RegulonDB RegulonDB 10.9: Gene Form
   

ybgI gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

dtpD ybgI pxpB pxpC TSS_836 TSS_836 TSS_835 (cluster) TSS_835 (cluster) ybgIp2 ybgIp2 dtpDp8 dtpDp8 TSS_833 TSS_833 dtpDp6 dtpDp6 dtpDp5 dtpDp5 ybgIp1 ybgIp1

Gene      
Name: ybgI    Texpresso search in the literature
Synonym(s): ECK0699, G6379, b0710
Genome position(nucleotides): 742827 --> 743570 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.49
External database links:  
ASAP:
ABE-0002424
ECHOBASE:
EB3089
ECOLIHUB:
ybgI
OU-MICROARRAY:
b0710
STRING:
511145.b0710
COLOMBOS: ybgI


Product      
Name: radiation resistance protein YbgI
Synonym(s): YbgI, conserved metal-binding protein
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 26.892
Isoelectric point: 4.851
Motif(s):
 
Type Positions Sequence
6 -> 234 LEQLINEKLNSAAISDYAPNGLQVEGKETVQKIVTGVTASQALLDEAVRLGADAVIVHHGYFWKGESPVIRGMKRNRLKTLLANDINLYGWHLPLDAHPELGNNAQLAALLGITVMGEIEPLVPWGELTMPVPGLELASWIEARLGRKPLWCGDTGPEVVQRVAWCTGGGQSFIDSAARFGVDAFITGEVSEQTIHSAREQGLHFYAAGHHATERGGIRALSEWLNENT

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0060187 - cell pole
molecular_function GO:0046872 - metal ion binding
GO:0042802 - identical protein binding
biological_process GO:0006281 - DNA repair
GO:0006974 - cellular response to DNA damage stimulus
GO:0010212 - response to ionizing radiation
GO:0034214 - protein hexamerization
Note(s): Note(s): ...[more].
Reference(s): [1] Rooney JP., et al., 2009
External database links:  
DIP:
DIP-36185N
ECOCYC:
G6379-MONOMER
ECOLIWIKI:
b0710
INTERPRO:
IPR036069
INTERPRO:
IPR002678
MODBASE:
P0AFP6
PANTHER:
PTHR13799
PDB:
1NMP
PDB:
1NMO
PFAM:
PF01784
PRIDE:
P0AFP6
REFSEQ:
NP_415238
SMR:
P0AFP6
SWISSMODEL:
P0AFP6
UNIPROT:
P0AFP6


Operon      
Name: ybgI-pxpBCA-nei         
Operon arrangement:
Transcription unit        Promoter
ybgIJKL-nei
ybgIJKL-nei
nei


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 dtpDp5 742622 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter dtpDp6 742623 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_833 742669 reverse nd [RS-EPT-CBR] [3]
  promoter dtpDp8 742670 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_835 (cluster) 743357 forward For this promoter, there
Read more >
[RS-EPT-CBR] [3]
  promoter TSS_836 743410 forward nd [RS-EPT-CBR] [3]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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



Reference(s)    

 [1] Rooney JP., George AD., Patil A., Begley U., Bessette E., Zappala MR., Huang X., Conklin DS., Cunningham RP., Begley TJ., 2009, Systems based mapping demonstrates that recovery from alkylation damage requires DNA repair, RNA processing, and translation associated networks., Genomics 93(1):42-51

 [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

 [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.


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