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Name: | hdeD | |||||||||
Gene(s): | hdeD Genome Browser M3D Gene expression COLOMBOS | |||||||||
Note(s): | The positive regulation of the hdeD gene by GadX is positively influenced by the transcriptional regulator GadW Tucker DL,2003. The transcription of hdeD appears to be increased under acidic growth conditions during stationary and exponential phases in a RcsB-dependent manner Johnson MD,2011 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 |
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Reference(s): |
[1] Hommais F., et al., 2004 [2] Yoshida T., et al., 1993 |
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Promoter | ||||||||||
Name: | hdeDp2 | |||||||||
+1: | 3656960 | |||||||||
Sigma Factor: | Sigma38 Sigmulon | |||||||||
Distance from start of the gene: | 35 | |||||||||
Sequence: |
taggaaatttttattaaatcgactgcattcttagacgcgtttttggcatagattgatagcAggggattttcttcttaattt |
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Evidence: |
[HIPP] [IEP] [IPI] [RS-EPT-CBR] [TIM] |
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Reference(s): |
[1] Hommais F., et al., 2004 [3] Itou J., et al., 2009 [4] Salgado H, et al., 2012 [5] Seo SW., et al., 2015 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | GadE | activator | hdeDp2 | 3656899 | 3656918 | -51.5 | gatactgcaaTTAGGAAATTTTTATTAAATcgactgcatt | nd | [AIBSCS], [BPP], [GEA], [RSE], [AIBSCS], [APIORCISFBSCS], [BPP], [CEEUMA], [IHBCE] | [1], [5], [8] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | GadX | activator | hdeDp2 | 3656835 | 3656854 | -115.5 | atgttgatggAAAATATCAAAATCAGATATttttatttca | nd | [APIORCISFBSCS], [BPP], [GEA], [AIBSCS], [APIORCISFBSCS], [BPP] | [1], [8], [9], [10] |
remote | GadX | activator | hdeDp2 | 3656856 | 3656875 | -94.5 | atcagatattTTTATTTCAATACAATGAGTtacagatgca | nd | [AIBSCS], [BPP], [GEA], [AIBSCS], [APIORCISFBSCS], [BPP] | [1], [8], [9], [10] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | PhoP-phosphorylated | activator | hdeDp2 | 3656815 | 3656831 | -137.0 | cctggttttcTGTATATGTCATGTTGAtggaaaatat | nd | [APIORCISFBSCS], [BPP], [GEA], [APIORCISFBSCS], [BPP] | [7] |
sRNA | TU Regulated | Function | Binding Sites | Regulatory Mechanism | Evidence (Confirmed, Strong, Weak) | Reference(s) | ||
---|---|---|---|---|---|---|---|---|
PosLeft | PosRight | Target sequence (mRNA) | ||||||
small regulatory RNA CyaR | hdeD | repressor | 3656985 | 3656994 | GGGUGGUUCU | TRANSLATION-BLOCKING, MRNA-DEGRADATION | [IEP], [IPI], [SM] | [6] |
small regulatory RNA RprA | hdeD | repressor | 3656960 | 3656970 | AGGGGAUUUUC | TRANSLATION-BLOCKING | [GEA], [SM] | [6] |
small regulatory RNA RprA | hdeD | repressor | 3656985 | 3656997 | GGGUGGUUCUAUG | TRANSLATION-BLOCKING | [IEP], [IMP] | [6] |
Name: | hdeD | |||||||||
Gene(s): | hdeD Genome Browser M3D Gene expression COLOMBOS | |||||||||
Note(s): | The positive regulation of the hdeD gene by GadX is positively influenced by the transcriptional regulator GadW Tucker DL,2003. The transcription of hdeD appears to be increased under acidic growth conditions during stationary and exponential phases in a RcsB-dependent manner Johnson MD,2011 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 |
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Reference(s): |
[1] Hommais F., et al., 2004 [2] Yoshida T., et al., 1993 |
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Promoter | ||||||||||
Name: | hdeDp | |||||||||
+1: | 3656960 | |||||||||
Sigma Factor: | Sigma70 Sigmulon | |||||||||
Distance from start of the gene: | 35 | |||||||||
Sequence: |
taggaaatttttattaaatcgactgcattcttagacgcgtttttggcatagattgatagcAggggattttcttcttaattt -35 -10 +1 |
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Evidence: |
[HIPP] [ICWHO] [IHBCE] [RS-EPT-CBR] [TIM] |
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Reference(s): |
[1] Hommais F., et al., 2004 [12] Huerta AM., et al., 2003 [3] Itou J., et al., 2009 [4] Salgado H, et al., 2012 [5] Seo SW., et al., 2015 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | GadE | activator | hdeDp | 3656899 | 3656918 | -51.5 | gatactgcaaTTAGGAAATTTTTATTAAATcgactgcatt | nd | [AIBSCS], [BPP], [GEA], [RSE], [AIBSCS], [APIORCISFBSCS], [BPP], [CEEUMA], [IHBCE] | [1], [5], [8] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | GadX | activator | hdeDp | 3656835 | 3656854 | -115.5 | atgttgatggAAAATATCAAAATCAGATATttttatttca | nd | [APIORCISFBSCS], [BPP], [GEA], [AIBSCS], [APIORCISFBSCS], [BPP] | [1], [8], [9], [10] |
remote | GadX | activator | hdeDp | 3656856 | 3656875 | -94.5 | atcagatattTTTATTTCAATACAATGAGTtacagatgca | nd | [AIBSCS], [BPP], [GEA], [AIBSCS], [APIORCISFBSCS], [BPP] | [1], [8], [9], [10] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | PhoP-phosphorylated | activator | hdeDp | 3656815 | 3656831 | -137.0 | cctggttttcTGTATATGTCATGTTGAtggaaaatat | nd | [APIORCISFBSCS], [BPP], [GEA], [APIORCISFBSCS], [BPP] | [7] |
sRNA | TU Regulated | Function | Binding Sites | Regulatory Mechanism | Evidence (Confirmed, Strong, Weak) | Reference(s) | ||
---|---|---|---|---|---|---|---|---|
PosLeft | PosRight | Target sequence (mRNA) | ||||||
small regulatory RNA CyaR | hdeD | repressor | 3656985 | 3656994 | GGGUGGUUCU | TRANSLATION-BLOCKING, MRNA-DEGRADATION | [IEP], [IPI], [SM] | [6] |
small regulatory RNA RprA | hdeD | repressor | 3656960 | 3656970 | AGGGGAUUUUC | TRANSLATION-BLOCKING | [GEA], [SM] | [6] |
small regulatory RNA RprA | hdeD | repressor | 3656985 | 3656997 | GGGUGGUUCUAUG | TRANSLATION-BLOCKING | [IEP], [IMP] | [6] |
Reference(s) |
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