RegulonDB RegulonDB 10.8: Gene Form
   

hdeD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

hdeD hdeA arrS GadX GadW YdeO GadX GadW Lrp GadX GadW H-NS Lrp GadE Lrp GadX GadW Lrp Lrp TorR GadX GadW MarA PhoP TorR Lrp GadE FliZ arrSp arrSp gadEp3 gadEp3 TSS_4124 (cluster) TSS_4124 (cluster) TSS_4123 (cluster) TSS_4123 (cluster) hdeDp hdeDp hdeAp hdeAp TSS_4120 TSS_4120 TSS_4119 TSS_4119 TSS_4118 TSS_4118

Gene      
Name: hdeD    Texpresso search in the literature
Synonym(s): ECK3495, EG11495, b3511, yhiA
Genome position(nucleotides): 3656995 --> 3657567 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
46.6
External database links:  
ASAP:
ABE-0011467
CGSC:
33737
ECHOBASE:
EB1458
OU-MICROARRAY:
b3511
PortEco:
hdeD
STRING:
511145.b3511
COLOMBOS: hdeD


Product      
Name: acid-resistance membrane protein
Synonym(s): HdeD, YhiA
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 20.903
Isoelectric point: 9.882
Motif(s):
 
Type Positions Sequence
77 -> 99 WPVLSGFLVAVAYLLIGYFFIRA
84 -> 153 LVAVAYLLIGYFFIRAPELGIFAIAAFIAGLFCVAGVIRLMSWYRQRSMKGSWLQLVIGVLDIVIAWIFL
139 -> 161 LVIGVLDIVIAWIFLGATPMVSV
27 -> 97 IAVLLFIVGLLCISFPFVSGDILSTVVGALLICSGIALIVGLFSNRSHNFWPVLSGFLVAVAYLLIGYFFI
26 -> 44 FIAVLLFIVGLLCISFPFV

 

Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.5 - adaptations --> 5.5.4 - pH
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0016021 - integral component of membrane
biological_process GO:0009268 - response to pH
Note(s): Note(s): ...[more].
Evidence: [IGI] Inferred from genetic interaction
Reference(s): [1] Masuda N., et al., 2003
External database links:  
DIP:
DIP-48170N
ECOCYC:
EG11495-MONOMER
ECOLIWIKI:
b3511
INTERPRO:
IPR005325
MINT:
MINT-1261306
PFAM:
PF03729
PRIDE:
P0AET5
PRODB:
PRO_000022870
REFSEQ:
NP_417968
UNIPROT:
P0AET5


Operon      
Name: hdeD         
Operon arrangement:
Transcription unit        Promoter
hdeD


Transcriptional Regulation      
Display Regulation             
Activated by: PhoP, GadX, RcsB, GadE
Repressed by: H-NS


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_4118 3656618 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_4119 3656719 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_4120 3656761 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_4123 (cluster) 3656977 forward For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter TSS_4124 (cluster) 3657010 forward For this promoter, there
Read more >
[RS-EPT-CBR] [2]


Evidence    

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



Reference(s)    

 [1] Masuda N., Church GM., 2003, Regulatory network of acid resistance genes in Escherichia coli., Mol Microbiol 48(3):699-712

 [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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