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Name: | ltaE-ybjT |
Gene(s): | ybjT, ltaE Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [IC] Inferred by curator |
Promoter | |
Name: | ltaEp |
+1: | 909320 |
Distance from start of the gene: | 26 |
Sequence: |
gacgcggtgatgaagtgatcgaactggcgaaaacaaactggctaaggtaaaaagggtggcAtttcccgtcataataaggac |
Evidence: |
[CV(RS-EPT-CBR)] [HTIM] [RS-EPT-CBR] |
Reference(s): |
[1] Mendoza-Vargas A., et al., 2009 [2] Salgado H, et al., 2012 |
Name: | poxB |
Gene(s): | poxB Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [IEP] Inferred from expression pattern |
Reference(s): | [3] Chang YY., et al., 1994 |
Promoter | |
Name: | poxBp |
+1: | 911076 |
Sigma Factor: | Sigma38, Sigma70 |
Distance from start of the gene: | 27 |
Sequence: |
ttagtgcctcctttctctcccatcccttccccctccgtcagatgaactaaacttgttaccGttatcacattcaggagatgg -35 -10 +1 |
Evidence: |
[CV(RS-EPT-CBR)] [CV(TIM)] [HTIM] [RS-EPT-CBR] [TIM] |
Reference(s): |
[3] Chang YY., et al., 1994 [4] Olvera L., et al., 2009 [2] Salgado H, et al., 2012 [5] Wise A., et al., 1996 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | MarA | activator | poxBp | 911127 | 911146 | -60.5 | ttcatcgggcTATTTAACCGTTAGTGCCTCctttctctcc | nd | [APIORCISFBSCS], [CV(GEA)], [GEA] | [6] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | SoxS | activator | poxBp | 911127 | 911146 | -60.5 | ttcatcgggcTATTTAACCGTTAGTGCCTCctttctctcc | nd | [APIORCISFBSCS], [CV(GEA)], [GEA] | [6] |
Name: | hcp-hcr | ||||
Gene(s): | hcr, hcp Genome Browser M3D Gene expression COLOMBOS | ||||
Note(s): | The expression of hcp-hcr is induced by nitrite and nitrate, and this induction is mediated by NarP and NarL van den Berg WA,2000. Vine CE,2011 and by nitrosative stress mediated by OxyR Seth D,2012. | ||||
Evidence: | [PM] Polar mutation | ||||
Reference(s): | [8] van den Berg WA., et al., 2000 | ||||
Promoter | |||||
Name: | hcpp | ||||
+1: | 913845 | ||||
Distance from start of the gene: | 31 | ||||
Sequence: |
Evidence: |
[TIM]
|
Reference(s): |
[9] Filenko NA., et al., 2005
|
|
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | FNR | activator | hcpp | 913911 | 913924 | -72.5 | gccgccaaaaTTGCGCTAAATCAAtctcccttaa | nd | [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] | [9], [10], [11] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | NarL-Phosphorylated | activator | hcpp | 913937 | 913952 | -100.0 | cgtaatacctCTCTGGCGGTAGATCCctgccgccaa | nd | [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [9], [10] |
remote | NarL-Phosphorylated | activator | hcpp | 913946 | 913961 | -109.0 | ttttctctgcGTAATACCTCTCTGGCggtagatccc | nd | [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [9], [10] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | NarP-Phosphorylated | activator | hcpp | 913937 | 913952 | -100.0 | cgtaatacctCTCTGGCGGTAGATCCctgccgccaa | nd | [APIORCISFBSCS], [CV(GEA)], [GEA] | [9] |
remote | NarP-Phosphorylated | activator | hcpp | 913946 | 913961 | -109.0 | ttttctctgcGTAATACCTCTCTGGCggtagatccc | nd | [APIORCISFBSCS], [CV(GEA)], [GEA] | [9] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | NsrR1 | repressor | hcpp | 913831 | 913849 | 6.0 | taaccttaaaCATGTATATTAAATATAACtttaaaaggt | nd | [APIORCISFBSCS], [BCE], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] | [10], [11], [12] |
Note(s): |
1NsrR plays a major role while the effects of NarL and NarP are minimal in the regulation of the hcp-hcr operon by nitrate and nitrite Chismon DL,2010.6NsrR plays a major role while the effects of NarL and NarP are minimal in the regulation of the hcp-hcr operon by nitrate and nitrite Chismon DL,2010. |
Name: | hcp-hcr-poxB | ||||
Gene(s): | poxB, hcr, hcp Genome Browser M3D Gene expression COLOMBOS | ||||
Note(s): | Based on transcriptome analysis and findings with an nrsR mutant, poxB was identified as an NsrR target due to readthrough transcription from the hcp-hcr genes Chhabra S,2015 | ||||
Evidence: | [ITC] Inferred through co-regulation | ||||
Reference(s): | [14] Chhabra S., et al., 2015 | ||||
Promoter | |||||
Name: | hcpp | ||||
+1: | 913845 | ||||
Distance from start of the gene: | 31 | ||||
Sequence: |
Evidence: |
[TIM]
|
Reference(s): |
[9] Filenko NA., et al., 2005
|
|
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | FNR | activator | hcpp | 913911 | 913924 | -72.5 | gccgccaaaaTTGCGCTAAATCAAtctcccttaa | nd | [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] | [9], [10], [11] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | NarL-Phosphorylated | activator | hcpp | 913937 | 913952 | -100.0 | cgtaatacctCTCTGGCGGTAGATCCctgccgccaa | nd | [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [9], [10] |
remote | NarL-Phosphorylated | activator | hcpp | 913946 | 913961 | -109.0 | ttttctctgcGTAATACCTCTCTGGCggtagatccc | nd | [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [9], [10] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | NarP-Phosphorylated | activator | hcpp | 913937 | 913952 | -100.0 | cgtaatacctCTCTGGCGGTAGATCCctgccgccaa | nd | [APIORCISFBSCS], [CV(GEA)], [GEA] | [9] |
remote | NarP-Phosphorylated | activator | hcpp | 913946 | 913961 | -109.0 | ttttctctgcGTAATACCTCTCTGGCggtagatccc | nd | [APIORCISFBSCS], [CV(GEA)], [GEA] | [9] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
proximal | NsrR1 | repressor | hcpp | 913831 | 913849 | 6.0 | taaccttaaaCATGTATATTAAATATAACtttaaaaggt | nd | [APIORCISFBSCS], [BCE], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] | [10], [11], [12] |
Note(s): |
1NsrR plays a major role while the effects of NarL and NarP are minimal in the regulation of the hcp-hcr operon by nitrate and nitrite Chismon DL,2010.6NsrR plays a major role while the effects of NarL and NarP are minimal in the regulation of the hcp-hcr operon by nitrate and nitrite Chismon DL,2010. |
Name: | hcp-hcr |
Gene(s): | hcr, hcp Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [ITC] Inferred through co-regulation [PM] Polar mutation |
Reference(s): |
[15] Rhodius VA., et al., 2005 [8] van den Berg WA., et al., 2000 |
Promoter | |
Name: | hcpp2 |
+1: | 914129 |
Sigma Factor: | Sigma24 Sigmulon |
Distance from start of the gene: | 315 |
Sequence: |
cgcggcgttttttaatgatctggcccgtgaactgattgctattatgttgatccctgggctGattcgccgcagccgctctac -35 -10 +1 |
Evidence: |
[AIPP] [TIM] |
Reference(s): | [15] Rhodius VA., et al., 2005 |
Gene(s): | ybjT, ltaE, poxB Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [ICWHO] Inferred computationally without human oversight |
Reference(s) |
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