RegulonDB RegulonDB 10.8: Gene Form
   

xynR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yagH argF xynR argL TSS_470 TSS_470 yagIp1 yagIp1

Gene      
Name: xynR    Texpresso search in the literature
Synonym(s): ECK0273, G6144, b0272, yagI
Genome position(nucleotides): 288404 <-- 289162 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 63.24
External database links:  
ASAP:
 ABE-0000933
ECHOBASE:
 EB3133
OU-MICROARRAY:
 b0272
PortEco:
 yagI
STRING:
 511145.b0272
COLOMBOS: xynR


Product      
Name: CP4-6 prophage; DNA-binding transcriptional repressor XynR
Synonym(s): XynR, YagI
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 27.838
Isoelectric point: 7.746
Motif(s):
 
Type Positions Sequence
81 -> 250 IRQKAKGWLTELSRRTGQTTHLGILDGREGVYIEKIEGKLAAIAYSRIGRRLPVHATAIGKVLIAWLGEAELNALLEGYQYTTFTPATLASREALMSALAQTREQGYALDSEENEQGVRCVAVPVWNHESRVIAALSLSTLTSRVDDAELANFREQLQQAGLALSRALGY
4 -> 66 IQSVERALQILDLFNEQATELKITDISKLMGLSKSTLHSLLKTLQLHGYIDQNPENGKYRLGM
25 -> 45 KITDISKLMGLSKSTLHSLLK
6 -> 57 SVERALQILDLFNEQATELKITDISKLMGLSKSTLHSLLKTLQLHGYIDQNP
123 -> 246 IAYSRIGRRLPVHATAIGKVLIAWLGEAELNALLEGYQYTTFTPATLASREALMSALAQTREQGYALDSEENEQGVRCVAVPVWNHESRVIAALSLSTLTSRVDDAELANFREQLQQAGLALSR

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
GO:0000976 - transcription regulatory region sequence-specific DNA binding
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:0045892 - negative regulation of transcription, DNA-templated
GO:0044010 - single-species biofilm formation
Note(s): Note(s): ...[more].
Evidence: [APPHINH] Assay of protein purified to homogeneity from its native host
[HIFS] Human inference of function from sequence
[ICWHO] Inferred computationally without human oversight
[IEP] Inferred from expression pattern
Reference(s): [1] Perez-Rueda E., et al., 2004
[2] Shimada T., et al., 2017
External database links:  
ECOCYC:
 G6144-MONOMER
ECOLIWIKI:
 b0272
INTERPRO:
 IPR029016
INTERPRO:
 IPR036390
INTERPRO:
 IPR036388
INTERPRO:
 IPR014757
INTERPRO:
 IPR005471
MODBASE:
 P77300
PFAM:
 PF09339
PFAM:
 PF01614
PRIDE:
 P77300
PROSITE:
 PS51078
PROSITE:
 PS51077
REFSEQ:
 NP_414806
SMART:
 SM00346
SMR:
 P77300
UNIPROT:
 P77300


Operon      
Name: xynR         
Operon arrangement:
Transcription unit        Promoter
 


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 yagIp1 289192 reverse Similarity to the consensus
Read more > 		[ICWHO] [3]
  promoter TSS_470 290115 reverse 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] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50

 [2] Shimada T., Momiyama E., Yamanaka Y., Watanabe H., Yamamoto K., Ishihama A., 2017, Regulatory role of XynR (YagI) in catabolism of xylonate in Escherichia coli K-12., FEMS Microbiol Lett 364(22)

 [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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