsulfate sulfotransferase | 0.763003 | TCTAATATTTATTTAAT | nd | / | 1100 | Subspecies 1 only? |
stfA | STM0195; S. typhimurium major fimbrial subunit StfA | 0.762241 | ATCAATTTTAATTTAAT | / | / | 1000 | Some Salmonella only |
atpF | STM3869; Ortholog of E. coli membrane-bound ATP synthase, F0 sector, subunit b (AAC76759.1); Blast hit to imembrane-bound ATP synthase, F0 sector, subunit b; Putative RBS for atpH; first gene of a putative operon encoding putative ATP synthase | 0.760841 | CAGAAGGTTAACTAGAT | m | + | 1111 | All nine genomes |
yegH/wza | STM2119; Ortholog of E. coli putative transport protein (AAC75124.1); Blast hit to putative inner membrane protein; intergenic shared with wza (putative polysaccharide export protein) | 0.760004 | ATTAATATTAAATGAAT | m | - | 1111 | All nine genomes |
yjgD/argI | STM4470; S. typhimurium hypothetical protein in argI-miaE intergenic region (ORF15.6). (SW:YJGD_SALTY) putative cytoplasmic protein; Putative binding site for ArgR; shared intergenic regions with argI (arginine ornithine transferase); first gene of a putative operon with miaE (tRNA hydroxylase) | 0.759514 | ATTAAAATTCACTTTAT | m | + | 1111 | All nine genomes |
sseJ/STM1630* | STM1631; S. typhimurium secreted effector; regulated by SPI-2; shared intergenic with STM1630 (putative inner membrane protein) | 0.758303 | CTTAAGAAATATTTAAT | / | / | 1000 | Some Salmonella only |
csrA | STM2826; S. typhimurium carbon storage regulator | 0.756990 | CTTAGGTTTAACAGAAT | m | + | 1111 | All nine genomes |
dinP/yafK | STM0313; Ortholog of E. coli damage-inducible protein P; putative tRNA synthetase (AAC73335.1); Blast hit to AAC73335.1 DNA polymerase IV, devoid of proofreading, damage-inducible protein P; intergenic shared with yafKJ (periplasmic protein, putative amido transferase) | 0.756938 | CATACTGTACACTTAAA | m | + | 1111 | All nine genomes |
STM0346 | Putative outer membrane protein; Homolog of ail and ompX | 0.756369 | CATTAGGTGCTCTTAAT | / | / | 1000 | Some Salmonella only |
ybfA/STM0707 | STM0708; Ortholog of E. coli orf, hypothetical protein (AAC73793.1); Blast hit to putative periplasmic protein; intergenic shared with STM0707 (hypothetical protein) | 0.754265 | ATTAGTATTAATTTAAC | m | + | 1111 | All nine genomes? |
yncD/STM1587 | STM1587; Ortholog of E. coli putative outer membrane receptor for iron transport (AAC74533.1); Blast hit to paral putative outer membrane receptor; intergenic shared with STM1586 (putative receptor) | 0.754063 | CATTTTCTTAACTTAAT | m | - | 1100 | All nine genomes |
yafC/STM0275 | STM0256; Ortholog of E. coli putative transcriptional regulator LysR-type (AAC73313.1); Blast hit to putative transcriptional regulator, LysR family; intergenic shared STM0275 (drug efflux protein) | 0.753257 | CAAAATATCAATTTAAT | m | - | 1111 | Other distributions |