RegulonDB RegulonDB 10.8: Gene Form
   

yjiR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yjiR mdtM rpnD yjiS terminator terminator yjiSp4 yjiSp4 yjiSp3 yjiSp3 TSS_5146 TSS_5146

Gene      
Name: yjiR    Texpresso search in the literature
Synonym(s): ECK4331, G7936, b4340
Genome position(nucleotides): 4570162 <-- 4571574 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
55.06
External database links:  
ASAP:
ABE-0014232
ECHOBASE:
EB2466
OU-MICROARRAY:
b4340
PortEco:
yjiR
STRING:
511145.b4340
COLOMBOS: yjiR


Product      
Name: fused putative DNA-binding transcriptional regulator/putative aminotransferase YjiR
Synonym(s): YjiR
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 53.047
Isoelectric point: 8.287
Motif(s):
 
Type Positions Sequence
1 -> 69 MTRYQHLATLLAERIEQGLYRHGEKLPSVRSLSQEHGVSISTVQQAYQTLETMKLITPQPRSGYFVAQR
4 -> 66 YQHLATLLAERIEQGLYRHGEKLPSVRSLSQEHGVSISTVQQAYQTLETMKLITPQPRSGYFV
132 -> 461 VQHNLQTVLGYDLLAGQRVLREQIARLMLDSGSVVTADDIIITSGCHNSMSLALMAVCKPGDIVAVESPCYYGSMQMLRGMGVKVIEIPTDPETGISVEALELALEQWPIKGIILVPNCNNPLGFIMPDARKRAVLSLAQRHDIVIFEDDVYGELATEYPRPRTIHSWDIDGRVLLCSSFSKSIAPGLRVGWVAPGRYHDKLMHMKYAISSFNVPSTQMAAATFVLEGHYHRHIRRMRQIYQRNLALYTCWIREYFPCEICITRPKGGFLLWIELPEQVDMVCVARQLCRMKIQVAAGSIFSASGKYRNCLRINCALPLSETYREALKQI

 

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
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003824 - catalytic activity
GO:0016740 - transferase activity
GO:0008483 - transaminase activity
GO:0003700 - DNA-binding transcription factor activity
GO:0030170 - pyridoxal phosphate binding
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:0009058 - biosynthetic process
GO:1901605 - alpha-amino acid metabolic process
Note(s): Note(s): ...[more].
Evidence: [HIFS] Human inference of function from sequence
Reference(s): [1] Kingston AW., et al., 2015
[2] Perez-Rueda E., et al., 2000
[3] Perez-Rueda E., et al., 2004
External database links:  
ECOCYC:
G7936-MONOMER
ECOLIWIKI:
b4340
INTERPRO:
IPR004839
INTERPRO:
IPR036388
INTERPRO:
IPR015424
INTERPRO:
IPR015422
INTERPRO:
IPR000524
INTERPRO:
IPR036390
INTERPRO:
IPR015421
MODBASE:
P39389
PFAM:
PF00155
PFAM:
PF00392
PRIDE:
P39389
PROSITE:
PS50949
REFSEQ:
NP_418760
SMART:
SM00345
SMR:
P39389
UNIPROT:
P39389


Operon      
Name: yjiR         
Operon arrangement:
Transcription unit        Promoter
yjiR


RNA cis-regulatory element    
Attenuation: Translational


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_5146 4569651 forward nd [RS-EPT-CBR] [4]
  promoter yjiSp3 4571705 forward Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter yjiSp4 4571720 forward Similarity to the consensus
Read more >
[ICWHO] [5]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Kingston AW., Roussel-Rossin C., Dupont C., Raleigh EA., 2015, Novel recA-Independent Horizontal Gene Transfer in Escherichia coli K-12., PLoS One 10(7):e0130813

 [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.

 [5] 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


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