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Name: | cydAB | ||||||||||
Synonym(s): | OP00140 | ||||||||||
Gene(s): | cydA, cydB Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The cydAB operon is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020. The expression of the gene cydB is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013 |
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Evidence: | [AS-TAS] Traceable author statement | ||||||||||
Reference(s): |
[1] Cotter PA., et al., 1990 [2] Ramseier TM., et al., 1996 |
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Promoter | |||||||||||
Name: | cydAp1 | ||||||||||
+1: | 771170 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 288 | ||||||||||
Sequence: |
ttgatatttatcaatgtataagtcttggaaatgggcatcaaaaagagataaattgttctcGatcaaattggctgaaaggcg -35 -10 +1 |
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Evidence: |
[COMP-AINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
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Reference(s): |
[3] Cotter PA., et al., 1997 [4] Huerta AM., et al., 2003 |
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 | FNR | repressor | cydAp1 | 771110 | 771123 | -53.5 | tttgtaggaaTTGATATTTATCAAtgtataagtc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [3], [7], [9], [11], [12], [13] |
proximal | FNR | repressor | cydAp1 | 771162 | 771175 | -1.5 | aagagataaaTTGTTCTCGATCAAattggctgaa | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [3], [7], [9], [12], [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 | ||||||||
nd | H-NS | repressor | cydAp1 | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [15] |
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 | HypT-Met-oxidized | activator | cydAp1 | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [14] |
Name: | cydAB | ||||||||||
Gene(s): | cydA, cydB Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The cydAB operon is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020. The expression of the gene cydB is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013 |
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Reference(s): | [2] Ramseier TM., et al., 1996 | ||||||||||
Promoter | |||||||||||
Name: | cydAp3 | ||||||||||
+1: | 771202 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 256 | ||||||||||
Sequence: |
gggcatcaaaaagagataaattgttctcgatcaaattggctgaaaggcggtaatttagctAtaaattgatcaccgtcgaaa -35 -10 +1 |
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Evidence: |
[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
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Reference(s): |
[12] Govantes F., et al., 2000 [4] Huerta AM., et al., 2003 |
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 | ArcA-phosphorylated | activator | cydAp3 | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [6], [7], [8], [12], [15] |
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 | FNR | repressor | cydAp3 | 771110 | 771123 | -85.5 | tttgtaggaaTTGATATTTATCAAtgtataagtc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [7], [12], [13] |
proximal | FNR | repressor | cydAp3 | 771162 | 771175 | -33.5 | aagagataaaTTGTTCTCGATCAAattggctgaa | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [7], [12], [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 | ||||||||
nd | H-NS | repressor | cydAp3 | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [15] |
Name: | cydAB | ||||||||||
Gene(s): | cydA, cydB Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The cydAB operon is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020. The expression of the gene cydB is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013 |
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Reference(s): | [2] Ramseier TM., et al., 1996 | ||||||||||
Promoter | |||||||||||
Name: | cydAp4 | ||||||||||
+1: | 771213 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 245 | ||||||||||
Sequence: |
agagataaattgttctcgatcaaattggctgaaaggcggtaatttagctataaattgatcAccgtcgaaaaatgcaaattt -35 -10 +1 |
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Evidence: |
[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
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Reference(s): |
[12] Govantes F., et al., 2000 [4] Huerta AM., et al., 2003 |
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 | ArcA-phosphorylated | activator | cydAp4 | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [6], [7], [8], [12], [15] |
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 | FNR | repressor | cydAp4 | 771110 | 771123 | -96.5 | tttgtaggaaTTGATATTTATCAAtgtataagtc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [7], [12], [13] |
proximal | FNR | repressor | cydAp4 | 771162 | 771175 | -44.5 | aagagataaaTTGTTCTCGATCAAattggctgaa | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [7], [12], [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 | ||||||||
nd | H-NS | repressor | cydAp4 | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [15] |
Name: | cydAB | ||||||||||
Gene(s): | cydA, cydB Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The cydAB operon is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020. The expression of the gene cydB is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013 |
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Reference(s): | [2] Ramseier TM., et al., 1996 | ||||||||||
Promoter | |||||||||||
Name: | cydAp2 | ||||||||||
+1: | 771284 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 174 | ||||||||||
Sequence: |
atgcaaatttgcttcaacaaaaacctgtttattgtaaggattttgcggcgtaatatatacGtgggatcaatttgagttttt -35 -10 +1 |
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Evidence: |
[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR] |
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Reference(s): |
[3] Cotter PA., et al., 1997 [4] Huerta AM., et al., 2003 [16] Ogasawara H., et al., 2005 [17] 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 | ArcA-phosphorylated | activator | cydAp2 | 771199 | 771213 | -77.5 | cggtaatttaGCTATAAATTGATCAccgtcgaaaa | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [6], [7], [8], [10] |
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 | FNR | activator | cydAp2 | 771110 | 771123 | -167.5 | tttgtaggaaTTGATATTTATCAAtgtataagtc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [7], [12], [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 | ||||||||
remote | FNR | repressor | cydAp2 | 771162 | 771175 | -115.5 | aagagataaaTTGTTCTCGATCAAattggctgaa | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [7], [12], [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 | ||||||||
nd | H-NS | repressor | cydAp2 | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [15] |
Name: | cydAB | ||||||||||
Gene(s): | cydA, cydB Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The cydAB operon is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020. The expression of the gene cydB is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013 |
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Reference(s): | [2] Ramseier TM., et al., 1996 | ||||||||||
Promoter | |||||||||||
Name: | cydAp5 | ||||||||||
+1: | 771368 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 90 | ||||||||||
Sequence: |
aacatgtttgcaacctttctttacgccgtttttgtgtgcattcacatggtatgatgaaagTgttcaaacaaatttctattg -35 -10 +1 |
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Evidence: |
[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
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Reference(s): |
[12] Govantes F., et al., 2000 [4] Huerta AM., et al., 2003 |
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 | Cra | activator | cydAp5 | 771225 | 771242 | -134.5 | cgtcgaaaaaTGCAAATTTGCTTCAACAaaaacctgtt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2] |
remote | Cra | activator | cydAp5 | 771254 | 771271 | -105.5 | aaacctgtttATTGTAAGGATTTTGCGGcgtaatatat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2] |
Reference(s) |
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