RegulonDB RegulonDB 10.7: Gene Form
   

yhiD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yhiD dctR hdeB anti-terminator terminator TSS_4117 TSS_4117 TSS_4116 TSS_4116 TSS_4115 TSS_4115 yhiDp1 yhiDp1 yhiDp8 yhiDp8

Gene      
Name: yhiD    Texpresso search in the literature
Synonym(s): ECK3492, EG11400, b3508, yhhE
Genome position(nucleotides): 3655255 <-- 3655902 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
45.52
External database links:  
ASAP:
ABE-0011456
ECHOBASE:
EB1372
OU-MICROARRAY:
b3508
PORTECO:
yhiD
REGULONDB:
b3508
STRING:
511145.b3508
M3D: yhiD
COLOMBOS: yhiD
PortEco: b3508


Product      
Name: inner membrane protein YhiD
Synonym(s): YhhE, YhiD
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 23.213
Isoelectric point: 7.161
Motif(s):
 
Type Positions Sequence
36 -> 56 VLIGMGSALFMIVSKYGFADV
9 -> 136 LILAAIACGAIGMERQMRGKGAGLRTHVLIGMGSALFMIVSKYGFADVLSLDHVGLDPSRIAAQVVTGVGFIGAGNILVRNQNIVGLTTAADIWVTAAIGMVIGSGMYELGIYGSVMTLLVLEVFHQL
67 -> 87 SRIAAQVVTGVGFIGAGNILV
1 -> 21 MTAEFIIRLILAAIACGAIGM
118 -> 138 LGIYGSVMTLLVLEVFHQLTF

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0016021 - integral component of membrane
Note(s): Note(s): ...[more].
External database links:  
ECOCYC:
EG11400-MONOMER
ECOLIWIKI:
b3508
INTERPRO:
IPR003416
PANTHER:
PTHR33778
PFAM:
PF02308
PRIDE:
P0AFV2
PRINTS:
PR01837
PROTEINMODELPORTAL:
P0AFV2
REFSEQ:
NP_417965
UNIPROT:
P0AFV2


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


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


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 yhiDp8 3656039 reverse Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter yhiDp1 3656110 reverse Similarity to the consensus
Read more >
[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]


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.


RegulonDB