RegulonDB RegulonDB 10.7: Gene Form
   

hupB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

lon ppiD hupB CpxR CpxR CpxR Fis CRP Fis Fis Fis terminator anti-terminator anti-anti-terminator terminator ybaVp3 ybaVp3 TSS_606 (cluster) TSS_606 (cluster) ppiDp1 ppiDp1 ppiDp2 ppiDp2 TSS_605 TSS_605 TSS_604 (cluster) TSS_604 (cluster) TSS_603 TSS_603 TSS_602 TSS_602 TSS_601 TSS_601 TSS_600 TSS_600 TSS_599 TSS_599 hupBp1 hupBp1 TSS_598 TSS_598 TSS_597 (cluster) TSS_597 (cluster) TSS_596 (cluster) TSS_596 (cluster) TSS_595 (cluster) TSS_595 (cluster) hupBp2 hupBp2 TSS_593 TSS_593 TSS_592 TSS_592 hupBp3 hupBp3 hupBp4 hupBp4 TSS_590 TSS_590

Gene      
Name: hupB    Texpresso search in the literature
Synonym(s): ECK0434, EG10467, b0440, dbhB, dpeA, hopD
Genome position(nucleotides): 461451 --> 461723 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
49.08
External database links:  
ASAP:
ABE-0001527
CGSC:
18235
ECHOBASE:
EB0462
OU-MICROARRAY:
b0440
PORTECO:
hupB
REGULONDB:
b0440
STRING:
511145.b0440
M3D: hupB
COLOMBOS: hupB
PortEco: b0440


Product      
Name: DNA-binding protein HU-β
Synonym(s): DbhB, DpeA, HopD, HupB, transcriptional dual regulator HU-beta;, NS1 (HU-1)
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 9.226
Isoelectric point: 10.496
Motif(s):
 
Type Positions Sequence
12 -> 12 A
26 -> 26 D
30 -> 30 A
37 -> 37 K
47 -> 47 F

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  2 - information transfer --> 2.3 - protein related --> 2.3.7 - nucleoproteins, basic proteins
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.2 - activator
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0042802 - identical protein binding
biological_process GO:0006351 - transcription, DNA-templated
GO:0030261 - chromosome condensation
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-31833N
ECOCYC:
EG10467-MONOMER
ECOLIWIKI:
b0440
INTERPRO:
IPR010992
INTERPRO:
IPR020816
INTERPRO:
IPR000119
MINT:
MINT-1236756
MODBASE:
P0ACF4
PANTHER:
PTHR33175
PDB:
4YFT
PDB:
4YEW
PDB:
4P3V
PDB:
2O97
PFAM:
PF00216
PRIDE:
P0ACF4
PRINTS:
PR01727
PRODB:
PRO_000022942
PROSITE:
PS00045
PROTEINMODELPORTAL:
P0ACF4
REFSEQ:
NP_414974
SMART:
SM00411
SMR:
P0ACF4
SWISSMODEL:
P0ACF4
UNIPROT:
P0ACF4


Operon      
Name: hupB         
Operon arrangement:
Transcription unit        Promoter
hupB
hupB
hupB
hupB


Transcriptional Regulation      
Display Regulation             
Activated by: CRP
Repressed by: Fis


RNA cis-regulatory element    
Attenuation: Transcriptional


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_590 458974 forward nd [RS-EPT-CBR] [1]
  promoter TSS_592 461391 forward nd [RS-EPT-CBR] [1]
  promoter TSS_593 461393 forward nd [RS-EPT-CBR] [1]
  promoter TSS_595 (cluster) 461430 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_596 (cluster) 461433 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_597 (cluster) 461436 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_598 461441 forward nd [RS-EPT-CBR] [1]
  promoter TSS_599 461445 forward nd [RS-EPT-CBR] [1]
  promoter TSS_600 461451 forward nd [RS-EPT-CBR] [1]
  promoter TSS_601 461455 forward nd [RS-EPT-CBR] [1]
  promoter TSS_602 461459 forward nd [RS-EPT-CBR] [1]
  promoter TSS_603 461478 forward nd [RS-EPT-CBR] [1]
  promoter TSS_604 (cluster) 461543 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_605 461552 forward nd [RS-EPT-CBR] [1]
  promoter TSS_606 (cluster) 461851 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter ybaVp3 463752 forward Similarity to the consensus
Read more >
[ICWHO] [2]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] 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.

 [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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