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Name: | dadAX | ||||||||||
Synonym(s): | dad | ||||||||||
Gene(s): | dadA, dadX Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The transcript of dadAX is decreased after σE induction, as observed in high-throughput analysis of gene expression Lacoux C,2020. dadAX operon expression is upregulated upon L-valine addition (isoleucine starvation) in the cellular growth medium Gummesson B, Shah SA, Borum AS, Fessler M, Mitarai N, Sørensen MA, Svenningsen SL,2020. A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for dadA . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020. |
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Evidence: | [EXP-IEP-COREGULATION] Inferred through co-regulation [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process |
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Reference(s): |
[1] Lobocka M., et al., 1994 [2] Wild J., et al., 1985 |
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Promoter | |||||||||||
Name: | dadAp2 | ||||||||||
+1: | 1237525 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 46 | ||||||||||
Sequence: |
cagctcaccataaaaaagccgcatgttgaataatattttcaactgagttatcaagatgtgAttagattattattcttttac -35 -10 +1 |
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Evidence: |
[COMP-AINF] [COMP-HINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
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Reference(s): |
[3] Huerta AM., et al., 2003 [1] Lobocka M., et al., 1994 [4] Mathew E., et al., 1996 [5] Zhi J., et al., 1999 [6] Zhi J., 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 | ||||||||
proximal | CRP-cyclic-AMP | activator | dadAp2 | 1237455 | 1237477 | -59.5 | agagtcagggAGATGTGAGCCAGCTCACCATAAaaaagccgca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [4], [5], [6] |
proximal | CRP-cyclic-AMP | activator | dadAp2 | 1237520 | 1237541 | 7.0 | agttatcaagATGTGATTAGATTATTATTCTTttactgtatc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | nd |
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 | Lrp | repressor | dadAp2 | 1237252 | 1237266 | -266.0 | acgcgcacctCATTGTTGTCGGCGCtctctgtgtg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7] |
remote | Lrp | repressor | dadAp2 | 1237277 | 1237291 | -241.0 | tctctgtgtgGAGCACCTCATTTCAagcatagaac | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7] |
remote | Lrp | repressor | dadAp2 | 1237325 | 1237339 | -193.0 | cgcgtcgccgGAGAATTTTTTTCTTtgcgatttct | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-MICROARRAY], [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7], [8] |
remote | Lrp | repressor | dadAp2 | 1237356 | 1237370 | -162.0 | ttcttattatCAGAGTGCCACTAATccgcttctga | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7] |
remote | Lrp | repressor | dadAp2 | 1237382 | 1237396 | -136.0 | cgcttctgaaCGGAATTTTATGCTGgataaaaagg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-MICROARRAY], [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7], [8] |
remote | Lrp | repressor | dadAp2 | 1237412 | 1237426 | -106.0 | aaagggcgttCAGCAGGAGATACTAaagacgccat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7] |
proximal | Lrp | repressor | dadAp2 | 1237450 | 1237464 | -68.0 | gccgcagagtCAGGGAGATGTGAGCcagctcacca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7] |
proximal | Lrp | repressor | dadAp2 | 1237495 | 1237509 | -23.0 | gcatgttgaaTAATATTTTCAACTGagttatcaag | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-MICROARRAY], [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7], [8] |
proximal | Lrp | repressor | dadAp2 | 1237527 | 1237541 | 10.0 | aagatgtgatTAGATTATTATTCTTttactgtatc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-MICROARRAY], [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7], [8] |
remote | Lrp | repressor | dadAp2 | 1237574 | 1237588 | 57.0 | agtggctatgCGAGTTGTCATACTGggaagtggtg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7] |
remote | Lrp | repressor | dadAp2 | 1237596 | 1237610 | 79.0 | ctgggaagtgGTGTGGTAGGCGTTGccagcgcctg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7] |
Name: | dadAX | ||||||||||
Gene(s): | dadA, dadX Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | dadAX operon expression is upregulated upon L-valine addition (isoleucine starvation) in the cellular growth medium Gummesson B, Shah SA, Borum AS, Fessler M, Mitarai N, Sørensen MA, Svenningsen SL,2020. A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for dadA. This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020. |
||||||||||
Evidence: | [EXP-IEP-COREGULATION] Inferred through co-regulation [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process |
||||||||||
Reference(s): |
[1] Lobocka M., et al., 1994 [2] Wild J., et al., 1985 |
||||||||||
Promoter | |||||||||||
Name: | dadAp3 | ||||||||||
+1: | 1237538 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 33 | ||||||||||
Sequence: |
aaaagccgcatgttgaataatattttcaactgagttatcaagatgtgattagattattatTcttttactgtatctaccgtt -35 -10 +1 |
||||||||||
Evidence: |
[COMP-AINF] [COMP-HINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
||||||||||
Reference(s): |
[3] Huerta AM., et al., 2003 [4] Mathew E., et al., 1996 [5] Zhi J., et al., 1999 [6] Zhi J., 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 | ||||||||
proximal | CRP-cyclic-AMP | activator | dadAp3 | 1237455 | 1237477 | -72.5 | agagtcagggAGATGTGAGCCAGCTCACCATAAaaaagccgca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [4], [5], [6] |
proximal | CRP-cyclic-AMP | activator | dadAp3 | 1237518 | 1237539 | -9.5 | tgagttatcaAGATGTGATTAGATTATTATTCttttactgta | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | S | [4], [5], [6] |
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 | Lrp | repressor | dadAp3 | 1237252 | 1237266 | -279.0 | acgcgcacctCATTGTTGTCGGCGCtctctgtgtg | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [EXP-IMP-SITE-MUTATION], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7] |
remote | Lrp | repressor | dadAp3 | 1237277 | 1237291 | -254.0 | tctctgtgtgGAGCACCTCATTTCAagcatagaac | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [EXP-IMP-SITE-MUTATION], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7] |
remote | Lrp | repressor | dadAp3 | 1237325 | 1237339 | -206.0 | cgcgtcgccgGAGAATTTTTTTCTTtgcgatttct | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-MICROARRAY], [EXP-IEP-RNA-SEQ], [EXP-IMP-SITE-MUTATION], [COMP-AINF-PATTERN-DISCOVERY], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7], [8] |
remote | Lrp | repressor | dadAp3 | 1237356 | 1237370 | -175.0 | ttcttattatCAGAGTGCCACTAATccgcttctga | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [EXP-IMP-SITE-MUTATION], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7] |
remote | Lrp | repressor | dadAp3 | 1237382 | 1237396 | -149.0 | cgcttctgaaCGGAATTTTATGCTGgataaaaagg | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-MICROARRAY], [EXP-IEP-RNA-SEQ], [EXP-IMP-SITE-MUTATION], [COMP-AINF-PATTERN-DISCOVERY], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7], [8] |
remote | Lrp | repressor | dadAp3 | 1237412 | 1237426 | -119.0 | aaagggcgttCAGCAGGAGATACTAaagacgccat | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [EXP-IMP-SITE-MUTATION], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7] |
proximal | Lrp | repressor | dadAp3 | 1237450 | 1237464 | -81.0 | gccgcagagtCAGGGAGATGTGAGCcagctcacca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7] |
proximal | Lrp | repressor | dadAp3 | 1237495 | 1237509 | -36.0 | gcatgttgaaTAATATTTTCAACTGagttatcaag | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-MICROARRAY], [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7], [8] |
proximal | Lrp | repressor | dadAp3 | 1237527 | 1237541 | -4.0 | aagatgtgatTAGATTATTATTCTTttactgtatc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-MICROARRAY], [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7], [8] |
remote | Lrp | repressor | dadAp3 | 1237574 | 1237588 | 44.0 | agtggctatgCGAGTTGTCATACTGggaagtggtg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7] |
remote | Lrp | repressor | dadAp3 | 1237596 | 1237610 | 66.0 | ctgggaagtgGTGTGGTAGGCGTTGccagcgcctg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [4], [5], [7] |
Evidence |
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Reference(s) |
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