RegulonDB RegulonDB 10.10: Gene Form
   

yidZ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

tnaB mdtL yidZ yieE TSS_4279 TSS_4279 yieEp yieEp

Gene      
Name: yidZ    Texpresso search in the literature
Synonym(s): ECK3704, EG11721, b3711
Genome position(nucleotides): 3892765 --> 3893724 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.19
External database links:  
ASAP:
ABE-0012141
ECHOBASE:
EB1672
ECOLIHUB:
yidZ
OU-MICROARRAY:
b3711
STRING:
511145.b3711
COLOMBOS: yidZ


Product      
Name: putative LysR-type transcriptional regulator YidZ
Synonym(s): YidZ
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 36.882
Isoelectric point: 7.629
Motif(s):
 
Type Positions Sequence
8 -> 65 LDLNLLLCLQLLMQERSVTKAAKRINVTPSAVSKSLAKLRAWFDDPLFVNSPLGLSPT
101 -> 313 LAAESPLMMIMLNALSKQIYQRYPQATIKLRNWDYDSLDAITRGEVDIGFSGRESHPRSRELLSSLPLAIDYEVLFSDVPCVWLRKDHPALHQTWNLDTFLRYPHISICWEQSDTWALDNVLQELGRERTIAMSLPEFEQSLFMAAQPDNLLLATAPRYCQYYNQLHQLPLVALPLPFDESQQKKLEVPFTLLWHKRNSHNPKIVWLRETIKN
25 -> 44 VTKAAKRINVTPSAVSKSLA
10 -> 66 LNLLLCLQLLMQERSVTKAAKRINVTPSAVSKSLAKLRAWFDDPLFVNSPLGLSPTP

 

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 --> 3.1.2.2 - activator
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [HIFS] Human inference of function from sequence
[IMP] Inferred from mutant phenotype
Reference(s): [1] Justino MC., et al., 2005
[2] Perez-Rueda E., et al., 2000
[3] Perez-Rueda E., et al., 2004
External database links:  
DIP:
DIP-12458N
ECOCYC:
EG11721-MONOMER
ECOLIWIKI:
b3711
INTERPRO:
IPR036390
INTERPRO:
IPR037402
INTERPRO:
IPR036388
INTERPRO:
IPR023746
INTERPRO:
IPR005119
INTERPRO:
IPR000847
MODBASE:
P31463
PFAM:
PF03466
PFAM:
PF00126
PRIDE:
P31463
PROSITE:
PS50931
REFSEQ:
NP_418167
SMR:
P31463
UNIPROT:
P31463


Operon      
Name: yidZ         
Operon arrangement:
Transcription unit        Promoter
yidZ


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 TSS_4279 3893852 forward nd [RS-EPT-CBR] [4]


Evidence    

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



Reference(s)    

 [1] Justino MC., Vicente JB., Teixeira M., Saraiva LM., 2005, New genes implicated in the protection of anaerobically grown Escherichia coli against nitric oxide., J Biol Chem 280(4):2636-43

 [2] Perez-Rueda E., Collado-Vides J., 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12., Nucleic Acids Res 28(8):1838-47

 [3] 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

 [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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