RegulonDB RegulonDB 10.10: Gene Form
   

hdeB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yhiD hdeA hdeB anti-terminator terminator terminator TSS_4119 TSS_4119 TSS_4118 TSS_4118 TSS_4117 TSS_4117 TSS_4116 TSS_4116 TSS_4115 TSS_4115 yhiDp1 yhiDp1 yhiDp8 yhiDp8

Gene      
Name: hdeB    Texpresso search in the literature
Synonym(s): ECK3493, EG11399, b3509, yhhD, yhiC
Genome position(nucleotides): 3655966 <-- 3656292 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 40.06
External database links:  
ASAP:
 ABE-0011458
CGSC:
 33731
ECHOBASE:
 EB1371
ECOLIHUB:
 hdeB
OU-MICROARRAY:
 b3509
STRING:
 511145.b3509
COLOMBOS: hdeB


Product      
Name: periplasmic acid stress chaperone HdeB
Synonym(s): 10K-L protein, HdeB, YhhD, YhiC
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 12.043
Isoelectric point: 5.817
Motif(s):
 
Type Positions Sequence
30 -> 108 ANESAKDMTCQEFIDLNPKAMTPVAWWMLHEETVYKGGDTVTLNETDLTQIPKVIEYCKKNPQKNLYTFKNQASNDLPN
55 -> 56 WW
95 -> 100 LYTFKN
1 -> 29 MNISSLRKAFIFMGAVAALSLVNAQSALA
50 -> 58 MTPVAWWML

 
Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.5 - adaptations --> 5.5.4 - pH
Gene Ontology Terms (GO)  
cellular_component GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
molecular_function GO:0051082 - unfolded protein binding
biological_process GO:0009268 - response to pH
GO:0010447 - response to acidic pH
GO:1990451 - cellular stress response to acidic pH
External database links:  
DIP:
 DIP-47949N
ECOCYC:
 EG11399-MONOMER
ECOLIWIKI:
 b3509
INTERPRO:
 IPR028623
INTERPRO:
 IPR010486
INTERPRO:
 IPR038303
PDB:
 2XUV
PDB:
 2MYJ
PFAM:
 PF06411
PRIDE:
 P0AET2
PRODB:
 PRO_000022869
REFSEQ:
 NP_417966
SMR:
 P0AET2
UNIPROT:
 P0AET2


Operon      
Name: hdeAB-yhiD         
Operon arrangement:
Transcription unit        Promoter
hdeAB-yhiD
hdeAB-yhiD
yhiD


Transcriptional Regulation      
Display Regulation             
Activated by: PhoP, GadX, GadW, TorR, GadE, RcsB
Repressed by: MarA, FliZ, GadX, H-NS, Lrp, GadW


RNA cis-regulatory element    
Attenuation: Translational


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 yhiDp8 3656039 reverse nd [ICWHO] [1]
  promoter yhiDp1 3656110 reverse nd [ICWHO] [1]
  promoter TSS_4115 3656259 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_4116 3656277 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_4117 3656279 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_4118 3656618 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_4119 3656719 reverse nd [RS-EPT-CBR] [2]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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


Reference(s)    

 [1] 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

 [2] 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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