RegulonDB RegulonDB 11.1: Gene Form
   

ygbE gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

cysC ygbE ftsB ygbEp3 ygbEp3 TSS_3038 TSS_3038 TSS_3037 TSS_3037 ftsBp ftsBp TSS_3036 TSS_3036

Gene      
Name: ygbE    Texpresso search in the literature
Synonym(s): ECK2744, EG12707, b2749
Genome position(nucleotides): 2873014 <-- 2873337
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 48.15
External database links:  
ASAP:
 ABE-0009021
ECHOBASE:
 EB2569
ECOLIHUB:
 ygbE
OU-MICROARRAY:
 b2749
STRING:
 511145.b2749
COLOMBOS: ygbE


Product      
Name: DUF3561 domain-containing inner membrane protein YgbE
Synonym(s): YgbE
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 12.017
Isoelectric point: 4.724
Motif(s):
 
Type Positions Sequence Comment
1 -> 107 MRNSHNITLTNNDSLTEDEETTWSLPGAVVGFISWLFALAMPMLIYGSNTLFFFIYTWPFFLALMPVAVVVGIALHSLMDGKLRYSIVFTLVTVGIMFGALFMWLLG
21 -> 43 TTWSLPGAVVGFISWLFALAMPM UniProt: Helical.
53 -> 75 FFIYTWPFFLALMPVAVVVGIAL UniProt: Helical.
67 -> 81 VAVVVGIALHSLMDG UniProt: In Ref. 1..
87 -> 106 IVFTLVTVGIMFGALFMWLL UniProt: Helical.

 
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:  
ALPHAFOLD:
 P46141
ECOCYC:
 EG12707-MONOMER
ECOLIWIKI:
 b2749
INTERPRO:
 IPR022721
PFAM:
 PF12084
PRIDE:
 P46141
REFSEQ:
 NP_417229
UNIPROT:
 P46141


Operon      
Name: ygbE         
Operon arrangement:
Transcription unit        Promoter
ygbE


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_3036 2872900 reverse nd [RS-EPT-CBR] [1]
  promoter ftsBp 2872901 reverse nd [COMP-AINF], [COMP-AINF-POSITIONAL-IDENTIFICATION] [2], [3]
  promoter TSS_3037 2872957 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3038 2872975 reverse nd [RS-EPT-CBR] [1]
  promoter ygbEp3 2873392 reverse nd [COMP-AINF] [3]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position


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] Gama-Castro S., Jimenez-Jacinto V., Peralta-Gil M., Santos-Zavaleta A., Penaloza-Spinola MI., Contreras-Moreira B., Segura-Salazar J., Muniz-Rascado L., Martinez-Flores I., Salgado H., Bonavides-Martinez C., Abreu-Goodger C., Rodriguez-Penagos C., Miranda-Rios J., Morett E., Merino E., Huerta AM., Trevino-Quintanilla L., Collado-Vides J., 2008, RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation., Nucleic Acids Res 36(Database issue):D120-4

 [3] 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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