RegulonDB RegulonDB 10.8: Gene Form
   

atl gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybaY atl ffs terminator TSS_610 TSS_610 ffsp7 ffsp7 ffsp5 ffsp5 ffsp6 ffsp6

Gene      
Name: atl    Texpresso search in the literature
Synonym(s): ECK0448, G6251, b0454, ybaZ
Genome position(nucleotides): 475982 <-- 476371 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.1
External database links:  
ASAP:
 ABE-0001576
ECHOBASE:
 EB3043
OU-MICROARRAY:
 b0454
PortEco:
 atl
STRING:
 511145.b0454
COLOMBOS: atl


Product      
Name: DNA base-flipping protein
Synonym(s): Atl, YbaZ
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 14.45
Isoelectric point: 9.487
Motif(s):
 
Type Positions Sequence
33 -> 112 FPQRVWQIVAAIPEGYVTTYGDVAKLAGSPRAARQVGGVLKRLPEGSTLPWHRVVNRHGTISLTGPDLQRQRQALLAEGV
83 -> 83 W

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.4 - DNA repair
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003824 - catalytic activity
GO:0005515 - protein binding
GO:0019899 - enzyme binding
GO:0003684 - damaged DNA binding
biological_process GO:0006281 - DNA repair
GO:0006974 - cellular response to DNA damage stimulus
Note(s): Note(s): ...[more].
Evidence: [APP] Assay of partially-purified protein
[APPH] Assay of protein purified to homogeneity
Reference(s): [1] Chen CS., et al., 2008
[2] Pearson SJ., et al., 2005
External database links:  
DIP:
 DIP-48135N
ECOCYC:
 G6251-MONOMER
ECOLIWIKI:
 b0454
INTERPRO:
 IPR036217
INTERPRO:
 IPR036388
INTERPRO:
 IPR014048
MINT:
 MINT-1239891
MODBASE:
 P0AFP2
PFAM:
 PF01035
PRIDE:
 P0AFP2
REFSEQ:
 NP_414988
SMR:
 P0AFP2
UNIPROT:
 P0AFP2


Operon      
Name: atl         
Operon arrangement:
Transcription unit        Promoter
ybaZ


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 ffsp6 476288 forward Similarity to the consensus
Read more > 		[ICWHO] [3]
  promoter ffsp5 476399 forward Similarity to the consensus
Read more > 		[ICWHO] [3]
  promoter ffsp7 476422 forward Similarity to the consensus
Read more > 		[ICWHO] [3]
  promoter TSS_610 476448 forward nd [RS-EPT-CBR] [4]


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] Chen CS., Korobkova E., Chen H., Zhu J., Jian X., Tao SC., He C., Zhu H., 2008, A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli., Nat Methods 5(1):69-74

 [2] Pearson SJ., Ferguson J., Santibanez-Koref M., Margison GP., 2005, Inhibition of O6-methylguanine-DNA methyltransferase by an alkyltransferase-like protein from Escherichia coli., Nucleic Acids Res 33(12):3837-44

 [3] 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

 [4] 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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