RegulonDB RegulonDB 11.1: Gene Form
   

ygjV gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

uxaA sstT ygjV ygjVp4 ygjVp4 TSS_3388 TSS_3388 TSS_3387 TSS_3387 TSS_3386 TSS_3386 TSS_3385 TSS_3385 TSS_3384 TSS_3384 TSS_3383 TSS_3383

Gene      
Name: ygjV    Texpresso search in the literature
Synonym(s): ECK3081, G7608, b3090
Genome position(nucleotides): 3241193 <-- 3241744
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.64
External database links:  
ASAP:
 ABE-0010161
ECHOBASE:
 EB2591
ECOLIHUB:
 ygjV
OU-MICROARRAY:
 b3090
STRING:
 511145.b3090
COLOMBOS: ygjV


Product      
Name: inner membrane protein
Synonym(s): YgjV
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 20.512
Isoelectric point: 10.394
Motif(s):
 
Type Positions Sequence Comment
3 -> 23 AYWLAQGVGVIAFLIGITTFF UniProt: Helical.
5 -> 163 WLAQGVGVIAFLIGITTFFNRDERRFKKQLSVYSAVIGVHFFLLGTYPAGASAILNAIRTLITLRTRSLWVMAIFIVLTGGIGLAKFHHPVELLPVIGTIVSTWALFCCKGLTMRCVMWFSTCCWVIHNFWAGSIGGTMIEGSFLLMNGLNIIRFWRMQ
39 -> 59 AVIGVHFFLLGTYPAGASAIL UniProt: Helical.
72 -> 92 SLWVMAIFIVLTGGIGLAKFH UniProt: Helical.
93 -> 113 HPVELLPVIGTIVSTWALFCC UniProt: Helical.

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane
Note(s): Note(s): ...[more].
Evidence: [EXP] Inferred from experiment
Reference(s): [1] Drew D., et al., 2002
[2] Serres MH., et al., 2001
External database links:  
ALPHAFOLD:
 P42603
ECOCYC:
 G7608-MONOMER
ECOLIWIKI:
 b3090
INTERPRO:
 IPR019629
INTERPRO:
 IPR026267
PFAM:
 PF10688
PRIDE:
 P42603
REFSEQ:
 NP_417561
UNIPROT:
 P42603


Operon      
Name: ygjV         
Operon arrangement:
Transcription unit        Promoter
ygjV


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_3383 3239984 forward nd [RS-EPT-CBR] [3]
  promoter TSS_3384 3240007 forward nd [RS-EPT-CBR] [3]
  promoter TSS_3385 3240085 forward nd [RS-EPT-CBR] [3]
  promoter TSS_3386 3240529 forward nd [RS-EPT-CBR] [3]
  promoter TSS_3387 3240567 forward nd [RS-EPT-CBR] [3]
  promoter TSS_3388 3240667 forward nd [RS-EPT-CBR] [3]
  promoter ygjVp4 3241819 reverse nd [COMP-AINF] [4]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Drew D., Sjostrand D., Nilsson J., Urbig T., Chin CN., de Gier JW., von Heijne G., 2002, Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis., Proc Natl Acad Sci U S A 99(5):2690-5

 [2] Serres MH., Gopal S., Nahum LA., Liang P., Gaasterland T., Riley M., 2001, A functional update of the Escherichia coli K-12 genome., Genome Biol 2(9):RESEARCH0035

 [3] 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.

 [4] 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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