RegulonDB RegulonDB 10.7: Operon Form
   

hydN-hypF operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: hypF
Gene(s): hypF   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Shimada T., et al., 2005
Promoter
Name: hypFp2
+1: 2838014
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 589
Sequence: aatgtattggttgccgtacctgtgaagtagcgtgcgtggtttctcatcaggaaaatcaggActgtgcatcgctgaccccgg
                           -35                     -10      +1                   
Evidence: [IDA]
Reference(s): [1] Shimada T., et al., 2005
TF binding sites (TFBSs)
[Cra,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Cra repressor hypFp2 2838090 2838107 -84.5 ctggagaattTGATGAACCGTTTCATCAttgctgacgc nd [APIORCISFBSCS], [BPP], [GEA] [1]


Transcription unit          
Name: hypF
Gene(s): hypF   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Shimada T., et al., 2005
Promoter
Name: hypFp3
+1: 2838105
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 680
Sequence: taaaaactggcatgatttgtgaatgtatcggcgcattaactgtcattgctggagaatttgAtgaaccgtttcatcattgct
                         -35                        -10     +1                   
Evidence: [IDA]
Reference(s): [1] Shimada T., et al., 2005
TF binding sites (TFBSs)
[Cra,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Cra repressor hypFp3 2838090 2838107 7.5 ctggagaattTGATGAACCGTTTCATCAttgctgacgc nd [APIORCISFBSCS], [BPP], [GEA] [1]


Transcription unit          
Name: hydN-hypF
Synonym(s): hydA
Gene(s): hypF, hydN   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [2] Maier T., et al., 1996
Promoter
Name: hydNp
+1: 2838132
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 27
Sequence: aattaatttccttaaataacagtaaattaaaaactggcatgatttgtgaatgtatcggcgCattaactgtcattgctggag
                                   -24         -12          +1                   
Evidence: [HIPP]
[TIM] ; Method: Primer Extension
[TIM]
Reference(s): [2] Maier T., et al., 1996
TF binding sites (TFBSs)
[FhlA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FhlA-formate activator hydNp nd nd nd nd nd [BPP], [GEA] [2]
[FlhDC,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FlhDC1 activator hydNp nd nd nd nd nd [GEA] [3]
Note(s): 1The regulatory effect of FlhDC in hydN operon transcription has been proved only by a microarray analysis by Pruss BM,2001.1The regulatory effect of FlhDC in hydN operon transcription has been proved only by a microarray analysis by Pruss BM,2001.


Transcription unit       
Name: hypF
Gene(s): hypF   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Shimada T., et al., 2005
Promoter
Name: hypFp1
+1: Unknown
Sigma Factor: Sigma70 Sigmulon
Evidence: [IDA]
Reference(s): [1] Shimada T., et al., 2005


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
Evidence: [ICA] Inferred by computational analysis
Reference(s): [4] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -14.0 2838205 2838240 ttgtcatcacATGTCATCGTCACTAGTGTCGATGACATCGTTTTTcctgcattac
  anti-terminator -4.6 2838231 2838260 ttgctccttcGCGATAAACATTGTCATCACATGTCATCGtcactagtgt
  anti-anti-terminator -4.52 2838246 2838280 gatccgccgcGACTCACTCATTGCTCCTTCGCGATAAACATTGTcatcacatgt
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"


Evidence    

 [IDA] Inferred from direct assay

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

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [HIPP] Human inference of promoter position

 [TIM] Transcription initiation mapping


Reference(s)    

 [1] Shimada T., Fujita N., Maeda M., Ishihama A., 2005, Systematic search for the Cra-binding promoters using genomic SELEX system., Genes Cells 10(9):907-18

 [2] Maier T., Binder U., Bock A., 1996, Analysis of the hydA locus of Escherichia coli: two genes (hydN and hypF) involved in formate and hydrogen metabolism., Arch Microbiol 165(5):333-41

 [3] Pruss BM., Liu X., Hendrickson W., Matsumura P., 2001, FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions., FEMS Microbiol Lett 197(1):91-7

 [4] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.

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