Skip to main content

Table 1 List of the putative PmrAB targets in S. typhimurium

From: In silico identification and experimental validation of PmrAB targets in Salmonella typhimuriumby regulatory motif detection

Name Description Score Instance Alignment Footprint Distribution (COG) Distribution [38]
Minus strand        
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 / /   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        
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
  1. 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.