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Name: | pdhR-aceEF-lpdA | ||||||||||
Gene(s): | pdhR, aceE, aceF, lpd Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The expression of this operon is enhanced during and after the switch from aerobic to anaerobic growth conditions Trotter EW, Rolfe MD, Hounslow AM, Craven CJ, Williamson MP, Sanguinetti G, Poole RK, Green J,2011 | ||||||||||
Evidence: | [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined | ||||||||||
Reference(s): | [1] Cunningham L., et al., 1998 | ||||||||||
Promoter | |||||||||||
Name: | pdhRp | ||||||||||
+1: | 122034 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 58 | ||||||||||
Sequence: |
ttcatgatttcaatcaaaacctgtatggacataaggtgaatactttgttactttagcgtcAcagacatgaaattggtaaga -35 -10 +1 |
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Note(s): | The genes are expressed from two major promoters: Ppdh, which generates a 7.4-kb pdhR-lpdA readthrough transcript, and Plpd, which generates an independent 1.7-kb lpda transcript. Like pdhRp, ndhp and cyoAp are repressed by PdhR and derepressed by the addition of pyruvate Ogasawara H,2007 |
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Evidence: |
[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR] |
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Reference(s): |
[1] Cunningham L., et al., 1998 [2] Huerta AM., et al., 2003 [3] Olvera L., et al., 2009 [4] Quail MA., et al., 1995 [5] Salgado H, et al., 2012 |
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Terminator(s) | |||||||||||
Type: | rho-independent | ||||||||||
Sequence: | tccggcaattAAAAAAGCGGCTAACCACGCCGCTTTTTTtacgtctgca | ||||||||||
Reference(s): | [6] Spencer ME., et al., 1985 |
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 | BtsR-Phosphorylated | repressor | pdhRp | 121826 | 121837 | -203.0 | tgaattaaaaATCACAAAATTGgtaagtgaat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-PATTERN-DISCOVERY], [EXP-GSELEX] | S | [8] |
remote | BtsR-Phosphorylated | repressor | pdhRp | 121841 | 121852 | -188.0 | aaaattggtaAGTGAATCGGTTcaattcggat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-PATTERN-DISCOVERY], [EXP-GSELEX] | S | [8] |
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 | CRP-cyclic-AMP | activator | pdhRp | 121646 | 121667 | -377.5 | tacatcaaagAAGTTTGAATTGTTACAAAAAGacttccgtca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
remote | CRP-cyclic-AMP | activator | pdhRp | 121913 | 121934 | -110.5 | taaagtctacATTTGTGCATAGTTACAACTTTgaaacgttat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
proximal | CRP-cyclic-AMP | activator | pdhRp | 121941 | 121962 | -82.5 | ctttgaaacgTTATATATGTCAAGTTGTTAAAatgtgcacag | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | [7], [11] |
proximal | CRP-cyclic-AMP | activator | pdhRp | 121953 | 121974 | -70.5 | atatatgtcaAGTTGTTAAAATGTGCACAGTTtcatgatttc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | [7], [11] |
proximal | CRP-cyclic-AMP | activator | pdhRp | 121961 | 121982 | -62.5 | caagttgttaAAATGTGCACAGTTTCATGATTtcaatcaaaa | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
proximal | CRP-cyclic-AMP | activator | pdhRp | 121973 | 121994 | -50.5 | atgtgcacagTTTCATGATTTCAATCAAAACCtgtatggaca | 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 | ||||||||
remote | Cra | repressor | pdhRp | 121840 | 121857 | -185.5 | caaaattggtAAGTGAATCGGTTCAATTcggattttta | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [9], [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 | ||||||||
proximal | FNR | activator | pdhRp | 121977 | 121990 | -50.5 | gcacagtttcATGATTTCAATCAAaacctgtatg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] | S | [11], [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 | ||||||||
proximal | FNR | repressor | pdhRp | 121977 | 121990 | -50.5 | gcacagtttcATGATTTCAATCAAaacctgtatg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] | S | [11], [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 | ||||||||
proximal | PdhR | repressor | pdhRp | 122044 | 122060 | 19.0 | acagacatgaAATTGGTAAGACCAATTgacttcggca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | C | [4], [11], [14], [15] |
Name: | pdhR-aceEF-lpdA | ||||||||||
Gene(s): | pdhR, aceE, aceF, lpd Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The expression of this operon is enhanced during and after the switch from aerobic to anaerobic growth conditions Trotter EW, Rolfe MD, Hounslow AM, Craven CJ, Williamson MP, Sanguinetti G, Poole RK, Green J,2011 | ||||||||||
Evidence: | [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined | ||||||||||
Reference(s): | [1] Cunningham L., et al., 1998 | ||||||||||
Promoter | |||||||||||
Name: | pdhRp2 | ||||||||||
+1: | 122034 | ||||||||||
Sigma Factor: | Sigma38 Sigmulon | ||||||||||
Distance from start of the gene: | 58 | ||||||||||
Sequence: |
ttcatgatttcaatcaaaacctgtatggacataaggtgaatactttgttactttagcgtcAcagacatgaaattggtaaga -35 -10 +1 |
||||||||||
Note(s): | The genes are expressed from two major promoters: Ppdh, which generates a 7.4-kb pdhR-lpdA readthrough transcript, and Plpd, which generates an independent 1.7-kb lpda transcript. Like pdhRp, ndhp and cyoAp are repressed by PdhR and derepressed by the addition of pyruvate Ogasawara H,2007 |
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Evidence: |
[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR] |
||||||||||
Reference(s): |
[1] Cunningham L., et al., 1998 [2] Huerta AM., et al., 2003 [3] Olvera L., et al., 2009 [4] Quail MA., et al., 1995 [5] Salgado H, et al., 2012 |
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Terminator(s) | |||||||||||
Type: | rho-independent | ||||||||||
Sequence: | tccggcaattAAAAAAGCGGCTAACCACGCCGCTTTTTTtacgtctgca | ||||||||||
Reference(s): | [6] Spencer ME., et al., 1985 |
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 | BtsR-Phosphorylated | repressor | pdhRp2 | 121826 | 121837 | -203.0 | tgaattaaaaATCACAAAATTGgtaagtgaat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-PATTERN-DISCOVERY], [EXP-GSELEX] | S | [8] |
remote | BtsR-Phosphorylated | repressor | pdhRp2 | 121841 | 121852 | -188.0 | aaaattggtaAGTGAATCGGTTcaattcggat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-PATTERN-DISCOVERY], [EXP-GSELEX] | S | [8] |
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 | CRP-cyclic-AMP | activator | pdhRp2 | 121646 | 121667 | -377.5 | tacatcaaagAAGTTTGAATTGTTACAAAAAGacttccgtca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
remote | CRP-cyclic-AMP | activator | pdhRp2 | 121913 | 121934 | -110.5 | taaagtctacATTTGTGCATAGTTACAACTTTgaaacgttat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
proximal | CRP-cyclic-AMP | activator | pdhRp2 | 121941 | 121962 | -82.5 | ctttgaaacgTTATATATGTCAAGTTGTTAAAatgtgcacag | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | [7], [11] |
proximal | CRP-cyclic-AMP | activator | pdhRp2 | 121953 | 121974 | -70.5 | atatatgtcaAGTTGTTAAAATGTGCACAGTTtcatgatttc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | [7], [11] |
proximal | CRP-cyclic-AMP | activator | pdhRp2 | 121961 | 121982 | -62.5 | caagttgttaAAATGTGCACAGTTTCATGATTtcaatcaaaa | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
proximal | CRP-cyclic-AMP | activator | pdhRp2 | 121973 | 121994 | -50.5 | atgtgcacagTTTCATGATTTCAATCAAAACCtgtatggaca | 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 | ||||||||
remote | Cra | repressor | pdhRp2 | 121840 | 121857 | -185.5 | caaaattggtAAGTGAATCGGTTCAATTcggattttta | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [9], [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 | ||||||||
proximal | FNR | activator | pdhRp2 | 121977 | 121990 | -50.5 | gcacagtttcATGATTTCAATCAAaacctgtatg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] | S | [11], [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 | ||||||||
proximal | FNR | repressor | pdhRp2 | 121977 | 121990 | -50.5 | gcacagtttcATGATTTCAATCAAaacctgtatg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] | S | [11], [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 | ||||||||
proximal | PdhR | repressor | pdhRp2 | 122044 | 122060 | 19.0 | acagacatgaAATTGGTAAGACCAATTgacttcggca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | C | [4], [11], [14], [15] |
Name: | aceEF | ||||||||||
Gene(s): | aceE, aceF Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The aceE gene expression is highly induced in the presence of pyruvate El-Mansi M, Phue JN, Shiloach J,2021. | ||||||||||
Evidence: | [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined | ||||||||||
Reference(s): | [6] Spencer ME., et al., 1985 | ||||||||||
Promoter | |||||||||||
Name: | aceEp2 | ||||||||||
+1: | 122969 | ||||||||||
Sigma Factor: | Sigma38 Sigmulon | ||||||||||
Distance from start of the gene: | 48 | ||||||||||
Sequence: |
aaagcgcggcaactaaacgtagaacctgtcttattgagctttccggcgagagttcaatggGacaggttccagaaaactcaa -35 -10 +1 |
||||||||||
Evidence: |
[COMP-AINF] [COMP-HINF] [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR] |
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Reference(s): |
[2] Huerta AM., et al., 2003 [3] Olvera L., et al., 2009 [5] Salgado H, et al., 2012 [6] Spencer ME., et al., 1985 |
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Terminator(s) | |||||||||||
Type: | rho-independent | ||||||||||
Sequence: | tgatgtaagtAAAAGAGCCGGCCCAACGGCCGGCTTTTTTctggtaatct | ||||||||||
Note(s): | This potential stem-loop structure is a pdhR-aceEF terminator or an mRNA processing site. | ||||||||||
Reference(s): | [16] Cunningham L., et al., 1998 |
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 | repressor | aceEp2 | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] | W | [18] |
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 | FNR | repressor | aceEp2 | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] | W | [11], [18] |
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 | NsrR | repressor | aceEp2 | 122883 | 122894 | -81.0 | aattatccagAAGATGTTGTAAatcaagcgca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | [17] |
Name: | aceEF | ||||||||||
Gene(s): | aceE, aceF Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The aceE gene expression is highly induced in the presence of pyruvate El-Mansi M, Phue JN, Shiloach J,2021. | ||||||||||
Evidence: | [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined | ||||||||||
Reference(s): | [6] Spencer ME., et al., 1985 | ||||||||||
Promoter | |||||||||||
Name: | aceEp1 | ||||||||||
+1: | 122969 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 48 | ||||||||||
Sequence: |
aaagcgcggcaactaaacgtagaacctgtcttattgagctttccggcgagagttcaatggGacaggttccagaaaactcaa -35 -10 +1 |
||||||||||
Evidence: |
[COMP-AINF] [COMP-HINF] [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR] |
||||||||||
Reference(s): |
[2] Huerta AM., et al., 2003 [3] Olvera L., et al., 2009 [5] Salgado H, et al., 2012 [6] Spencer ME., et al., 1985 |
||||||||||
Terminator(s) | |||||||||||
Type: | rho-independent | ||||||||||
Sequence: | tgatgtaagtAAAAGAGCCGGCCCAACGGCCGGCTTTTTTctggtaatct | ||||||||||
Note(s): | This potential stem-loop structure is a pdhR-aceEF terminator or an mRNA processing site. | ||||||||||
Reference(s): | [16] Cunningham L., et al., 1998 |
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 | repressor | aceEp1 | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] | W | [18] |
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 | FNR | repressor | aceEp1 | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] | W | [11], [18] |
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 | NsrR | repressor | aceEp1 | 122883 | 122894 | -81.0 | aattatccagAAGATGTTGTAAatcaagcgca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | [17] |
Name: | lpdA | ||||||||||
Gene(s): | lpd Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | Under nitrogen-rich growth conditions, the expression of the lpdA gene increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased Kumar R,2011 | ||||||||||
Evidence: | [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined | ||||||||||
Reference(s): | [1] Cunningham L., et al., 1998 | ||||||||||
Promoter | |||||||||||
Name: | lpdAp | ||||||||||
+1: | 127717 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 195 | ||||||||||
Sequence: |
tagacaaatcggttgccgtttgttgtttaaaaattgttaacaattttgtaaaataccgacGgatagaacgacccggtggtg -35 -10 +1 |
||||||||||
Evidence: |
[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
||||||||||
Reference(s): |
[16] Cunningham L., et al., 1998 [1] Cunningham L., et al., 1998 [2] Huerta AM., et al., 2003 [11] Quail MA., et al., 1994 |
||||||||||
Terminator(s) | |||||||||||
Type: | rho-independent | ||||||||||
Sequence: | tccggcaattAAAAAAGCGGCTAACCACGCCGCTTTTTTtacgtctgca | ||||||||||
Reference(s): | [6] Spencer ME., et al., 1985 |
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 | repressor | lpdAp | 127683 | 127697 | -27.0 | cgtttgttgtTTAAAAATTGTTAACaattttgtaa | nd | [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-CHIP] | S | [19] |
proximal | ArcA-phosphorylated | repressor | lpdAp | 127692 | 127706 | -18.0 | tttaaaaattGTTAACAATTTTGTAaaataccgac | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-CHIP], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | C | [11], [16], [19], [20] |
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 | CRP-cyclic-AMP | repressor | lpdAp | 127688 | 127709 | -18.5 | gttgtttaaaAATTGTTAACAATTTTGTAAAAtaccgacgga | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [1], [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 | ||||||||
nd | FNR | activator | lpdAp | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [13], [21] |
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 | FNR | repressor | lpdAp | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [13], [21] |
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 | Fis | activator | lpdAp | 127681 | 127695 | -29.0 | gccgtttgttGTTTAAAAATTGTTAacaattttgt | nd | [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | nd | [1], [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 | ||||||||
nd | Fur-Fe2+ | activator | lpdAp | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] | W | [21] |
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 | Fur-Fe2+ | repressor | lpdAp | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] | W | [21] |
Reference(s) |
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