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Name: | alkA | ||||||||||
Synonym(s): | OP00002 | ||||||||||
Gene(s): | alkA Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | Both the unmethylated and methylated forms of the Ada protein can activate alkA transcription in vivo and in vitro Landini P,1999 | ||||||||||
Evidence: | [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit | ||||||||||
Reference(s): |
[1] Nakabeppu Y., et al., 1984 [2] Volkert MR. 1988 |
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Promoter | |||||||||||
Name: | alkAp2 | ||||||||||
+1: | 2147559 | ||||||||||
Sigma Factor: | Sigma38 Sigmulon | ||||||||||
Distance from start of the gene: | 19 | ||||||||||
Sequence: |
tcgcgacaaccggaatatgaaagcaaagcgcagcgtctgaataacgtttatgctgaaagcGgatgaataaggagatgcgat -35 -10 +1 |
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Note(s): | σ70 is the sigma factor principally responsible for the alkA transcription. However alkA is highly dependent on alternative factor σ38 (RpoS) during the stationary phase. In contrast, the transcription factor Ada in its methylated state negatively regulates σ38-dependent transcription Landini P,1999. EσS is more efficient than Eσ70 in carrying out transcription from the alkA promoter in the absence of Ada (Ada is a repressor for EσS) Landini P,1999 |
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Evidence: |
[COMP-AINF] [EXP-IDA] [EXP-IDA-RNA-POLYMERASE-FOOTPRINTING] [EXP-IEP] [RS-EPT-CBR] |
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Reference(s): |
[3] Huerta AM., et al., 2003 [4] Lai CF., et al., 1999 [5] Landini P., et al., 1999 [6] Landini P., et al., 1999 [7] 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 | Ada | activator | alkAp2 | 2147589 | 2147613 | -41.5 | gccgtcgcgaCAACCGGAATATGAAAGCAAAGCGCagcgtctgaa | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [5], [6], [8], [9], [10], [11], [12], [13] |
Name: | alkA | ||||||||||
Synonym(s): | OP00002 | ||||||||||
Gene(s): | alkA Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | Both the unmethylated and methylated forms of the Ada protein can activate alkA transcription in vivo and in vitro Landini P,1999 | ||||||||||
Evidence: | [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit | ||||||||||
Reference(s): |
[1] Nakabeppu Y., et al., 1984 [2] Volkert MR. 1988 |
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Promoter | |||||||||||
Name: | alkAp | ||||||||||
+1: | 2147559 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 19 | ||||||||||
Sequence: |
tcgcgacaaccggaatatgaaagcaaagcgcagcgtctgaataacgtttatgctgaaagcGgatgaataaggagatgcgat -35 -10 +1 |
||||||||||
Note(s): | σ70 is the sigma factor principally responsible for the alkA transcription. However alkA is highly dependent on alternative factor σ38 (RpoS) during the stationary phase. In contrast, the transcription factor Ada in its methylated state negatively regulates σ38-dependent transcription Landini P,1999. EσS is more efficient than Eσ70 in carrying out transcription from the alkA promoter in the absence of Ada (Ada is a repressor for EσS) Landini P,1999 |
||||||||||
Evidence: |
[COMP-AINF] [EXP-IDA] [EXP-IDA-RNA-POLYMERASE-FOOTPRINTING] [EXP-IEP] [RS-EPT-CBR] |
||||||||||
Reference(s): |
[3] Huerta AM., et al., 2003 [4] Lai CF., et al., 1999 [5] Landini P., et al., 1999 [6] Landini P., et al., 1999 [7] 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 | Ada | activator | alkAp | 2147589 | 2147613 | -41.5 | gccgtcgcgaCAACCGGAATATGAAAGCAAAGCGCagcgtctgaa | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [5], [6], [8], [9], [10], [11], [12], [13] |
RNA cis-regulatory element | ![]() |
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Regulation, transcriptional elongation | |
Attenuator type: | Transcriptional |
Strand: | reverse |
Structure type | Energy | LeftPos | RightPos | Sequence (RNA-strand) | |
---|---|---|---|---|---|
terminator | -9.3 | 2147747 | 2147780 | gcaaagcattGAAGGCAGCAGCGTGCTGTCGTTTTCCATTTTTagcaaatgcg | |
anti-terminator | -12.9 | 2147768 | 2147815 | tacagccattCGCTTACCGCTTCACGCGTTGGCGCGCAAAGCATTGAAGGCAGCAGCgtgctgtcgt | |
anti-anti-terminator | -8.0 | 2147813 | 2147841 | cgtctgccggAACATCATGATGGCGGTACAGCCATTCGcttaccgctt |
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos" |
Reference(s) |
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