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Name: | hdeAB-yhiD | ||||||||||
Gene(s): | yhiD, hdeB, hdeA Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The hdeAB-yhiD operon is induced under stationary phase Shin M,2005. Weber H,2005 and at acid pH Hayes ET,2006. Tucker DL,2003. Marzan LW,2013 in a RcsB-dependent manner Johnson MD,2011 Lrp represses the hdeAB-yhiD operon only in the exponential phase at pH 7.0, and MarA reduces this repression Ruiz C,2008. The hdeAB genes are upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020. Indole enhances the expression of several genes related to acid resistance, such as gadA, gadB, gadC, hdeA, hdeB, hdeD, slp, and gadE Hirakawa H, Hayashi-Nishino M, Yamaguchi A, Nishino K,2010 The acid resistance phenotype induced by indoles is mainly due to increased expression of the glutamine decarboxylase system Hirakawa H, Hayashi-Nishino M, Yamaguchi A, Nishino K,2010 The mdtEF-tolC, malEFG, gadBC, treBC, entCEBA-ybdB, hdeAB-yhiD, and alaE operons were differentially regulated after induction of the nonnative organic acid citramalate Webb J,2019 The expression of hdeB appears to be slightly repressed by Rob under butanol stress Wang Z,2020. |
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Evidence: | [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined [EXP-IEP-COREGULATION] Inferred through co-regulation |
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Reference(s): |
[1] Arnqvist A., et al., 1994 [2] Tucker DL., et al., 2003 [3] Yoshida T., et al., 1993 |
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Promoter | |||||||||||
Name: | hdeAp2 | ||||||||||
+1: | 3656791 | ||||||||||
Sigma Factor: | Sigma38 Sigmulon | ||||||||||
Distance from start of the gene: | 51 | ||||||||||
Sequence: |
tctgattttgatattttccatcaacatgacatatacagaaaaccaggttataacctcagtGtcgaaattgattcgtgacgg -35 -10 +1 |
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Note(s): | The same transcriptional start site for this promoter is used in hns rpoS mutant strains as well as strains wild type for H-NS and σ38. This indicates that the same promoter can be utilized by both σ38 and σ70 in vivo. This promoter has significant homology to the consensus of a σ70 promoter even though it is dependent upon σ38 Arnqvist A,1994. | ||||||||||
Evidence: |
[COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP] [RS-EPT-CBR] |
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Reference(s): |
[1] Arnqvist A., et al., 1994 [4] Dudin O., et al., 2013 [5] Itou J., et al., 2009 [6] Salgado H, et al., 2012 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | FliZ | repressor | hdeAp2 | 3656757 | 3656812 | 8.0 | catatacagaAAACCAGGTTATAACCTCAGTGTCGAAATTGATTCGTGACGGCTCTTTCACTTTATagttgaggat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [16] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | GadE | activator | hdeAp2 | 3656773 | 3656792 | 9.5 | ataacctcagTGTCGAAATTGATTCGTGACggctctttca | nd | [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL] | S | [11] |
remote | GadE | activator | hdeAp2 | 3656899 | 3656918 | -117.5 | aatgcagtcgATTTAATAAAAATTTCCTAAttgcagtatc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | C | [7], [10], [11] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | GadW | activator | hdeAp2 | 3656835 | 3656854 | -53.5 | tgaaataaaaATATCTGATTTTGATATTTTccatcaacat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [7], [12] |
proximal | GadW | activator | hdeAp2 | 3656856 | 3656875 | -74.5 | tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [7], [12] |
remote | GadW | activator | hdeAp2 | 3656908 | 3656927 | -126.5 | gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [2], [7] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | GadW | repressor | hdeAp2 | 3656835 | 3656854 | -53.5 | tgaaataaaaATATCTGATTTTGATATTTTccatcaacat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [7], [12] |
proximal | GadW | repressor | hdeAp2 | 3656856 | 3656875 | -74.5 | tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [7], [12] |
remote | GadW | repressor | hdeAp2 | 3656908 | 3656927 | -126.5 | gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [2], [7] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | GadX | activator | hdeAp2 | 3656835 | 3656854 | -53.5 | tgaaataaaaATATCTGATTTTGATATTTTccatcaacat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [7], [10], [12] |
proximal | GadX | activator | hdeAp2 | 3656856 | 3656875 | -74.5 | tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [7], [10], [12] |
remote | GadX | activator | hdeAp2 | 3656908 | 3656927 | -126.5 | gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [2], [7] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | GadX | repressor | hdeAp2 | 3656835 | 3656854 | -53.5 | tgaaataaaaATATCTGATTTTGATATTTTccatcaacat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [7], [10], [12] |
proximal | GadX | repressor | hdeAp2 | 3656856 | 3656875 | -74.5 | tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [7], [10], [12] |
remote | GadX | repressor | hdeAp2 | 3656908 | 3656927 | -126.5 | gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [2], [7] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
remote | H-NS | repressor | hdeAp2 | 3656902 | 3656916 | -118.0 | tgcagtcgatTTAATAAAAATTTCCtaattgcagt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | C | [3], [8], [9] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | Lrp-L-leucine | repressor | hdeAp2 | 3656802 | 3656817 | -18.0 | catgacatatACAGAAAACCAGGTTAtaacctcagt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
proximal | Lrp-L-leucine | repressor | hdeAp2 | 3656839 | 3656854 | -55.0 | tgaaataaaaATATCTGATTTTGATAttttccatca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
proximal | Lrp-L-leucine | repressor | hdeAp2 | 3656848 | 3656863 | -64.0 | tcattgtattGAAATAAAAATATCTGattttgatat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
remote | Lrp-L-leucine | repressor | hdeAp2 | 3656881 | 3656896 | -97.0 | tttcctaattGCAGTATCTGATGCATctgtaactca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
remote | Lrp-L-leucine | repressor | hdeAp2 | 3656900 | 3656915 | -116.0 | gcagtcgattTAATAAAAATTTCCTAattgcagtat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
remote | Lrp-L-leucine | repressor | hdeAp2 | 3656943 | 3656958 | -159.0 | aaatcccctgCTATCAATCTATGCCAaaaacgcgtc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | MarA | repressor | hdeAp2 | 3656820 | 3656839 | -39.0 | tgattttgatATTTTCCATCAACATGACATatacagaaaa | nd | [EXP-IDA-PURIFIED-PROTEIN], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-PURIFIED-PROTEIN], [EXP-IMP-SITE-MUTATION] | W | [13] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | PhoP-phosphorylated | activator | hdeAp2 | 3656815 | 3656831 | -32.0 | atattttccaTCAACATGACATATACAgaaaaccagg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [14] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
nd | RcsB-phosphorylated | activator | hdeAp2 | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] | W | [17] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | TorR-phosphorylated | activator | hdeAp2 | 3656814 | 3656823 | -27.5 | catcaacatgACATATACAGaaaaccaggt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7], [15] |
proximal | TorR-phosphorylated | activator | hdeAp2 | 3656838 | 3656847 | -51.5 | aaaatatctgATTTTGATATtttccatcaa | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
Name: | hdeAB-yhiD | ||||||||||
Gene(s): | yhiD, hdeB, hdeA Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The hdeAB-yhiD operon is induced under stationary phase Shin M,2005. Weber H,2005 and at acid pH Hayes ET,2006. Tucker DL,2003. Marzan LW,2013 in a RcsB-dependent manner Johnson MD,2011 Lrp represses the hdeAB-yhiD operon only in the exponential phase at pH 7.0, and MarA reduces this repression Ruiz C,2008. The hdeAB genes are upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020. Indole enhances the expression of several genes related to acid resistance, such as gadA, gadB, gadC, hdeA, hdeB, hdeD, slp, and gadE Hirakawa H, Hayashi-Nishino M, Yamaguchi A, Nishino K,2010 The acid resistance phenotype induced by indoles is mainly due to increased expression of the glutamine decarboxylase system Hirakawa H, Hayashi-Nishino M, Yamaguchi A, Nishino K,2010 The mdtEF-tolC, malEFG, gadBC, treBC, entCEBA-ybdB, hdeAB-yhiD, and alaE operons were differentially regulated after induction of the nonnative organic acid citramalate Webb J,2019 The expression of hdeB appears to be slightly repressed by Rob under butanol stress Wang Z,2020. |
||||||||||
Evidence: | [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined [EXP-IEP-COREGULATION] Inferred through co-regulation |
||||||||||
Reference(s): |
[1] Arnqvist A., et al., 1994 [2] Tucker DL., et al., 2003 [3] Yoshida T., et al., 1993 |
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Promoter | |||||||||||
Name: | hdeAp | ||||||||||
+1: | 3656791 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 51 | ||||||||||
Sequence: |
tctgattttgatattttccatcaacatgacatatacagaaaaccaggttataacctcagtGtcgaaattgattcgtgacgg -35 -10 +1 |
||||||||||
Note(s): | The same transcriptional start site for this promoter is used in hns rpoS mutant strains as well as strains wild type for H-NS and σ38. This indicates that the same promoter can be utilized by both σ38 and σ70 in vivo. This promoter has significant homology to the consensus of a σ70 promoter even though it is dependent upon σ38 Arnqvist A,1994. | ||||||||||
Evidence: |
[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [COMP-HINF-SIMILAR-TO-CONSENSUS] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR] |
||||||||||
Reference(s): |
[1] Arnqvist A., et al., 1994 [4] Dudin O., et al., 2013 [18] Huerta AM., et al., 2003 [5] Itou J., et al., 2009 [6] Salgado H, et al., 2012 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | FliZ | repressor | hdeAp | 3656757 | 3656812 | 8.0 | catatacagaAAACCAGGTTATAACCTCAGTGTCGAAATTGATTCGTGACGGCTCTTTCACTTTATagttgaggat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [16] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | GadE | activator | hdeAp | 3656773 | 3656792 | 9.5 | ataacctcagTGTCGAAATTGATTCGTGACggctctttca | nd | [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL] | S | [11] |
remote | GadE | activator | hdeAp | 3656899 | 3656918 | -117.5 | aatgcagtcgATTTAATAAAAATTTCCTAAttgcagtatc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | C | [7], [10], [11] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | GadW | activator | hdeAp | 3656835 | 3656854 | -53.5 | tgaaataaaaATATCTGATTTTGATATTTTccatcaacat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [7], [12] |
proximal | GadW | activator | hdeAp | 3656856 | 3656875 | -74.5 | tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [7], [12] |
remote | GadW | activator | hdeAp | 3656908 | 3656927 | -126.5 | gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [2], [7] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | GadW | repressor | hdeAp | 3656835 | 3656854 | -53.5 | tgaaataaaaATATCTGATTTTGATATTTTccatcaacat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [7], [12] |
proximal | GadW | repressor | hdeAp | 3656856 | 3656875 | -74.5 | tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [7], [12] |
remote | GadW | repressor | hdeAp | 3656908 | 3656927 | -126.5 | gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [2], [7] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | GadX | activator | hdeAp | 3656835 | 3656854 | -53.5 | tgaaataaaaATATCTGATTTTGATATTTTccatcaacat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [7], [10], [12] |
proximal | GadX | activator | hdeAp | 3656856 | 3656875 | -74.5 | tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [7], [10], [12] |
remote | GadX | activator | hdeAp | 3656908 | 3656927 | -126.5 | gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [2], [7] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | GadX | repressor | hdeAp | 3656835 | 3656854 | -53.5 | tgaaataaaaATATCTGATTTTGATATTTTccatcaacat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [7], [10], [12] |
proximal | GadX | repressor | hdeAp | 3656856 | 3656875 | -74.5 | tgcatctgtaACTCATTGTATTGAAATAAAaatatctgat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [7], [10], [12] |
remote | GadX | repressor | hdeAp | 3656908 | 3656927 | -126.5 | gcgtctaagaATGCAGTCGATTTAATAAAAatttcctaat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [2], [7] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
remote | H-NS | repressor | hdeAp | 3656902 | 3656916 | -118.0 | tgcagtcgatTTAATAAAAATTTCCtaattgcagt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | C | [3], [8], [9] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | Lrp-L-leucine | repressor | hdeAp | 3656802 | 3656817 | -18.0 | catgacatatACAGAAAACCAGGTTAtaacctcagt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
proximal | Lrp-L-leucine | repressor | hdeAp | 3656839 | 3656854 | -55.0 | tgaaataaaaATATCTGATTTTGATAttttccatca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
proximal | Lrp-L-leucine | repressor | hdeAp | 3656848 | 3656863 | -64.0 | tcattgtattGAAATAAAAATATCTGattttgatat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
remote | Lrp-L-leucine | repressor | hdeAp | 3656881 | 3656896 | -97.0 | tttcctaattGCAGTATCTGATGCATctgtaactca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
remote | Lrp-L-leucine | repressor | hdeAp | 3656900 | 3656915 | -116.0 | gcagtcgattTAATAAAAATTTCCTAattgcagtat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
remote | Lrp-L-leucine | repressor | hdeAp | 3656943 | 3656958 | -159.0 | aaatcccctgCTATCAATCTATGCCAaaaacgcgtc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | MarA | repressor | hdeAp | 3656820 | 3656839 | -39.0 | tgattttgatATTTTCCATCAACATGACATatacagaaaa | nd | [EXP-IDA-PURIFIED-PROTEIN], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-PURIFIED-PROTEIN], [EXP-IMP-SITE-MUTATION] | W | [13] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | PhoP-phosphorylated | activator | hdeAp | 3656815 | 3656831 | -32.0 | atattttccaTCAACATGACATATACAgaaaaccagg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [14] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
nd | RcsB-phosphorylated | activator | hdeAp | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] | W | [17] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | TorR-phosphorylated | activator | hdeAp | 3656814 | 3656823 | -27.5 | catcaacatgACATATACAGaaaaccaggt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7], [15] |
proximal | TorR-phosphorylated | activator | hdeAp | 3656838 | 3656847 | -51.5 | aaaatatctgATTTTGATATtttccatcaa | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
Name: | yhiD |
Gene(s): | yhiD Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [COMP-AINF] Inferred computationally without human oversight |
RNA cis-regulatory element | ![]() |
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Regulation, transcriptional elongation | |
Attenuator type: | Transcriptional |
Strand: | reverse |
Structure type | Energy | LeftPos | RightPos | Sequence (RNA-strand) | |
---|---|---|---|---|---|
terminator | -17.3 | 3655903 | 3655948 | caagtaaaaaGGAGTAGCAAGTTGAGCCATCTTGCTGCTCCTTTTTGCATTTTTAtatgacagca | |
terminator | -8.7 | 3656300 | 3656331 | agctattcctCCTGTTCATATATAATCTCTATATTGAATGGgttacaaaat | |
anti-terminator | -9.06 | 3655933 | 3656001 | tttgtataccTTCAAAAATCAAGCATCTAATGACTTGCCGAATTAATGAGGTGCAAGTAAAAAGGAGTAGCAAGTTGAgccatcttgc |
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos" |
Reference(s) |
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