RegulonDB RegulonDB 11.1: Gene Form
   

queD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

cysJ ygcN queD ygcO IHF CysB terminator terminator ygcNp3 ygcNp3 TSS_3054 TSS_3054 cysJp cysJp TSS_3053 TSS_3053 TSS_3052 TSS_3052 TSS_3051 (cluster) TSS_3051 (cluster) TSS_3050 TSS_3050

Gene      
Name: queD    Texpresso search in the literature
Synonym(s): ECK2760, G7431, b2765, sscR, ygcM
Genome position(nucleotides): 2892214 --> 2892579
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.45
External database links:  
ASAP:
 ABE-0009068
ECHOBASE:
 EB2921
ECOLIHUB:
 queD
MIM:
 261640
OU-MICROARRAY:
 b2765
STRING:
 511145.b2765
COLOMBOS: queD


Product      
Name: 6-carboxy-5,6,7,8-tetrahydropterin synthase
Synonym(s): QueD, SscR, YgcM
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 13.773
Isoelectric point: 6.504
Motif(s):
 
Type Positions Sequence Comment
6 -> 121 LFKDFTFEAAHRLPHVPEGHKCGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRGE

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.3 - RNA modification
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0016829 - lyase activity
GO:0046872 - metal ion binding
GO:0008270 - zinc ion binding
GO:0042802 - identical protein binding
GO:0070497 - 6-carboxy-5,6,7,8-tetrahydropterin synthase activity
biological_process GO:0008616 - queuosine biosynthetic process
External database links:  
ALPHAFOLD:
 P65870
ECOCYC:
 G7431-MONOMER
ECOLIWIKI:
 b2765
INTERPRO:
 IPR038418
INTERPRO:
 IPR007115
MODBASE:
 P65870
PANTHER:
 PTHR12589
PDB:
 4NTN
PDB:
 4NTK
PDB:
 3QNA
PDB:
 3QN9
PDB:
 4NTM
PDB:
 3QN0
PFAM:
 PF01242
PRIDE:
 P65870
REFSEQ:
 NP_417245
SMR:
 P65870
UNIPROT:
 P65870


Operon      
Name: queD         
Operon arrangement:
Transcription unit        Promoter
queD


RNA cis-regulatory element    
Attenuation: Translational


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_3050 2890373 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3051 (cluster) 2891032 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3052 2891818 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3053 2891963 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3054 2892190 forward nd [RS-EPT-CBR] [1]
  promoter ygcNp3 2892572 forward nd [COMP-AINF] [2]


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] 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] 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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