RegulonDB RegulonDB 11.1: Gene Form
   

ycdU gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ycdU ymdE insEF4 insE4 serX insF4 Cis-reg Cis-reg TSS_1320 TSS_1320 ycdUp11 ycdUp11 ycdUp1 ycdUp1 ycdUp9 ycdUp9 insFp4 insFp4 insFp5 insFp5

Gene      
Name: ycdU    Texpresso search in the literature
Synonym(s): ECK1017, G6536, b1029
Genome position(nucleotides): 1095843 --> 1096829
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
40.53
External database links:  
ASAP:
ABE-0003489
ECHOBASE:
EB3627
ECOLIHUB:
ycdU
OU-MICROARRAY:
b1029
STRING:
511145.b1029
COLOMBOS: ycdU


Product      
Name: uncharacterized protein YcdU
Synonym(s): YcdU
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 38.668
Isoelectric point: 9.677
Motif(s):
 
Type Positions Sequence Comment
17 -> 37 LIYIYAIGLILIGFYWKNAGF UniProt: Helical.
44 -> 64 IGVVSGILALVLYNFIFDLKA UniProt: Helical.
96 -> 116 LVAGFLSLIMLSAMSWGLYQL UniProt: Helical.
118 -> 138 PSLYALFLISLLGPLVIFLLF UniProt: Helical.
165 -> 185 YVLLSVCISTVVNLLTISPLR 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:
P75910
ECOCYC:
G6536-MONOMER
ECOLIWIKI:
b1029
PRIDE:
P75910
REFSEQ:
NP_415548
SMR:
P75910
UNIPROT:
P75910


Operon      
Name: ymdE-ycdU         
Operon arrangement:
Transcription unit        Promoter
ymdE-ycdU


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 insFp5 1095155 reverse nd [COMP-AINF] [1]
  promoter insFp4 1095196 reverse nd [COMP-AINF] [1]
  promoter ycdUp9 1095633 forward nd [COMP-AINF] [1]
  promoter ycdUp1 1095693 forward nd [COMP-AINF] [1]
  promoter ycdUp11 1095759 forward nd [COMP-AINF] [1]
  promoter TSS_1320 1097652 reverse nd [RS-EPT-CBR] [2]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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



Reference(s)    

 [1] 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

 [2] 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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