RegulonDB RegulonDB 11.1: Operon Form
   

agaS-kbaY-agaBCDI operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: agaS-kbaY-agaBCDI
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: agaSYBCDI
Synonym(s): agaSkbaYagaBCDI
Gene(s): agaS, kbaY, agaB, agaC, agaD, agaI   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Brinkkotter A., et al., 2000
Promoter
Name: agaSp
+1: 3281889
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 87
Sequence: tcgttttatttcttttttctccattgaactttcagtttcttttctatagattttaatcaaCgaaagacatcaccaagtgaa
                        -35                  -10            +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[3] Ray WK., et al., 2004
TF binding sites (TFBSs)
[AgaR,-] Phrase
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 AgaR repressor agaSp 3281605 3281624 -274.5 ctggattcagGGTCAATTAGCTTCGTTTTGatagtttgct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
remote AgaR repressor agaSp 3281668 3281687 -211.5 ccgtaaggccTTTCTTTTTCTTTCGTTTTGatctgtgcag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
remote AgaR repressor agaSp 3281785 3281804 -94.5 gcatccagcaATCCCTTTTGCTTCCTTTATcttttctttc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
proximal AgaR repressor agaSp 3281827 3281846 -52.5 cgatcacaaaTTTCGTTTTATTTCTTTTTTctccattgaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
proximal AgaR repressor agaSp 3281858 3281877 -21.5 tccattgaacTTTCAGTTTCTTTTCTATAGattttaatca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
proximal AgaR repressor agaSp 3281901 3281920 22.5 aaagacatcaCCAAGTGAAATGAAACGAAAggcaagtgaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins


Reference(s)    

 [1] Brinkkotter A., Kloss H., Alpert C., Lengeler JW., 2000, Pathways for the utilization of N-acetyl-galactosamine and galactosamine in Escherichia coli., Mol Microbiol 37(1):125-35

 [2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [3] Ray WK., Larson TJ., 2004, Application of AgaR repressor and dominant repressor variants for verification of a gene cluster involved in N-acetylgalactosamine metabolism in Escherichia coli K-12., Mol Microbiol 51(3):813-26

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