RegulonDB RegulonDB 10.9: Gene Form
   

rtcR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rtcR rtcB glpG glpR IHF IHF glpRp1 glpRp1 glpRp2 glpRp2 rtcBp rtcBp rtcAp2 rtcAp2 rtcAp6 rtcAp6 rtcAp1 rtcAp1

Gene      
Name: rtcR    Texpresso search in the literature
Synonym(s): ECK3408, EG12356, b3422, yhgB
Genome position(nucleotides): 3558268 --> 3559866 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 55.78
External database links:  
ASAP:
 ABE-0011174
ECHOBASE:
 EB2259
ECOLIHUB:
 rtcR
OU-MICROARRAY:
 b3422
STRING:
 511145.b3422
COLOMBOS: rtcR


Shine dalgarno      
Sequence: gtcttttataAGGATAtctaagATG


Product      
Name: DNA-binding transcriptional activator RtcR
Synonym(s): RtcR, YhgB
Sequence: Get amino acid sequence Fasta Format
Regulator Family: EBP
Cellular location: cytosol
Molecular weight: 60.299
Isoelectric point: 7.102
Motif(s):
 
Type Positions Sequence
485 -> 504 KSLSAAGRQLFDVSRQGKAS
2 -> 185 RKTVAFGFVGTVLDYAGRGSQRWSKWRPTLCLCQQESLVIDRLELLHDARSRSLFETLKRDIASVSPETEVVSVEIELHNPWDFEEVYACLHDFARGYEFQPEKEDYLIHITTGTHVAQICWFLLAEARYLPARLIQSSPPRKKEQPRGPGEVTIIDLDLSRYNAIASRFAEERQQTLDFLKSG
186 -> 424 IATRNPHFNRMIEQIEKVAIKSRAPILLNGPTGAGKSFLARRILELKQARHQFSGAFVEVNCATLRGDTAMSTLFGHVKGAFTGARESREGLLRSANGGMLFLDEIGELGADEQAMLLKAIEEKTFYPFGSDRQVSSDFQLIAGTVRDLRQLVAEGKFREDLYARINLWTFTLPGLRQRQEDIEPNLDYEVERHASLTGDSVRFNTEARRAWLAFATSPQATWRGNFRELSASVTRMAT
187 -> 354 ATRNPHFNRMIEQIEKVAIKSRAPILLNGPTGAGKSFLARRILELKQARHQFSGAFVEVNCATLRGDTAMSTLFGHVKGAFTGARESREGLLRSANGGMLFLDEIGELGADEQAMLLKAIEEKTFYPFGSDRQVSSDFQLIAGTVRDLRQLVAEGKFREDLYARINLW
215 -> 222 GPTGAGKS

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.1 - operon
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0008134 - transcription factor binding
GO:0003700 - DNA-binding transcription factor activity
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0045893 - positive regulation of transcription, DNA-templated
GO:0000160 - phosphorelay signal transduction system
Note(s): Note(s): ...[more].
Evidence: [GEA] Gene expression analysis
[HIFS] Human inference of function from sequence
Reference(s): [1] Genschik P., et al., 1998
External database links:  
DIP:
 DIP-10812N
ECOCYC:
 EG12356-MONOMER
ECOLIWIKI:
 b3422
INTERPRO:
 IPR017183
INTERPRO:
 IPR027417
INTERPRO:
 IPR025943
INTERPRO:
 IPR009715
INTERPRO:
 IPR003593
INTERPRO:
 IPR002078
MODBASE:
 P38035
PANTHER:
 PTHR32071:SF14
PFAM:
 PF06956
PFAM:
 PF00158
PRIDE:
 P38035
PRODB:
 PRO_000023893
PROSITE:
 PS00676
PROSITE:
 PS50045
REFSEQ:
 NP_417880
SMART:
 SM00382
SMR:
 P38035
UNIPROT:
 P38035


Operon      
Name: rtcR         
Operon arrangement:
Transcription unit        Promoter
rtcR


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter rtcAp1 3556880 reverse Similarity to the consensus
Read more > 		[ICWHO] [2]
  promoter rtcAp6 3556948 reverse Similarity to the consensus
Read more > 		[ICWHO] [2]
  promoter rtcAp2 3557002 reverse Similarity to the consensus
Read more > 		[ICWHO] [2]


Evidence    

 [ICWHO] Inferred computationally without human oversight


Reference(s)    

 [1] Genschik P., Drabikowski K., Filipowicz W., 1998, Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase and its sigma54-regulated operon., J Biol Chem 273(39):25516-26

 [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

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