RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit       
Name: narK
Gene(s): narK, narS   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: narKp2
+1: 1277821
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 136
Sequence: cgctttacatcggtaagggtagggattttacagcaccgtgaaaaatctcataatttttatGaagtcactgtactcactatg
                           -35                     -10      +1                   
Note(s): The activity of narKp2 promoter is unaffected by the presence of oxygen and nitrate Bonnefoy V,1992
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Bonnefoy V., et al., 1992
[2] Huerta AM., et al., 2003


Transcription unit          
Name: narK
Synonym(s): OP00061
Gene(s): narK, narS   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [3] Li J., et al., 1994
Promoter
Name: narKp1
+1: 1277932
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 25
Sequence: ttatcttatcgtttgatttacatcaaattgcctttagctacagacactaaggtggcagacAtcgaaacgagtatcagaggt
                      -35                       -10         +1                   
Note(s): The activity of the narKp1 promoter is induced by anaerobiosis and nitrate Bonnefoy V,1992
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Bonnefoy V., et al., 1992
[2] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[FNR,+] 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
proximal FNR activator narKp1 1277846 1277859 -79.5 actatgggtaATGATAAATATCAAtgatagataa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] W [5]
proximal FNR activator narKp1 1277884 1277897 -41.5 atcttatcgtTTGATTTACATCAAattgccttta nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [7], [8]
[Fis,-] 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
proximal Fis repressor narKp1 1277880 1277899 -43.0 agttatcttaTCGTTTGATTTACATCAAATtgcctttagc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [6]
[IHF,+] 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 IHF activator narKp1 1277796 1277808 -130.0 ttttacagcaCCGTGAAAAATCTcataattttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [4]
[NarL,+] 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 NarL-phosphorylated activator narKp1 1277715 1277721 -214.0 ggctgaagtaTACCCATacccggaaag nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3]
remote NarL-phosphorylated activator narKp1 1277735 1277741 -194.0 cggaaagagtTACTCCTtatttgccgt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [3]
remote NarL-phosphorylated activator narKp1 1277752 1277758 -177.0 tatttgccgtGTGGTTAgtcgctttac nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3]
remote NarL-phosphorylated activator narKp1 1277769 1277775 -160.0 gtcgctttacATCGGTAagggtaggga nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3]
remote NarL-phosphorylated activator narKp1 1277775 1277781 -154.0 ttacatcggtAAGGGTAgggattttac nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3]
remote NarL-phosphorylated activator narKp1 1277826 1277832 -103.0 tttatgaagtCACTGTActcactatgg nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3]
remote NarL-phosphorylated activator narKp1 1277831 1277837 -98.0 gaagtcactgTACTCACtatgggtaat nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3]
proximal NarL-phosphorylated activator narKp1 1277839 1277845 -90.0 tgtactcactATGGGTAatgataaata nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3]
proximal NarL-phosphorylated activator narKp1 1277849 1277855 -80.0 atgggtaatgATAAATAtcaatgatag nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3]
proximal NarL-phosphorylated activator narKp1 1277862 1277868 -67.0 aatatcaatgATAGATAaagttatctt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [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

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-IEP-MICROARRAY] high throughput expression microarray evidence

 [COMP-AINF-PATTERN-DISCOVERY] Automated inference based on sequence pattern discovery

 [EXP-CHIP-CHIP] high throughput ChIP-chip evidence

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

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

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


Reference(s)    

 [1] Bonnefoy V., DeMoss JA., 1992, Identification of functional cis-acting sequences involved in regulation of narK gene expression in Escherichia coli., Mol Microbiol 6(23):3595-602

 [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] Li J., Kustu S., Stewart V., 1994, In vitro interaction of nitrate-responsive regulatory protein NarL with DNA target sequences in the fdnG, narG, narK and frdA operon control regions of Escherichia coli K-12., J Mol Biol 241(2):150-65

 [4] Kolesnikow T., Schroder I., Gunsalus RP., 1992, Regulation of narK gene expression in Escherichia coli in response to anaerobiosis, nitrate, iron, and molybdenum., J Bacteriol 174(22):7104-11

 [5] Walker MS., DeMoss JA., 1992, Role of alternative promoter elements in transcription from the nar promoter of Escherichia coli., J Bacteriol 174(4):1119-23

 [6] Bradley MD., Beach MB., de Koning AP., Pratt TS., Osuna R., 2007, Effects of Fis on Escherichia coli gene expression during different growth stages., Microbiology 153(Pt 9):2922-40

 [7] Federowicz S., Kim D., Ebrahim A., Lerman J., Nagarajan H., Cho BK., Zengler K., Palsson B., 2014, Determining the control circuitry of redox metabolism at the genome-scale., PLoS Genet 10(4):e1004264

 [8] Melville SB., Gunsalus RP., 1996, Isolation of an oxygen-sensitive FNR protein of Escherichia coli: interaction at activator and repressor sites of FNR-controlled genes., Proc Natl Acad Sci U S A 93(3):1226-31

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