RegulonDB RegulonDB 10.7: Gene Form
   

ycbX gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rlmL ycbX pyrD zapC Cis-reg; leader terminator anti-terminator terminator TSS_1248 TSS_1248 rlmLp rlmLp ycbWp4 ycbWp4 TSS_1247 (cluster) TSS_1247 (cluster) ycbWp6 ycbWp6

Gene      
Name: ycbX    Texpresso search in the literature
Synonym(s): ECK0938, G6487, b0947
Genome position(nucleotides): 1006491 <-- 1007600 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.45
External database links:  
ASAP:
 ABE-0003206
ECHOBASE:
 EB3480
OU-MICROARRAY:
 b0947
PORTECO:
 ycbX
REGULONDB:
 b0947
STRING:
 511145.b0947
M3D: ycbX
COLOMBOS: ycbX
PortEco: b0947


Product      
Name: 6-N-hydroxylaminopurine resistance protein
Synonym(s): YcbX, protein involved in base analog detoxification
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 40.644
Isoelectric point: 7.717
Motif(s):
 
Type Positions Sequence
115 -> 264 SREVQLRWVGPQMTRRVKRHNTVPLSFADGYPYLLANEASLRDLQQRCPASVKMEQFRPNLVVSGASAWEEDRWKVIRIGDVVFDVVKPCSRCIFTTVSPEKGQKHPAGEPLKTLQSFRTAQDNGDVDFGQNLIARNSGVIRVGDEVEIL
1 -> 116 MATLIRLFIHPVKSMRGIGLTHALADVSGLAFDRIFMITEPDGTFITARQFPQMVRFTPSPVHDGLHLTAPDGSSAYVRFADFATQDAPTEVWGTHFTARIAPDAINKWLSGFFSR
296 -> 362 QGQAFRGNNQQVLLEQLENQGIRIPYSCRAGICGSCRVQLLEGEVTPLKKSAMGDDGTILCCSCVPK
139 -> 262 LSFADGYPYLLANEASLRDLQQRCPASVKMEQFRPNLVVSGASAWEEDRWKVIRIGDVVFDVVKPCSRCIFTTVSPEKGQKHPAGEPLKTLQSFRTAQDNGDVDFGQNLIARNSGVIRVGDEVE
289 -> 369 ANVDIDWQGQAFRGNNQQVLLEQLENQGIRIPYSCRAGICGSCRVQLLEGEVTPLKKSAMGDDGTILCCSCVPKTALKLAR

 
Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.6 - protection --> 5.6.2 - detoxification
Gene Ontology Terms (GO)  
cellular_component GO:0030288 - outer membrane-bounded periplasmic space
molecular_function GO:0003824 - catalytic activity
GO:0005515 - protein binding
GO:0009055 - electron transfer activity
GO:0030170 - pyridoxal phosphate binding
GO:0051536 - iron-sulfur cluster binding
GO:0051537 - 2 iron, 2 sulfur cluster binding
GO:0030151 - molybdenum ion binding
biological_process GO:0009636 - response to toxic substance
GO:0009407 - toxin catabolic process
GO:0022900 - electron transport chain
Note(s): Note(s): ...[more].
Evidence: [IMP] Inferred from mutant phenotype
Reference(s): [1] Kozmin SG., et al., 2008
External database links:  
DIP:
 DIP-28068N
ECOCYC:
 G6487-MONOMER
ECOLIWIKI:
 b0947
INTERPRO:
 IPR006058
INTERPRO:
 IPR011037
INTERPRO:
 IPR036010
INTERPRO:
 IPR005303
INTERPRO:
 IPR005302
INTERPRO:
 IPR001041
INTERPRO:
 IPR012675
MODBASE:
 P75863
PFAM:
 PF00111
PFAM:
 PF03476
PFAM:
 PF03473
PRIDE:
 P75863
PROSITE:
 PS51340
PROSITE:
 PS51085
PROSITE:
 PS00197
PROTEINMODELPORTAL:
 P75863
REFSEQ:
 NP_415467
SMR:
 P75863
UNIPROT:
 P75863


Operon      
Name: ycbX         
Operon arrangement:
Transcription unit        Promoter
ycbX


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 ycbWp6 1005850 forward Similarity to the consensus
Read more > 		[ICWHO] [2]
  promoter TSS_1247 (cluster) 1005852 forward For this promoter, there
Read more > 		[RS-EPT-CBR] [3]
  promoter ycbWp4 1005890 forward Similarity to the consensus
Read more > 		[ICWHO] [2]
  promoter TSS_1248 1008970 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] Kozmin SG., Leroy P., Pavlov YI., Schaaper RM., 2008, YcbX and yiiM, two novel determinants for resistance of Escherichia coli to N-hydroxylated base analogues., Mol Microbiol 68(1):51-65

 [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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