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Name: | csiD-ygaF-gabDTP | |||||||||
Synonym(s): | csiD | |||||||||
Gene(s): | glaH, lhgD, gabD, gabT, gabP Genome Browser M3D Gene expression COLOMBOS | |||||||||
Note(s): | This transcription unit is induced under stationary phase Metzner M,2004, and it is part of a complex operon that contains three promoters, two of which are internal. The glaH-lhgO-gabDTP operon is induced in stationary phase (carbon starvation) Knorr S,2018 |
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Evidence: | [ITCR] Inferred through co-regulation [PM] Polar mutation |
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Reference(s): | [1] Metzner M., et al., 2004 | |||||||||
Promoter | ||||||||||
Name: | csiDp | |||||||||
+1: | 2788927 | |||||||||
Sigma Factor: | Sigma38 Sigmulon | |||||||||
Distance from start of the gene: | 58 | |||||||||
Sequence: |
ataagaaaacaatatgtcgcttttgtgcgcatttttcagaaatgtagatatttttagattAtggctacgaaatgagcatcg -35 -10 +1 |
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Evidence: |
[ICWHO] [TIM] |
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Reference(s): |
[2] Huerta AM., et al., 2003 [3] Marschall C., et al., 1998 [1] Metzner M., et al., 2004 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | CRP-cyclic-AMP | activator | csiDp | 2788848 | 2788869 | -68.5 | atgttactaaTTTGTTGCTTTTGATCACAATAagaaaacaat | nd | [GEA], [AIBSCS], [BPP] | [3], [4] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | GlaR | repressor | csiDp | 2788889 | 2788902 | -32.0 | tatgtcgcttTTGTGCGCATTTTTcagaaatgta | nd | [GEA], [IEP], [BPP] | [1], [5] |
proximal | GlaR | repressor | csiDp | 2788908 | 2788921 | -13.0 | tttttcagaaATGTAGATATTTTTagattatggc | nd | [GEA], [IEP], [RSE], [AIBSPD], [BPP], [CSE] | [1], [5], [6] |
Evidence: | [EME] Expression microarray evidence |
Reference(s): | [7] Traxler MF., et al., 2008 |
Name: | gabDTP |
Gene(s): | gabD, gabT, gabP Genome Browser M3D Gene expression COLOMBOS |
Note(s): | This transcription unit is part of a complex operon that contains three promoters, two of which are internal. Although Schneider BL,2002 et al. suggested that the csiR gene is part of the gabDTP operon because they saw a polar effect of an insertion in gabT on gabC, Metzner M,2004 et al. saw that the presence or absence of the gabD promoters did not affect the csiR expression and therefore concluded that the csiR gene is transcribed in another transcription unit. For this reason, this gene was not included in the operon. The gabDTP operon is induced in response to nitrogen starvation Knorr S,2018 |
Evidence: | [ITCR] Inferred through co-regulation [PM] Polar mutation |
Reference(s): | [1] Metzner M., et al., 2004 |
Promoter | |
Name: | gabDp2 |
+1: | 2790912 |
Sigma Factor: | Sigma38 Sigmulon |
Distance from start of the gene: | 361 |
Sequence: |
gagattttgggctcgtcggggattcgccgggtgctgcaaaaccatctacgctcaggactgGgcgagatgaaaaactcgctg -35 -10 +1 |
Evidence: |
[HIPP] [ICWHO] [IEP] [IHBCE] [TIM] |
Reference(s): |
[2] Huerta AM., et al., 2003 [8] Maciag A., et al., 2011 [1] Metzner M., et al., 2004 |
Name: | gabDTP | |||||||||
Gene(s): | gabD, gabT, gabP Genome Browser M3D Gene expression COLOMBOS | |||||||||
Note(s): | This transcription unit is part of a complex operon that contains three promoters, two of which are internal. Although Schneider BL,2002 et al. suggested that the csiR gene is part of the gabDTP operon because they saw a polar effect of an insertion in gabT on gabC, Metzner M,2004 et al. saw that the presence or absence of the gabD promoters did not affect the csiR expression and therefore concluded that the csiR gene is transcribed in another transcription unit. For this reason, this gene was not included in the operon. The gabDTP operon is induced in response to nitrogen starvation Knorr S,2018 |
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Evidence: | [ITCR] Inferred through co-regulation [PM] Polar mutation |
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Reference(s): |
[1] Metzner M., et al., 2004 [9] Schneider BL., et al., 2002 |
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Promoter | ||||||||||
Name: | gabDp1 | |||||||||
+1: | 2791172 | |||||||||
Sigma Factor: | Sigma70 Sigmulon | |||||||||
Distance from start of the gene: | 101 | |||||||||
Sequence: |
ggcagcgacatcagcaattcctattggtgcgcatattgtcagcaaggtacaaacgctgttGgcaagccagagtaaccccgg -35 -10 +1 |
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Evidence: |
[HIPP] [ICWHO] [IEP] [IHBCE] [TIM] |
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Reference(s): |
[2] Huerta AM., et al., 2003 [8] Maciag A., et al., 2011 [9] Schneider BL., et al., 2002 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | Nac | activator | gabDp1 | 2791121 | 2791135 | -44.0 | cggcagcgacATCAGCAATTCCTATtggtgcgcat | nd | [GEA], [RSE], [AIBSPD], [APIORCISFBSCS], [CSE] | [6], [9], [10] |
Name: | gabDTP | |||||||||
Gene(s): | gabD, gabT, gabP Genome Browser M3D Gene expression COLOMBOS | |||||||||
Note(s): | This transcription unit is part of a complex operon that contains three promoters, two of which are internal. Although Schneider BL,2002 et al. suggested that the csiR gene is part of the gabDTP operon because they saw a polar effect of an insertion in gabT on gabC, Metzner M,2004 et al. saw that the presence or absence of the gabD promoters did not affect the csiR expression and therefore concluded that the csiR gene is transcribed in another transcription unit. For this reason, this gene was not included in the operon. The gabDTP operon is induced in response to nitrogen starvation Knorr S,2018 |
|||||||||
Evidence: | [ITCR] Inferred through co-regulation [PM] Polar mutation |
|||||||||
Reference(s): |
[1] Metzner M., et al., 2004 [9] Schneider BL., et al., 2002 |
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Promoter | ||||||||||
Name: | gabDp | |||||||||
+1: | 2791172 | |||||||||
Sigma Factor: | Sigma38 Sigmulon | |||||||||
Distance from start of the gene: | 101 | |||||||||
Sequence: |
ggcagcgacatcagcaattcctattggtgcgcatattgtcagcaaggtacaaacgctgttGgcaagccagagtaaccccgg -35 -10 +1 |
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Evidence: |
[HIPP] [ICWHO] [IEP] [IHBCE] [TIM] |
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Reference(s): |
[2] Huerta AM., et al., 2003 [8] Maciag A., et al., 2011 [9] Schneider BL., et al., 2002 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | Nac | activator | gabDp | 2791121 | 2791135 | -44.0 | cggcagcgacATCAGCAATTCCTATtggtgcgcat | nd | [GEA], [RSE], [AIBSPD], [APIORCISFBSCS], [CSE] | [6], [9], [10] |
Reference(s) |
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