RegulonDB RegulonDB 10.8: Gene Form
   

ygdR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

tas ygdQ ygdR MgrR terminator anti-terminator anti-anti-terminator TSS_3135 TSS_3135 tasp4 tasp4 TSS_3134 (cluster) TSS_3134 (cluster) ygdRp5 ygdRp5 TSS_3133 TSS_3133

Gene      
Name: ygdR    Texpresso search in the literature
Synonym(s): ECK2829, G7461, b2833
Genome position(nucleotides): 2971271 --> 2971489 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
43.38
External database links:  
ASAP:
ABE-0009293
ECHOBASE:
EB2886
OU-MICROARRAY:
b2833
PortEco:
ygdR
STRING:
511145.b2833
COLOMBOS: ygdR


Product      
Name: DUF903 domain-containing lipoprotein YgdR
Synonym(s): YgdR
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space,inner membrane
Molecular weight: 7.877
Isoelectric point: 4.393
Motif(s):
 
Type Positions Sequence
20 -> 72 CSSDYVMATKDGRMILTDGKPEIDDDTGLVSYHDQQGNAMQINRDDVSQIIER
23 -> 71 DYVMATKDGRMILTDGKPEIDDDTGLVSYHDQQGNAMQINRDDVSQIIE
1 -> 19 MKKWAVIISAVGLAFAVSG

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0030288 - outer membrane-bounded periplasmic space
GO:0005886 - plasma membrane
Note(s): Note(s): ...[more].
External database links:  
ECOCYC:
G7461-MONOMER
ECOLIWIKI:
b2833
INTERPRO:
IPR010920
INTERPRO:
IPR010305
PANTHER:
PTHR37011
PDB:
2JN0
PDB:
3FIF
PFAM:
PF06004
PRIDE:
P65294
PROSITE:
PS51257
REFSEQ:
NP_417310
SMR:
P65294
UNIPROT:
P65294


Operon      
Name: ygdR         
Operon arrangement:
Transcription unit        Promoter
 


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_3133 2971238 forward nd [RS-EPT-CBR] [1]
  promoter ygdRp5 2971247 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_3134 (cluster) 2971565 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter tasp4 2971569 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_3135 2971604 forward nd [RS-EPT-CBR] [1]


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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