RegulonDB RegulonDB 10.10: Gene Form
   

yedD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

amyA yedE yedD yedF yedDp5 yedDp5 TSS_2269 TSS_2269 yedEp8 yedEp8 TSS_2268 TSS_2268 TSS_2267 (cluster) TSS_2267 (cluster)

Gene      
Name: yedD    Texpresso search in the literature
Synonym(s): ECK1927, EG11659, b1928
Genome position(nucleotides): 2007677 <-- 2008090 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 57.0
External database links:  
ASAP:
 ABE-0006416
ECHOBASE:
 EB1611
ECOLIHUB:
 yedD
OU-MICROARRAY:
 b1928
STRING:
 511145.b1928
COLOMBOS: yedD


Product      
Name: lipoprotein YedD
Synonym(s): YedD
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 14.983
Isoelectric point: 4.596
Motif(s):
 
Type Positions Sequence
16 -> 137 CAEVENYNNVVKTPAPDWLAGYWQTKGPQRALVSPEAIGSLIVTKEGDTLDCRQWQRVIAVPGKLTLMSDDLTNVTVKRELYEVERDGNTIEYDGMTMERVDRPTAECAAALDKAPLPTPLP
25 -> 129 VVKTPAPDWLAGYWQTKGPQRALVSPEAIGSLIVTKEGDTLDCRQWQRVIAVPGKLTLMSDDLTNVTVKRELYEVERDGNTIEYDGMTMERVDRPTAECAAALDK
1 -> 15 MKKLAIAGALLLLAG

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
Note(s): Note(s): ...[more].
Reference(s): [1] Paradis-Bleau C., et al., 2014
[2] Rao S., et al., 2020
External database links:  
DIP:
 DIP-11838N
ECOCYC:
 EG11659-MONOMER
ECOLIWIKI:
 b1928
INTERPRO:
 IPR025596
INTERPRO:
 IPR038624
PFAM:
 PF13987
PRIDE:
 P31063
PROSITE:
 PS51257
REFSEQ:
 NP_416438
SMR:
 P31063
UNIPROT:
 P31063


Operon      
Name: yedD         
Operon arrangement:
Transcription unit        Promoter
yedD


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_2267 (cluster) 2008115 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_2268 2008117 reverse nd [RS-EPT-CBR] [3]
  promoter yedEp8 2008155 forward nd [ICWHO] [4]
  promoter TSS_2269 2008240 forward nd [RS-EPT-CBR] [3]
  promoter yedDp5 2008261 reverse nd [ICWHO] [4]


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] Paradis-Bleau C., Kritikos G., Orlova K., Typas A., Bernhardt TG., 2014, A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism., PLoS Genet 10(1):e1004056

 [2] Rao S., Bates GT., Matthews CR., Newport TD., Vickery ON., Stansfeld PJ., 2020, Characterizing Membrane Association and Periplasmic Transfer of Bacterial Lipoproteins through Molecular Dynamics Simulations., Structure 28(4):475-487.e3

 [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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