RegulonDB RegulonDB 10.10: Operon Form
   

idnK operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: idnK
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: idnK
Gene(s): idnK   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Bausch C., et al., 2004
Promoter
Name: idnKp
+1: 4494597
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 26
Sequence: tcttatcagtagaaataaaaaaacgtgaaattattatgccgccaggcgtagtatcgcagcAggtaagatgattcaggagat
                         -35                     -10        +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [1] Bausch C., et al., 2004
[2] Huerta AM., et al., 2003
[3] Tsunedomi R., et al., 2003
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cyclic-AMP activator idnKp 4494466 4494488 -120.5 aactgtcattATTTGTGATGAAGATCACGTCAGaaaattgtta nd [GEA], [AIBSCS], [APIORCISFBSCS] [1], [3], [4]
proximal CRP-cyclic-AMP activator idnKp 4494516 4494537 -70.5 atgttacgcaTAACGTGATGTGCCTTGTAATTcttatcagta nd [GEA], [APIORCISFBSCS] [1], [3]
[GntR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote GntR repressor idnKp 4494484 4494503 -103.5 tgaagatcacGTCAGAAAATTGTTACATTActatgttacg nd [GEA], [APIORCISFBSCS] [3]
proximal GntR repressor idnKp 4494504 4494523 -83.5 tgttacattaCTATGTTACGCATAACGTGAtgtgccttgt nd [GEA], [AIBSCS], [APIORCISFBSCS] [3]
proximal GntR repressor idnKp 4494534 4494553 -53.5 tgtgccttgtAATTCTTATCAGTAGAAATAaaaaaacgtg nd [GEA], [AIBSCS], [APIORCISFBSCS] [3]
[IdnR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IdnR activator idnKp 4494506 4494521 -83.5 ttacattactATGTTACGCATAACGTgatgtgcctt nd [GEA], [AIBSCS] [3], [5]


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.


Reference(s)    

 [1] Bausch C., Ramsey M., Conway T., 2004, Transcriptional organization and regulation of the L-idonic acid pathway (GntII system) in Escherichia coli., J Bacteriol 186(5):1388-97

 [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] Tsunedomi R., Izu H., Kawai T., Yamada M., 2003, Dual control by regulators, GntH and GntR, of the GntII genes for gluconate metabolism in Escherichia coli., J Mol Microbiol Biotechnol 6(1):41-56

 [4] Tsai MJ., Wang JR., Yang CD., Kao KC., Huang WL., Huang HY., Tseng CP., Huang HD., Ho SY., 2018, PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli., Sci Rep 8(1):951

 [5] Bausch C., Peekhaus N., Utz C., Blais T., Murray E., Lowary T., Conway T., 1998, Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for L-idonic acid catabolism in Escherichia coli., J Bacteriol 180(14):3704-10

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