RegulonDB RegulonDB 11.1: Gene Form
   

yqjD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yqjE yqjC yqjD yqjK TSS_3404 TSS_3404 TSS_3403 (cluster) TSS_3403 (cluster) TSS_3402 (cluster) TSS_3402 (cluster) TSS_3401 TSS_3401

Gene      
Name: yqjD    Texpresso search in the literature
Synonym(s): ECK3089, G7612, b3098
Genome position(nucleotides): 3249375 --> 3249680
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.9
External database links:  
ASAP:
 ABE-0010192
ECHOBASE:
 EB2599
ECOLIHUB:
 yqjD
OU-MICROARRAY:
 b3098
STRING:
 511145.b3098
COLOMBOS: yqjD


Product      
Name: ribosome- and membrane-associated DUF883 domain-containing protein YqjD
Synonym(s): YqjD, inner membrane protein associated with the ribosome
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 11.051
Isoelectric point: 9.663
Motif(s):
 
Type Positions Sequence Comment
1 -> 12 MSKEHTTEHLRA UniProt: Required for binding to 30S subunits in vitro; Sequence Annotation Type: region of interest.
8 -> 60 EHLRAELKSLSDTLEEVLSSSGEKSKEELSKIRSKAEQALKQSRYRLGETGDA
72 -> 101 ADEYVRENPWTGVGIGAAIGVVLGVLLSRR
81 -> 98 WTGVGIGAAIGVVLGVLL 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
GO:0060187 - cell pole
molecular_function GO:0005515 - protein binding
GO:0043022 - ribosome binding
GO:0043024 - ribosomal small subunit binding
Note(s): Note(s): ...[more].
Evidence: [EXP-IMP] Inferred from mutant phenotype
Reference(s): [1] Lutfullahoglu-Bal G., et al., 2017
[2] Szoke T., et al., 2021
[3] Yoshida H., et al., 2012
External database links:  
ALPHAFOLD:
 P64581
DIP:
 DIP-47920N
ECOCYC:
 G7612-MONOMER
ECOLIWIKI:
 b3098
INTERPRO:
 IPR010279
INTERPRO:
 IPR043604
INTERPRO:
 IPR043605
PANTHER:
 PTHR35893
PFAM:
 PF05957
PFAM:
 PF19029
PRIDE:
 P64581
REFSEQ:
 NP_417569
UNIPROT:
 P64581


Operon      
Name: yqjCDEK         
Operon arrangement:
Transcription unit        Promoter
yqjCDEK


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_3401 3248969 forward nd [RS-EPT-CBR] [4]
  promoter TSS_3402 (cluster) 3249228 forward nd [RS-EPT-CBR] [4]
  promoter TSS_3403 (cluster) 3249266 forward nd [RS-EPT-CBR] [4]
  promoter TSS_3404 3249284 forward nd [RS-EPT-CBR] [4]


Evidence    

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


Reference(s)    

 [1] Lutfullahoglu-Bal G., Keskin A., Seferoglu AB., Dunn CD., 2017, Bacterial tail anchors can target to the mitochondrial outer membrane., Biol Direct 12(1):16

 [2] Szoke T., Nussbaum-Shochat A., Amster-Choder O., 2021, Evolutionarily conserved mechanism for membrane recognition from bacteria to mitochondria., FEBS Lett 595(22):2805-2815

 [3] Yoshida H., Maki Y., Furuike S., Sakai A., Ueta M., Wada A., 2012, YqjD Is an Inner Membrane Protein Associated with Stationary-Phase Ribosomes in Escherichia coli., J Bacteriol 194(16):4178-83

 [4] 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.

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