RegulonDB RegulonDB 11.1: Gene Form
   

yfbR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yfbS alaA yfbR terminator TSS_2578 (cluster) TSS_2578 (cluster) TSS_2577 TSS_2577 TSS_2576 TSS_2576 TSS_2575 (cluster) TSS_2575 (cluster) TSS_2574 TSS_2574 TSS_2573 (cluster) TSS_2573 (cluster) TSS_2572 TSS_2572 TSS_2571 TSS_2571 TSS_2570 (cluster) TSS_2570 (cluster) yfbRp4 yfbRp4 yfbRp3 yfbRp3

Gene      
Name: yfbR    Texpresso search in the literature
Synonym(s): ECK2285, G7185, b2291
Genome position(nucleotides): 2408862 --> 2409461
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.33
External database links:  
ASAP:
 ABE-0007563
ECHOBASE:
 EB3855
ECOLIHUB:
 yfbR
OU-MICROARRAY:
 b2291
STRING:
 511145.b2291
COLOMBOS: yfbR


Product      
Name: dCMP phosphohydrolase
Synonym(s): YfbR
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 22.708
Isoelectric point: 5.601
Motif(s):
 
Type Positions Sequence Comment
5 -> 186 HFFAHLSRLKLINRWPLMRNVRTENVSEHSLQVAMVAHALAAIKNRKFGGNVNAERIALLAMYHDASEVLTGDLPTPVKYFNSQIAQEYKAIEKIAQQKLVDMVPEELRDIFAPLIDEHAYSDEEKSLVKQADALCAYLKCLEELAAGNNEFLLAKTRLEATLEARRSQEMDYFMEIFVPSF
18 -> 18 R UniProt: Shows negligible enzymatic activity..
30 -> 30 V UniProt: Shows reduced activity and affinity compared to the wild-type..
33 -> 33 H UniProt: Shows negligible enzymatic activity..
68 -> 68 H UniProt: Shows negligible enzymatic activity..

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.2 - nucleotides --> 1.5.2.2 - pyrimidine biosynthesis
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0002953 - 5'-deoxynucleotidase activity
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0016791 - phosphatase activity
GO:0000166 - nucleotide binding
GO:0042802 - identical protein binding
GO:0050897 - cobalt ion binding
biological_process GO:0016311 - dephosphorylation
GO:0006226 - dUMP biosynthetic process
GO:0010139 - pyrimidine deoxyribonucleotide salvage
Note(s): Note(s): ...[more].
External database links:  
ALPHAFOLD:
 P76491
DIP:
 DIP-28107N
ECOCYC:
 G7185-MONOMER
ECOLIWIKI:
 b2291
INTERPRO:
 IPR022971
INTERPRO:
 IPR039356
INTERPRO:
 IPR003607
PANTHER:
 PTHR11845
PDB:
 2PAR
PDB:
 2PAQ
PDB:
 2PAU
PFAM:
 PF12917
PRIDE:
 P76491
PROSITE:
 PS51831
REFSEQ:
 NP_416794
SMART:
 SM00471
SMR:
 P76491
UNIPROT:
 P76491


Operon      
Name: alaA-yfbR         
Operon arrangement:
Transcription unit        Promoter
alaA
yfbR
alaA-yfbR


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 yfbRp4 2408835 forward nd [COMP-AINF] [1]
  promoter TSS_2570 (cluster) 2409942 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_2571 2409945 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_2572 2409947 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_2573 (cluster) 2409960 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_2574 2410159 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_2575 (cluster) 2410629 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_2576 2410812 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_2577 2410818 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_2578 (cluster) 2411098 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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