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Name: | actP |
Gene(s): | actP Genome Browser M3D Gene expression COLOMBOS |
Promoter | |
Name: | actPp |
+1: | 4284935 |
Sigma Factor: | Sigma54 Sigmulon |
Distance from start of the gene: | 33 |
Sequence: |
gatctcctttgttctcaccggtatctacatctggcgggcgaacggcgaattcgaccgtctTaataatgaagtcctgcatga -24 -12 +1 |
Note(s): | This promoter was identified by microarray assays with a mutant σ54 strain and a σ54-overexpressing strain, and by σ54-related promoter element identification Zhao K,2010 We assigned a putative transcription start site to this promoter based on the observation that the majority of the σ54-dependent promoters, whose transcription start sites were determined experimentally, present a distance of 11 nucleotides between the transcription start site and the -12 box Barrios H,1999. |
Evidence: |
[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IEP] |
Reference(s): |
[1] Huerta AM., et al., 2003 [2] Zhao K., et al., 2010 |
Name: | acs-yjcHG | ||||||||||
Gene(s): | actP, yjcH, acs Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | Transcription of acs may be negatively regulated by IclR through an indirect effect Kumari S,2000Shin S, Song SG, Lee DS, Pan JG, Park C,1997. Fnr activates the transcription of acs by binding to two sites located close to the transcription start site. This has been demonstrated by gene expression analysis and protein binding to the region, but the specific sequences of the sites were not reported Kumari S,2000. Based on arcA deletion experiments, it appears that ArcA-P represses the acs-yjcH-actP operon, resulting in a lower rate of acetate uptake and assimilation Veeravalli K, Schindler T, Dong E, Yamada M, Hamilton R, Laird MW,2018 The expression of the gene acs is diminished under oxygen limitation Kawaguchi H, Miyagawa H, Nakamura-Tsuruta S, Takaya N, Ogino C, Kondo A,2019, and it is highly increased in the presence of pyruvate El-Mansi M, Phue JN, Shiloach J,2021. |
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Evidence: | [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined | ||||||||||
Reference(s): |
[3] Gimenez R., et al., 2003 [4] Kumari S., et al., 2000 |
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Promoter | |||||||||||
Name: | acsp | ||||||||||
+1: | 4287391 | ||||||||||
Sigma Factor: | Sigma38 Sigmulon | ||||||||||
Distance from start of the gene: | 20 | ||||||||||
Sequence: |
atactaaacaaaactgccaatacccctacatttaacgcttatgccacatattattaacatCctacaaggagaacaaaagca -35 -10 +1 |
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Note(s): | The effect of RpoS is likely indirect and may be mediated by competing with σ70 for core polymerase Kumari S,2000. Shin S, Song SG, Lee DS, Pan JG, Park C,1997 | ||||||||||
Evidence: |
[COMP-AINF-POSITIONAL-IDENTIFICATION] [COMP-HINF] [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] |
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Reference(s): |
[5] Beatty CM., et al., 2003 [6] Kumari S., et al., 2000 [7] Olvera L., et al., 2009 |
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 | activator | acsp | 4287450 | 4287471 | -69.5 | aattctacttTTGCGTGATCTGTCGCCCAAATactaaacaaa | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [11] |
remote | CRP-cyclic-AMP | activator | acsp | 4287503 | 4287524 | -122.5 | ttaatcaactTTTGTTGCTGACCTTCAAAAATtaccctgccg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [11] |
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 | repressor | acsp | 4287443 | 4287457 | -59.0 | gtgatctgtcGCCCAAATACTAAACaaaactgcca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [8] |
remote | Fis | repressor | acsp | 4287482 | 4287496 | -98.0 | aaattaccctGCCGTTTATTTGCACaattctactt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [8] |
remote | Fis | repressor | acsp | 4287649 | 4287663 | -265.0 | tcgcccctatGTGTAACAAATAACCacactgtgaa | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [8], [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 | ||||||||
remote | IHF | repressor | acsp | 4287538 | 4287550 | -153.0 | tgcataactgCATGTTCCTCAAAgaattaatca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [8], [11] |
remote | IHF | repressor | acsp | 4287565 | 4287577 | -180.0 | tcagtatcttCCTCTTTTTCAACagcatgcata | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [8] |
remote | IHF | repressor | acsp | 4287610 | 4287622 | -225.0 | ctttaatcaaTTGTAAGTGCATGtaaaatacca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [8], [9], [10] |
Name: | acs-yjcHG | ||||||||||
Gene(s): | actP, yjcH, acs Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | Transcription of acs may be negatively regulated by IclR through an indirect effect Kumari S,2000. Shin S, Song SG, Lee DS, Pan JG, Park C,1997 Fnr activates the transcription of acs by binding to two sites located close to the transcription start site. This has been demonstrated by gene expression analysis and protein binding to the region, but the specific sequences of the sites were not reported Kumari S,2000. Based on arcA deletion experiments, it appears that ArcA-P represses the acs-yjcH-actP operon, resulting in a lower rate of acetate uptake and assimilation Veeravalli K, Schindler T, Dong E, Yamada M, Hamilton R, Laird MW,2018. The expression of the gene acs is diminished under oxygen limitation Kawaguchi H, Miyagawa H, Nakamura-Tsuruta S, Takaya N, Ogino C, Kondo A,2019, and it is highly increased 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): |
[3] Gimenez R., et al., 2003 [4] Kumari S., et al., 2000 |
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Promoter | |||||||||||
Name: | acsp2 | ||||||||||
+1: | 4287391 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 20 | ||||||||||
Sequence: |
atactaaacaaaactgccaatacccctacatttaacgcttatgccacatattattaacatCctacaaggagaacaaaagca -35 -10 +1 |
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Note(s): | The effect of RpoS is likely indirect and may be mediated by competing with σ70 for core polymerase Kumari S,2000. Shin S, Song SG, Lee DS, Pan JG, Park C,1997 | ||||||||||
Evidence: |
[COMP-AINF-POSITIONAL-IDENTIFICATION] [COMP-HINF] [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] |
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Reference(s): |
[5] Beatty CM., et al., 2003 [6] Kumari S., et al., 2000 [7] Olvera L., et al., 2009 |
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 | activator | acsp2 | 4287450 | 4287471 | -69.5 | aattctacttTTGCGTGATCTGTCGCCCAAATactaaacaaa | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [11] |
remote | CRP-cyclic-AMP | activator | acsp2 | 4287503 | 4287524 | -122.5 | ttaatcaactTTTGTTGCTGACCTTCAAAAATtaccctgccg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [11] |
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 | repressor | acsp2 | 4287443 | 4287457 | -59.0 | gtgatctgtcGCCCAAATACTAAACaaaactgcca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [8] |
remote | Fis | repressor | acsp2 | 4287482 | 4287496 | -98.0 | aaattaccctGCCGTTTATTTGCACaattctactt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [8] |
remote | Fis | repressor | acsp2 | 4287649 | 4287663 | -265.0 | tcgcccctatGTGTAACAAATAACCacactgtgaa | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [8], [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 | ||||||||
remote | IHF | repressor | acsp2 | 4287538 | 4287550 | -153.0 | tgcataactgCATGTTCCTCAAAgaattaatca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [8], [11] |
remote | IHF | repressor | acsp2 | 4287565 | 4287577 | -180.0 | tcagtatcttCCTCTTTTTCAACagcatgcata | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [8] |
remote | IHF | repressor | acsp2 | 4287610 | 4287622 | -225.0 | ctttaatcaaTTGTAAGTGCATGtaaaatacca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [8], [9], [10] |
Name: | acs-yjcHG | ||||||||||
Gene(s): | actP, yjcH, acs Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | Transcription of acs may be negatively regulated by IclR through an indirect effect Kumari S,2000Shin S, Song SG, Lee DS, Pan JG, Park C,1997. Fnr activates the transcription of acs by binding to two sites located close to the transcription start site. This has been demonstrated by gene expression analysis and protein binding to the region, but the specific sequences of the sites were not reported Kumari S,2000. The expression of the gene acs is diminished under oxygen limitation Kawaguchi H, Miyagawa H, Nakamura-Tsuruta S, Takaya N, Ogino C, Kondo A,2019, and it is highly increased 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): |
[3] Gimenez R., et al., 2003 [4] Kumari S., et al., 2000 |
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Promoter | |||||||||||
Name: | acsp1 | ||||||||||
+1: | 4287595 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 224 | ||||||||||
Sequence: |
aataaccacactgtgaatgttgtctttaatcaattgtaagtgcatgtaaaataccactttAgagttagtcagtatcttcct -35 -10 +1 |
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Note(s): | The effect by RpoS is likely indirect and might be mediated by competing with σ70 for core polymerase Kumari S,2000. Shin S, Song SG, Lee DS, Pan JG, Park C,1997 | ||||||||||
Evidence: |
[COMP-AINF] [COMP-AINF-POSITIONAL-IDENTIFICATION] |
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Reference(s): |
[9] Browning DF., et al., 2002 [1] Huerta AM., et al., 2003 [6] Kumari S., et al., 2000 |
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 | repressor | acsp1 | 4287649 | 4287663 | -61.0 | tcgcccctatGTGTAACAAATAACCacactgtgaa | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [8], [9] |
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 | IHF | repressor | acsp1 | 4287610 | 4287622 | -21.0 | ctttaatcaaTTGTAAGTGCATGtaaaatacca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [8], [9] |
Reference(s) |
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