RegulonDB RegulonDB 11.1: Gene Form
   

rcdB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yhjD rcdB yhjB anti-anti-terminator anti-terminator terminator TSS_4132 (cluster) TSS_4132 (cluster) yhjDp5 yhjDp5 yhjCp yhjCp yhjBp4 yhjBp4

Gene      
Name: rcdB    Texpresso search in the literature
Synonym(s): ECK3506, EG12247, b3521, yhjC
Genome position(nucleotides): 3672414 --> 3673313
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.33
External database links:  
ASAP:
 ABE-0011503
ECHOBASE:
 EB2158
ECOLIHUB:
 yhjC
OU-MICROARRAY:
 b3521
STRING:
 511145.b3521
COLOMBOS: rcdB


Product      
Name: putative DNA-binding transcriptional regulator YhjC
Synonym(s): RcdB, YhjC
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 33.33
Isoelectric point: 8.639
Motif(s):
 
Type Positions Sequence Comment
1 -> 59 MDKIHAMQLFIKVAELESFSRAADFFALPKGSVSRQIQALEHQLGTQLLQRTTRRVKLT UniProt: HTH lysR-type.
5 -> 62 HAMQLFIKVAELESFSRAADFFALPKGSVSRQIQALEHQLGTQLLQRTTRRVKLTPEG
19 -> 38 FSRAADFFALPKGSVSRQIQ UniProt: H-T-H motif.
89 -> 292 SISGKLRIDIPPGIAKSLLLPRLSEFLYLHPGIELELSSHDRPVDILHDGFDCVIRTGALPEDGVIARPLGKLTMVNCASPHYLTRFGYPQSPDDLTSHAIVRYTPHLGVHPLGFEVASVNGVQWFKSGGMLTVNSSENYLTAGLAGLGIIQIPRIAVREALRAGRLIEVLPGYRAEPLSLSLVYPQRRELSRRVNLFMQWLAG

 
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
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
GO:0043565 - sequence-specific DNA binding
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [COMP-HINF-FN-FROM-SEQ] Human inference of function from sequence
Reference(s): [1] Perez-Rueda E., et al., 2000
[2] Perez-Rueda E., et al., 2004
External database links:  
ALPHAFOLD:
 P37641
DIP:
 DIP-12378N
ECOCYC:
 EG12247-MONOMER
ECOLIWIKI:
 b3521
INTERPRO:
 IPR036388
INTERPRO:
 IPR036390
INTERPRO:
 IPR005119
INTERPRO:
 IPR000847
MODBASE:
 P37641
PFAM:
 PF00126
PFAM:
 PF03466
PRIDE:
 P37641
PROSITE:
 PS50931
REFSEQ:
 NP_417978
SMR:
 P37641
UNIPROT:
 P37641


Operon      
Name: rcdB         
Operon arrangement:
Transcription unit        Promoter
yhjC


Transcriptional Regulation      
Display Regulation             
Activated by: PhoB


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 yhjBp4 3672045 reverse nd [COMP-AINF] [3]
  promoter yhjDp5 3673330 forward nd [COMP-AINF] [3]
  promoter TSS_4132 (cluster) 3673331 forward nd [RS-EPT-CBR] [4]


Evidence    

 [COMP-AINF] 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., 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12., Nucleic Acids Res 28(8):1838-47

 [2] 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

 [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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