RegulonDB RegulonDB 10.6.3: Gene Form
   

hdeA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

hdeD hdeA hdeB Lrp GadX GadW H-NS Lrp GadE Lrp GadX GadW Lrp Lrp TorR GadX GadW MarA PhoP TorR Lrp GadE FliZ anti-terminator terminator 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 TSS_4117 TSS_4117 TSS_4116 TSS_4116 TSS_4115 TSS_4115 yhiDp1 yhiDp1 yhiDp8 yhiDp8

Gene      
Name: hdeA    Texpresso search in the literature
Synonym(s): ECK3494, EG11398, b3510, yhhC, yhiB
Genome position(nucleotides): 3656408 <-- 3656740 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
42.94
External database links:  
ASAP:
ABE-0011464
CGSC:
33734
ECHOBASE:
EB1370
ECOCYC:
EG11398
ECOLIHUB:
hdeA
OU-MICROARRAY:
b3510
REGULONDB:
b3510
STRING:
511145.b3510
M3D: hdeA
COLOMBOS: hdeA
PortEco: b3510


Shine dalgarno      
Sequence: ctttatagttGAGGATattacGAT


Product      
Name: periplasmic acid stress chaperone HdeA
Synonym(s): HdeA, HdeA monomer, chaperone active form, YhhC, YhiB
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 11.858
Isoelectric point: 4.825
Motif(s):
 
Type Positions Sequence
1 -> 21 MKKVLGVILGGLLLLPVVSNA
12 -> 96 LLLLPVVSNAADAQKAADNKKPVNSWTCEDFLAVDESFQPTAVGFAEALNNKDKPEDAVLDVQGIATVTPAIVQACTQDKQANFK
22 -> 110 ADAQKAADNKKPVNSWTCEDFLAVDESFQPTAVGFAEALNNKDKPEDAVLDVQGIATVTPAIVQACTQDKQANFKDKVKGEWDKIKKDM

 

Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.10 - defense/survival
  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:0042802 - identical protein binding
GO:0042803 - protein homodimerization activity
GO:0051087 - chaperone binding
biological_process GO:0071468 - cellular response to acidic pH
GO:1990451 - cellular stress response to acidic pH
Note(s): Note(s): ...[more].
Reference(s): [1] Arnqvist A., et al., 1994
[2] Holland RD., et al., 1999
[3] Liwo A., et al., 1999
[4] Spory A., et al., 2002
[5] Yoshida T., et al., 1993
External database links:  
DIP:
DIP-47945N
ECOCYC:
EG11398-MONOMER
ECOLIWIKI:
b3510
INTERPRO:
IPR038303
INTERPRO:
IPR036831
INTERPRO:
IPR024972
INTERPRO:
IPR010486
MODBASE:
P0AES9
PDB:
1DJ8
PDB:
1BG8
PFAM:
PF06411
PRIDE:
P0AES9
PRODB:
PRO_000022868
PRODOM:
PD065392
PROTEINMODELPORTAL:
P0AES9
REFSEQ:
NP_417967
SMR:
P0AES9
SWISSMODEL:
P0AES9
UNIPROT:
P0AES9


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


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


Regulation by small RNA    
  Display Regulation
small RNA oxyS


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 Similarity to the consensus
Read more >
[ICWHO] [6]
  promoter yhiDp1 3656110 reverse Similarity to the consensus
Read more >
[ICWHO] [6]
  promoter TSS_4115 3656259 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_4116 3656277 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_4117 3656279 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_4118 3656618 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_4119 3656719 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_4120 3656761 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_4123 (cluster) 3656977 forward For this promoter, there
Read more >
[RS-EPT-CBR] [7]
  promoter TSS_4124 (cluster) 3657010 forward For this promoter, there
Read more >
[RS-EPT-CBR] [7]


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] Arnqvist A., Olsen A., Normark S., 1994, Sigma S-dependent growth-phase induction of the csgBA promoter in Escherichia coli can be achieved in vivo by sigma 70 in the absence of the nucleoid-associated protein H-NS., Mol Microbiol 13(6):1021-32

 [2] Holland RD., Duffy CR., Rafii F., Sutherland JB., Heinze TM., Holder CL., Voorhees KJ., Lay JO., 1999, Identification of bacterial proteins observed in MALDI TOF mass spectra from whole cells., Anal Chem 71(15):3226-30

 [3] Liwo A., Lee J., Ripoll DR., Pillardy J., Scheraga HA., 1999, Protein structure prediction by global optimization of a potential energy function., Proc Natl Acad Sci U S A 96(10):5482-5

 [4] Spory A., Bosserhoff A., von Rhein C., Goebel W., Ludwig A., 2002, Differential regulation of multiple proteins of Escherichia coli and Salmonella enterica serovar Typhimurium by the transcriptional regulator SlyA., J Bacteriol 184(13):3549-59

 [5] Yoshida T., Ueguchi C., Mizuno T., 1993, Physical map location of a set of Escherichia coli genes (hde) whose expression is affected by the nucleoid protein H-NS., J Bacteriol 175(23):7747-8

 [6] 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

 [7] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Mu¿¿iz-Rascado L, Garc¿¿a-Sotelo JS, Weiss V, Solano-Lira H, Mart¿¿nez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hern¿¿ndez S, Alquicira-Hern¿¿ndez K, L¿¿pez-Fuentes A, Porr¿¿n-Sotelo L, Huerta AM, Bonavides-Mart¿¿nez C, Balderas-Mart¿¿nez YI, Pannier L, Olvera M, Labastida A, Jim¿¿nez-Jacinto V, Vega-Alvarado L, Del Moral-Ch¿¿vez V, Hern¿¿ndez-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.


RegulonDB