RegulonDB RegulonDB 10.10: Gene Form
   

rdcB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rdcA proP rdcB yjdM Fis Fis CRP CRP TSS_4918 TSS_4918 TSS_4917 TSS_4917 TSS_4916 TSS_4916 TSS_4915 TSS_4915 TSS_4914 TSS_4914 proPp2 proPp2 TSS_4913 TSS_4913 TSS_4912 TSS_4912 proPp1 proPp1 TSS_4910 TSS_4910 rdcAp1 rdcAp1 rdcAp2 rdcAp2 yjdMp5 yjdMp5 TSS_4909 (cluster) TSS_4909 (cluster)

Gene      
Name: rdcB    Texpresso search in the literature
Synonym(s): ECK4103, G7823, b4110, yjcZ
Genome position(nucleotides): 4329360 --> 4330238 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
56.88
External database links:  
ASAP:
ABE-0013459
ECHOBASE:
EB2354
ECOLIHUB:
yjcZ
OU-MICROARRAY:
b4110
STRING:
511145.b4110
COLOMBOS: rdcB


Product      
Name: regulator of diguanylate cyclase RdcB
Synonym(s): RdcB, YjcZ
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 32.899
Isoelectric point: 8.244
Motif(s):
 
Type Positions Sequence
21 -> 287 LVDLAQGDDARLPQAHQQQFRERLMQELLSRVQLQTWTNGGMLNAPLSLRLTLVEKLASMLDPGHLALTQIAQHLALLQKMDHRQHSAFPELPQQIAALYEWFSARCRWKEKALTQRGLLVQAGDQSEQIFTRWRAGAYNAWSLPGRCFIVLEELRWGAFGDACRLGSPQAVALLLGDLLEKATQHLAESINAAPTTRHYYHQWFASSTVPTGGEHADFLSWLGKWTTADKQPVCWSVTQRWQTVALGMPRLCSAQRLAGAMLEEIF

 

Classification:
Multifun Terms (GenProtEC)  
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.3 - inhibition / activation of enzymes
Gene Ontology Terms (GO)  
molecular_function GO:0005515 - protein binding
biological_process GO:1900231 - regulation of single-species biofilm formation on inanimate substrate
Note(s): Note(s): ...[more].
Evidence: [IMP] Inferred from mutant phenotype
Reference(s): [1] Pfiffer V., et al., 2019
External database links:  
ECOCYC:
G7823-MONOMER
ECOLIWIKI:
b4110
INTERPRO:
IPR025599
PFAM:
PF13990
PRIDE:
P39267
REFSEQ:
NP_418534
SMR:
P39267
UNIPROT:
P39267


Operon      
Name: rdcAB         
Operon arrangement:
Transcription unit        Promoter
rdcAB
rdcAB


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_4909 (cluster) 4326796 reverse nd [RS-EPT-CBR] [2]
  promoter yjdMp5 4326836 reverse nd [ICWHO] [3]
  promoter TSS_4910 4329587 forward nd [RS-EPT-CBR] [2]
  promoter TSS_4912 4330352 forward nd [RS-EPT-CBR] [2]
  promoter TSS_4913 4330392 forward nd [RS-EPT-CBR] [2]
  promoter TSS_4914 4330838 forward nd [RS-EPT-CBR] [2]
  promoter TSS_4915 4330987 forward nd [RS-EPT-CBR] [2]
  promoter TSS_4916 4331343 forward nd [RS-EPT-CBR] [2]
  promoter TSS_4917 4331353 forward nd [RS-EPT-CBR] [2]
  promoter TSS_4918 4331355 forward nd [RS-EPT-CBR] [2]


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] Pfiffer V., Sarenko O., Possling A., Hengge R., 2019, Genetic dissection of Escherichia coli's master diguanylate cyclase DgcE: Role of the N-terminal MASE1 domain and direct signal input from a GTPase partner system., PLoS Genet 15(4):e1008059

 [2] 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.

 [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


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