Curation Information

Publication
Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ⁵⁴ (RpoN) regulon of Salmonella Typhimurium LT2.;Samuels DJ, Frye JG, Porwollik S, McClelland M, Mrázek J, Hoover TR, Karls AC;BMC genomics 2013 Sep 5; 14():602 [24007446]
TF
RpoN [P26979, view regulon]
Reported TF sp.
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Reported site sp.
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Created by
Dinara Sagitova
Curation notes
-

Experimental Process

Microarray analysis identified RpoN-dependent genes by comparing gene expression levels in wild-type S. Typhimurium LT2 and its rpoN deletion mutant. ChIP-chip assay combined with in silico analysis (PSSM site search) identified RpoN binding sites in S. Typhimurium LT2 genome. Promoter-lacZ fusion assays with seven of the 29 intergenic RpoN binding sites confirmed the functionality of RpoN binding sites identified by the ChIP-chip and PSSM analyses.

ChIP assay conditions
100 ml cultures of S. Typhimurium strains MS1868 (WT) and TRH134 (ΔrpoN) were grown overnight in NB at 37°C and sub-cultured in fresh medium the next day. Once cultures reached mid-log phase (OD600 ≈ 0.7), cells were treated with formaldehyde (3 ml of a 37% solution per 100 ml of culture) for 10 min. at room temperature to cross-link proteins to DNA. Cross-linking was quenched by the addition of glycine (10 ml of 1.33 M solution per 100 ml of culture) and incubation at 4°C for 30 min. Cells were harvested, washed and lysed in accordance with kit instructions. Cells were lysed in two passages through a French pressure cell at 10,000 psi. Cell extracts were clarified and pre-cleared with the provided protein A-Sepharose bead slurry per the kit instructions. 0.6 ml of the resulting extracts were mixed with 2 μl of rabbit anti-serum against S. Typhimurium σ54[73] and incubated with gentle shaking overnight at 4°C. The next day, 50 μl of protein A-Sepharose bead slurry was added to each sample, incubated 1 hr at room temperature and collected by centrifugation. The beads were washed, and protein-DNA complexes were eluted from the beads and disrupted per the supplier’s instructions. DNA was purified from each sample using the Qiagen PCR purification kit.
ChIP notes
Purified ChIP DNA was amplified by ligation-mediated PCR, adapting the procedure found at [http://www.flychip.org.uk/protocols/archive_protocols/lm_pcr.php]. Linkers consisting of complementary oligonucleotides (LM-PCR; Additional file 3) were ligated to the ends of purified DNA repaired with T4 DNA polymerase. Ligated was purified using the Qiagen PCR purification kit and the DNA was amplified with Taq polymerase (Fermentas; Burlington, ON) using LM-PCR-R as the PCR primer and the following cycling conditions: 55°C—2 min (1×); 72°C—5 min (1×); 94°C—5 min (1×); 94°C—1 min, 55°C—1 min, 72°C—1 min (24×); 72°C—5 min (1×); 4°C—hold. The resulting amplicons, most of which were 300–800 bp, were purified using the Qiagen PCR purification kit and to prepare dye-labeled DNA (Cy3 or Cy5) for hybridization to the S. Typhimurium complete ORF microarray. Microarrays were scanned and analyzed as above. ChIP-chip was performed on three biological replicates for the WT and ΔrpoN strains; the statistical analysis of the data was performed as described for the microarray data.

Transcription Factor Binding Sites


TGGCATAGCCTTTGCTTT
TGTCACGTATTTTGCATG
TGGCACATCCTTTGCAAT
TGGCACGCCGTTTGCCAT
TGGCACGCCTTTTGATTA
TGGCACGTCTATTGCTTT
TGGCATGATTTTTTCATT
TGGCATGAGAGTTGCTTT
TGGCACGAATGCTGCAAT
TGGCACGCAAATTGTATT
TGGCATAAGACCTGCATG
TGGCATGCCTTTTGCTTT
TGGCACAATTACTGCATA
TGGCATGAATATTGCGAG
TGGCACACTAGCTGCAAT
TGGCACGATTCGTGTATA
TGGCATGGAAAATGCTTA
TGGCATAAATATTGCTTT
TGGCACGCTGGTTGCAAT
TGGCACGGTTGTTGCTCG
TGGCACAACCTTTGCTCT
TGGCACGTTATGTGCAAT
TGGCACAGATTTCGCTTT
TGGCACGGAAGATGCAAG
TGGCATGATCTCTGCTTA
TGGCATGATTTTTGTAAG
TGGCATAAAACATGCATA
TGGCAGATATTTTGCTTG
TGGCACGCCGCTTGCTCT
TGGAACGCGTCTTGCAGG
CGGCATGGCATTTGCCAG
CGGCACAGTTTATGCAAG
TGGCCAGAAATATGCTTA
TGGCATTAATGCTGCATC
TGGCATCGATATTGCAAA
TGGCAGGAGTTTTTCAAT
CGGCACGATTTTTTCCAT
TGGCATGAAACTTGTCAC
TGGCCTGAATCTTGCTAA
TGGCATGAAAGCTGCTCA
TGGCATTCTTTATGCTCA
TGGCATCATTATTGCCTA
TGGCATGAAGGTTCATCG
TGGCAAGAATATTGCCAT
TGGCACACGTTTTGCGCT
TGGCATCATTTTTTCAAG
TGGCAAACCTGTGGTATA
TGGCAGGAGCGTTTTATT
TGGCGCGCTTTTTGCCTT
CGGTATAAATAATGCACG
TGGCATATAAATTGAGAT
AGGCATTTTTCTTGCATC
TGGCATCACTGTTGCAGT
TGGCACATCAGGCAAAAG
TGGCAGGTCACCTGCAAT
TGGTACGGATCTTGCCAT
CGGCGTAATTTTTGCATC
CGGCACAGCTCTTGCATC
TGGAACGCTTTTCGCATT
TGGCCCATTGAATGCATC
TGGCATGATGGTCGCCAG
AGGCATGTTTTATGCAAA
TGGTACGTAAAATGCACG
TGGCGCGATTATTGCCAG
TGGCCTGCTATTTGCCCT
TGGCGCGGAAATTGCACA
TGGCATAAAACCTGAAAA
AGGCGCGAATAATGCATC
TGGCCTGATTTTTGCAGG
TGGCGTGGCGATTTCAAT
TGGCATAGCCTTTGCTTT
TGTCACGTATTTTGCATG
TGGCACATCCTTTGCAAT
TGGCACGCCGTTTGCCAT
TGGCACGCCTTTTGATTA
TGGCACGTCTATTGCTTT
TGGCATGATTTTTTCATT
TGGCATGAGAGTTGCTTT
TGGCACGAATGCTGCAAT
TGGCACGCAAATTGTATT
TGGCATAAGACCTGCATG
TGGCATGCCTTTTGCTTT
TGGCACAATTACTGCATA
TGGCATGAATATTGCGAG
TGGCACACTAGCTGCAAT
TGGCACGATTCGTGTATA
TGGCATGGAAAATGCTTA
TGGCATAAATATTGCTTT
TGGCACGCTGGTTGCAAT
TGGCACGGTTGTTGCTCG
TGGCACAACCTTTGCTCT
TGGCACGTTATGTGCAAT
TGGCACAGATTTCGCTTT
TGGCACGGAAGATGCAAG
TGGCATGATCTCTGCTTA
TGGCATGATTTTTGTAAG
TGGCATAAAACATGCATA
TGGCAGATATTTTGCTTG
TGGCACGCCGCTTGCTCT
TGGAACGCGTCTTGCAGG
CGGCATGGCATTTGCCAG
CGGCACAGTTTATGCAAG
TGGCCAGAAATATGCTTA
TGGCATTAATGCTGCATC
TGGCATCGATATTGCAAA
TGGCAGGAGTTTTTCAAT
CGGCACGATTTTTTCCAT
TGGCATGAAACTTGTCAC
TGGCCTGAATCTTGCTAA
TGGCATGAAAGCTGCTCA
TGGCATTCTTTATGCTCA
TGGCATCATTATTGCCTA
TGGCATGAAGGTTCATCG
TGGCAAGAATATTGCCAT
TGGCACACGTTTTGCGCT
TGGCATCATTTTTTCAAG
TGGCAAACCTGTGGTATA
TGGCAGGAGCGTTTTATT
TGGCGCGCTTTTTGCCTT
CGGTATAAATAATGCACG
TGGCATATAAATTGAGAT
AGGCATTTTTCTTGCATC
TGGCATCACTGTTGCAGT
TGGCACATCAGGCAAAAG
TGGCAGGTCACCTGCAAT
TGGTACGGATCTTGCCAT
CGGCGTAATTTTTGCATC
CGGCACAGCTCTTGCATC
TGGAACGCTTTTCGCATT
TGGCCCATTGAATGCATC
TGGCATGATGGTCGCCAG
AGGCATGTTTTATGCAAA
TGGTACGTAAAATGCACG
TGGCGCGATTATTGCCAG
TGGCCTGCTATTTGCCCT
TGGCGCGGAAATTGCACA
TGGCATAAAACCTGAAAA
AGGCGCGAATAATGCATC
TGGCCTGATTTTTGCAGG
TGGCGTGGCGATTTCAAT

Quantitative data format: PSSM score

TGGCATAGCCTTTGCTTT 20.7
TGTCACGTATTTTGCATG 14.6
TGGCACATCCTTTGCAAT 20.0
TGGCACGCCGTTTGCCAT 17.9
TGGCACGCCTTTTGATTA 18.7
TGGCACGTCTATTGCTTT 22.1
TGGCATGATTTTTTCATT 20.8
TGGCATGAGAGTTGCTTT 21.5
TGGCACGAATGCTGCAAT 21.7
TGGCACGCAAATTGTATT 20.3
TGGCATAAGACCTGCATG 16.2
TGGCATGCCTTTTGCTTT 23.6
TGGCACAATTACTGCATA 20.6
TGGCATGAATATTGCGAG 14.6
TGGCACACTAGCTGCAAT 20.1
TGGCACGATTCGTGTATA 17.1
TGGCATGGAAAATGCTTA 17.9
TGGCATAAATATTGCTTT 22.4
TGGCACGCTGGTTGCAAT 21.2
TGGCACGGTTGTTGCTCG 18.9
TGGCACAACCTTTGCTCT 20.3
TGGCACGTTATGTGCAAT 19.5
TGGCACAGATTTCGCTTT 19.2
TGGCACGGAAGATGCAAG 17.4
TGGCATGATCTCTGCTTA 20.1
TGGCATGATTTTTGTAAG 19.4
TGGCATAAAACATGCATA 18.2
TGGCAGATATTTTGCTTG 14.1
TGGCACGCCGCTTGCTCT 18.3
TGGAACGCGTCTTGCAGG 6.2
CGGCATGGCATTTGCCAG 9.5
CGGCACAGTTTATGCAAG 11.3
TGGCCAGAAATATGCTTA 8.1
TGGCATTAATGCTGCATC 9.1
TGGCATCGATATTGCAAA 13.7
TGGCAGGAGTTTTTCAAT 12.1
CGGCACGATTTTTTCCAT 10.0
TGGCATGAAACTTGTCAC 11.7
TGGCCTGAATCTTGCTAA 13.7
TGGCATGAAAGCTGCTCA 17.7
TGGCATTCTTTATGCTCA 11.6
TGGCATCATTATTGCCTA 12.9
TGGCATGAAGGTTCATCG 6.5
TGGCAAGAATATTGCCAT 13.5
TGGCACACGTTTTGCGCT 13.4
TGGCATCATTTTTTCAAG 11.7
TGGCAAACCTGTGGTATA 5.9
TGGCAGGAGCGTTTTATT 8.1
TGGCGCGCTTTTTGCCTT 14.4
CGGTATAAATAATGCACG 2.2
TGGCATATAAATTGAGAT 9.5
AGGCATTTTTCTTGCATC 4.9
TGGCATCACTGTTGCAGT 11.7
TGGCACATCAGGCAAAAG 1.0
TGGCAGGTCACCTGCAAT 12.7
TGGTACGGATCTTGCCAT 11.1
CGGCGTAATTTTTGCATC 6.8
CGGCACAGCTCTTGCATC 10.9
TGGAACGCTTTTCGCATT 14.5
TGGCCCATTGAATGCATC 6.9
TGGCATGATGGTCGCCAG 12.6
AGGCATGTTTTATGCAAA 11.6
TGGTACGTAAAATGCACG 8.3
TGGCGCGATTATTGCCAG 11.1
TGGCCTGCTATTTGCCCT 11.0
TGGCGCGGAAATTGCACA 11.8
TGGCATAAAACCTGAAAA 13.6
AGGCGCGAATAATGCATC 4.2
TGGCCTGATTTTTGCAGG 10.1
TGGCGTGGCGATTTCAAT 8.2
TGGCATAGCCTTTGCTTT 20.7
TGTCACGTATTTTGCATG 14.6
TGGCACATCCTTTGCAAT 20.0
TGGCACGCCGTTTGCCAT 17.9
TGGCACGCCTTTTGATTA 18.7
TGGCACGTCTATTGCTTT 22.1
TGGCATGATTTTTTCATT 20.8
TGGCATGAGAGTTGCTTT 21.5
TGGCACGAATGCTGCAAT 21.7
TGGCACGCAAATTGTATT 20.3
TGGCATAAGACCTGCATG 16.2
TGGCATGCCTTTTGCTTT 23.6
TGGCACAATTACTGCATA 20.6
TGGCATGAATATTGCGAG 14.6
TGGCACACTAGCTGCAAT 20.1
TGGCACGATTCGTGTATA 17.1
TGGCATGGAAAATGCTTA 17.9
TGGCATAAATATTGCTTT 22.4
TGGCACGCTGGTTGCAAT 21.2
TGGCACGGTTGTTGCTCG 18.9
TGGCACAACCTTTGCTCT 20.3
TGGCACGTTATGTGCAAT 19.5
TGGCACAGATTTCGCTTT 19.2
TGGCACGGAAGATGCAAG 17.4
TGGCATGATCTCTGCTTA 20.1
TGGCATGATTTTTGTAAG 19.4
TGGCATAAAACATGCATA 18.2
TGGCAGATATTTTGCTTG 14.1
TGGCACGCCGCTTGCTCT 18.3
TGGAACGCGTCTTGCAGG 6.2
CGGCATGGCATTTGCCAG 9.5
CGGCACAGTTTATGCAAG 11.3
TGGCCAGAAATATGCTTA 8.1
TGGCATTAATGCTGCATC 9.1
TGGCATCGATATTGCAAA 13.7
TGGCAGGAGTTTTTCAAT 12.1
CGGCACGATTTTTTCCAT 10.0
TGGCATGAAACTTGTCAC 11.7
TGGCCTGAATCTTGCTAA 13.7
TGGCATGAAAGCTGCTCA 17.7
TGGCATTCTTTATGCTCA 11.6
TGGCATCATTATTGCCTA 12.9
TGGCATGAAGGTTCATCG 6.5
TGGCAAGAATATTGCCAT 13.5
TGGCACACGTTTTGCGCT 13.4
TGGCATCATTTTTTCAAG 11.7
TGGCAAACCTGTGGTATA 5.9
TGGCAGGAGCGTTTTATT 8.1
TGGCGCGCTTTTTGCCTT 14.4
CGGTATAAATAATGCACG 2.2
TGGCATATAAATTGAGAT 9.5
AGGCATTTTTCTTGCATC 4.9
TGGCATCACTGTTGCAGT 11.7
TGGCACATCAGGCAAAAG 1.0
TGGCAGGTCACCTGCAAT 12.7
TGGTACGGATCTTGCCAT 11.1
CGGCGTAATTTTTGCATC 6.8
CGGCACAGCTCTTGCATC 10.9
TGGAACGCTTTTCGCATT 14.5
TGGCCCATTGAATGCATC 6.9
TGGCATGATGGTCGCCAG 12.6
AGGCATGTTTTATGCAAA 11.6
TGGTACGTAAAATGCACG 8.3
TGGCGCGATTATTGCCAG 11.1
TGGCCTGCTATTTGCCCT 11.0
TGGCGCGGAAATTGCACA 11.8
TGGCATAAAACCTGAAAA 13.6
AGGCGCGAATAATGCATC 4.2
TGGCCTGATTTTTGCAGG 10.1
TGGCGTGGCGATTTCAAT 8.2

Gene Regulation

Regulated genes for each binding site are displayed below. Gene regulation diagrams show binding sites, positively-regulated genes, negatively-regulated genes, both positively and negatively regulated genes, genes with unspecified type of regulation. For each indvidual site, experimental techniques used to determine the site are also given.

Site sequence Regulated genes Gene diagram Experimental techniques TF function TF type
TGGCATAGCCTTTGCTTT prpB,
... ... prpB prpR prpC prpD prpE
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGTCACGTATTTTGCATG clpP
... ... clpP
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCACATCCTTTGCAAT glnK,
... ... glnK amtB
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCACGCCGTTTGCCAT STM0577,
... ... STM0577 STM0576 STM0575 STM0574 STM0573 STM0572
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCACGCCTTTTGATTA STM0649.S,
... ... STM0649.S leuS rlpB holA nadD STM0650 STM0651 STM0652 ybeL
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCACGTCTATTGCTTT gltI
... ... gltI
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCATGATTTTTTCATT glnH,
... ... glnH glnP glnQ ybiO
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCATGAGAGTTGCTTT yeaG,
... ... yeaG yeaH mipA
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCACGAATGCTGCAAT argD,
... ... argD xthA STM1301 astA astD astB astE
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCACGCAAATTGTATT pspA,
... ... pspA pspB pspC pspD pspE ycjX ycjF tyrR pspF sapA sapB sapC sapD sapF
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCATAAGACCTGCATG argT
... ... argT
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCATGCCTTTTGCTTT STM2360,
... ... STM2360 STM2359 STM2358 STM2357 ubiX STM2361
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCACAATTACTGCATA
... ... yfhK yfhG yfhA glnB
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCATGAATATTGCGAG proV,
... ... proV proW proX
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCACACTAGCTGCAAT STM2840,
... ... STM2840 ygaA ygbD
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCACGATTCGTGTATA hydN,
... ... hydN hypF
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCATGGAAAATGCTTA hycA,
... ... 3000000 hycA hycB hycC hycD hycE hycF hycG hycH hycI STM2844 hypA hypB hypC hypD hypE
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCATAAATATTGCTTT hypA,
... ... 3000000 hypA hycA hycB hycC hycD hycE hycF hycG hycH hycI STM2844 hypB hypC hypD hypE
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCACGCTGGTTGCAAT STM3521,
... ... STM3521 STM3519.1N rtcR
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCACGGTTGTTGCTCG rpoH
... ... rpoH
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCACAACCTTTGCTCT STM3772,
... ... STM3772 STM3771 STM3770 STM3769.S STM3768 STM3767
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCACGTTATGTGCAAT
... ... proM
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCACAGATTTCGCTTT glnA,
... ... glnA typA
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCACGGAAGATGCAAG zraP,
... ... zraP hydH hydG
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCATGATCTCTGCTTA hydH,
... ... hydH zraP hydG
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCATGATTTTTGTAAG pspG
... ... pspG
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCATAAAACATGCATA fdhF
... ... fdhF
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCAGATATTTTGCTTG yjeB,
... ... yjeB vacB yjfH yjfI yjfJ STM4372 yjfK yjfL yjfM yjfC aidB
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGCACGCCGCTTGCTCT STM4535,
... ... STM4535 STM4536 STM4537 STM4538 STM4539 STM4540.S
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGGAACGCGTCTTGCAGG
... ... ftsQ ftsA ftsZ lpxC
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
CGGCATGGCATTTGCCAG
... ... STM0155
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
CGGCACAGTTTATGCAAG
... ... proA thrW
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCCAGAAATATGCTTA
... ... STM0332 STM0333
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCATTAATGCTGCATC
... ... allC ylbA
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCATCGATATTGCAAA
... ... STM0699
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCAGGAGTTTTTCAAT
... ... potH potI ybjO rumB
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
CGGCACGATTTTTTCCAT
... ... ulaA STM0885 STM0886
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCATGAAACTTGTCAC
... ... STM0901 STM0902 STM0903
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCCTGAATCTTGCTAA
... ... ybjX ybjY ybjZ
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCATGAAAGCTGCTCA
... ... lolA ycaJ
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCATTCTTTATGCTCA
... ... ydiM ydiN aroE aroD
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCATCATTATTGCCTA
... ... orf242 orf319
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCATGAAGGTTCATCG
... ... ssaI ssaJ STM1410 ssaK ssaL ssaM ssaV ssaN ssaO ssaP ssaQ ssaR ssaS ssaT ssaU
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCAAGAATATTGCCAT
... ... STM1586 STM1585 yncD
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCACACGTTTTGCGCT
... ... srfB srfC
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCATCATTTTTTCAAG
... ... STM1665 STM1664 STM1666
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCAAACCTGTGGTATA
... ... 2000000 yecN yecO yecP
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCAGGAGCGTTTTATT
... ... otsA
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCGCGCTTTTTGCCTT
... ... yedA yedI STM1988.S
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
CGGTATAAATAATGCACG
... ... cbiC cbiD cbiE cbiT cbiF cbiG cbiH cbiJ cbiK cbiL cbiM cbiN cbiQ cbiO cbiP cobU cobS cobT erfK
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCATATAAATTGAGAT
... ... wcaA wcaB wcaC wcaD wcaE wcaF gmd wcaG wcaH wcaI manC cpsG wcaJ wzxC wcaK wcaL wcaM
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
AGGCATTTTTCTTGCATC
... ... yohJ yohK
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCATCACTGTTGCAGT
... ... cysK ptsH ptsI crr
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCACATCAGGCAAAAG
... ... STM2475
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCAGGTCACCTGCAAT
... ... ypfG STM2475
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGTACGGATCTTGCCAT
... ... sinH sinI ratA
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
CGGCGTAATTTTTGCATC
... ... yfhG yfhA glnB
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
CGGCACAGCTCTTGCATC
... ... ygcH STM2938 ygbF
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGAACGCTTTTCGCATT
... ... rumA relA barA
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCCCATTGAATGCATC
... ... STM3072 STM3073 STM3074 STM3075
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCATGATGGTCGCCAG
... ... yhbE obgE
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
AGGCATGTTTTATGCAAA
... ... glgA glgP
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGTACGTAAAATGCACG
... ... rfaP yibR rfaB rfaI rfaJ rfaY rfaZ rfaK
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCGCGATTATTGCCAG
... ... STM3863 glmU
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCCTGCTATTTGCCCT
... ... wzzE wecB wecC rffG rffH wecD wecE wzxE STM3927 wecF wecG
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCGCGGAAATTGCACA
... ... wecD wecE wzxE STM3927 wecF wecG
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCATAAAACCTGAAAA
... ... STM4013.S STM4012 STM4011 STM4010
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
AGGCGCGAATAATGCATC
... ... yjbA
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCCTGATTTTTGCAGG
... ... proP phnA phnB
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGCGTGGCGATTTCAAT
... ... stjB STM4571
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified