RegulonDB RegulonDB 10.10: Gene Form
   

rpoD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rpoD dnaG mug TSS_3377 TSS_3377 TSS_3376 TSS_3376 TSS_3375 TSS_3375 TSS_3374 (cluster) TSS_3374 (cluster) TSS_3373 TSS_3373 TSS_3372 TSS_3372 rpoDp4 rpoDp4 rpoDp3 rpoDp3 rpoDp2 rpoDp2 rpoDp1 rpoDp1

Gene      
Name: rpoD    Texpresso search in the literature
Synonym(s): ECK3057, EG10896, alt, b3067
Genome position(nucleotides): 3213047 --> 3214888 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.99
External database links:  
ASAP:
 ABE-0010070
CGSC:
 231
ECHOBASE:
 EB0889
ECOLIHUB:
 rpoD
OU-MICROARRAY:
 b3067
STRING:
 511145.b3067
COLOMBOS: rpoD


Product      
Name: RNA polymerase, sigma 70 (sigma D) factor
Synonym(s): sigma;70, Alt, RpoD, sigma 70 factor, sigma D factor
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 70.263
Isoelectric point: 4.418
Motif(s):
 
Type Positions Sequence
4 -> 79 NPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAENTADEDAAEA
96 -> 126 DPVRMYMREMGTVELLTREGEIDIAKRIEDG
547 -> 600 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRH
2 -> 80 EQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAENTADEDAAEAA
137 -> 348 YPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIE

 
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 --> 3.1.2.1 - sigma factors, anti-sigmafactors
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.3 - stimulon
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0016987 - sigma factor activity
GO:0003700 - DNA-binding transcription factor activity
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0009408 - response to heat
GO:0006352 - DNA-templated transcription, initiation
GO:0010468 - regulation of gene expression
GO:2000142 - regulation of DNA-templated transcription, initiation
GO:0001123 - transcription initiation from bacterial-type RNA polymerase promoter
Note(s): Note(s): ...[more].
Reference(s): [1] Silverstone AE., et al., 1972
[2] Zhi H., et al., 2003
External database links:  
DIP:
 DIP-10773N
ECOCYC:
 RPOD-MONOMER
ECOLIWIKI:
 b3067
INTERPRO:
 IPR000943
INTERPRO:
 IPR007127
INTERPRO:
 IPR007624
INTERPRO:
 IPR007627
INTERPRO:
 IPR007630
INTERPRO:
 IPR007631
INTERPRO:
 IPR042189
INTERPRO:
 IPR012760
INTERPRO:
 IPR013324
INTERPRO:
 IPR013325
INTERPRO:
 IPR014284
INTERPRO:
 IPR028630
INTERPRO:
 IPR036388
INTERPRO:
 IPR009042
MODBASE:
 P00579
PDB:
 4YFK
PDB:
 6WR6
PDB:
 6PB6
PDB:
 6PB5
PDB:
 6PB4
PDB:
 6P18
PDB:
 6K4Y
PDB:
 6JNX
PDB:
 6CUX
PDB:
 6CA0
PDB:
 6C9Y
PDB:
 1SIG
PDB:
 1TLH
PDB:
 2P7V
PDB:
 3IYD
PDB:
 3T72
PDB:
 4JK1
PDB:
 4JK2
PDB:
 4JKR
PDB:
 4KMU
PDB:
 4KN4
PDB:
 4KN7
PDB:
 4LJZ
PDB:
 4LK0
PDB:
 4LK1
PDB:
 4LLG
PDB:
 4MEX
PDB:
 4MEY
PDB:
 4XSX
PDB:
 4XSY
PDB:
 4XSZ
PDB:
 6WRD
PDB:
 4YFN
PDB:
 4YFX
PDB:
 4YG2
PDB:
 4YLN
PDB:
 4YLO
PDB:
 4YLP
PDB:
 4ZH2
PDB:
 4ZH3
PDB:
 4ZH4
PDB:
 5UAC
PDB:
 5UAG
PDB:
 5UAH
PDB:
 5UAJ
PDB:
 5UAL
PDB:
 5UAQ
PDB:
 5VSW
PDB:
 5VT0
PDB:
 5W1S
PDB:
 5W1T
PDB:
 6B6H
PDB:
 6BYU
PFAM:
 PF04542
PFAM:
 PF00140
PFAM:
 PF03979
PFAM:
 PF04539
PFAM:
 PF04545
PFAM:
 PF04546
PRIDE:
 P00579
PRINTS:
 PR00046
PRODB:
 PRO_000023847
PROSITE:
 PS00715
PROSITE:
 PS00716
REFSEQ:
 NP_417539
SMR:
 P00579
SWISSMODEL:
 P00579
UNIPROT:
 P00579


Operon      
Name: rpsU-dnaG-rpoD         
Operon arrangement:
Transcription unit        Promoter
rpsU
rpsU-dnaG-rpoD
rpsU-dnaG-rpoD
rpsU-dnaG-rpoD
rpoD
rpoD
rpoD
rpoD


Transcriptional Regulation      
Display Regulation             
Repressed by: LexA


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 TSS_3372 3212730 forward nd [RS-EPT-CBR] [3]
  promoter TSS_3373 3212852 forward nd [RS-EPT-CBR] [3]
  promoter TSS_3374 (cluster) 3212941 forward nd [RS-EPT-CBR] [3]
  promoter TSS_3375 3213189 forward nd [RS-EPT-CBR] [3]
  promoter TSS_3376 3213454 forward nd [RS-EPT-CBR] [3]
  promoter TSS_3377 3214325 forward nd [RS-EPT-CBR] [3]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Silverstone AE., Goman M., Scaife JG., 1972, ALT: a new factor involved in the synthesis of RNA by Escherichia coli., Mol Gen Genet 118(3):223-34

 [2] Zhi H., Jin DJ., 2003, Purification of highly-active and soluble Escherichia coli sigma 70 polypeptide overproduced at low temperature., Methods Enzymol 370:174-80

 [3] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

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