RegulonDB RegulonDB 10.8: Gene Form
   

rbfA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

infB truB rbfA rpsO ppGpp Cis-reg; leader anti-anti-terminator anti-terminator terminator anti-anti-terminator anti-terminator TSS_3465 TSS_3465 TSS_3464 (cluster) TSS_3464 (cluster) TSS_3463 TSS_3463 TSS_3462 TSS_3462 TSS_3461 TSS_3461 TSS_3460 TSS_3460 TSS_3459 TSS_3459 TSS_3458 TSS_3458 TSS_3457 TSS_3457 TSS_3456 TSS_3456 TSS_3455 TSS_3455 TSS_3454 TSS_3454 TSS_3453 TSS_3453 rpsOp rpsOp

Gene      
Name: rbfA    Texpresso search in the literature
Synonym(s): ECK3156, EG11178, b3167, sdr-43, yhbB
Genome position(nucleotides): 3312777 <-- 3313178 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.99
External database links:  
ASAP:
 ABE-0010406
CGSC:
 36919
ECHOBASE:
 EB1165
OU-MICROARRAY:
 b3167
PortEco:
 rbfA
STRING:
 511145.b3167
COLOMBOS: rbfA


Product      
Name: 30S ribosome binding factor
Synonym(s): RbfA, YhbB
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 15.154
Isoelectric point: 5.982
Motif(s):
 
Type Positions Sequence
2 -> 133 AKEFGRPQRVAQEMQKEIALILQREIKDPRLGMMTTVSGVEMSRDLAYAKVYVTFLNDKDEDAVKAGIKALQEASGFIRSLLGKAMRLRIVPELTFFYDNSLVEGMRMSNLVTSVVKHDEERRVNPDDSKED
100 -> 100 D
109 -> 133 MSNLVTSVVKHDEERRVNPDDSKED
84 -> 84 G
7 -> 112 RPQRVAQEMQKEIALILQREIKDPRLGMMTTVSGVEMSRDLAYAKVYVTFLNDKDEDAVKAGIKALQEASGFIRSLLGKAMRLRIVPELTFFYDNSLVEGMRMSNL

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.6 - rRNA, stable RNA
  5 - cell processes --> 5.5 - adaptations --> 5.5.2 - temperature extremes
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0043024 - ribosomal small subunit binding
biological_process GO:0006974 - cellular response to DNA damage stimulus
GO:0042254 - ribosome biogenesis
GO:0009409 - response to cold
GO:0006364 - rRNA processing
GO:0030490 - maturation of SSU-rRNA
Note(s): Note(s): ...[more].
Evidence: [IE] Inferred from experiment
Reference(s): [1] Bylund GO., et al., 1998
[2] Leong V., et al., 2013
External database links:  
ECOCYC:
 EG11178-MONOMER
ECOLIWIKI:
 b3167
INTERPRO:
 IPR020053
INTERPRO:
 IPR023799
INTERPRO:
 IPR015946
INTERPRO:
 IPR000238
MINT:
 MINT-1265558
PANTHER:
 PTHR33515
PDB:
 1KKG
PFAM:
 PF02033
PRIDE:
 P0A7G2
PRODB:
 PRO_000023681
PRODOM:
 PD007327
PROSITE:
 PS01319
REFSEQ:
 NP_417636
SMR:
 P0A7G2
UNIPROT:
 P0A7G2


Operon      
Name: metY-rimP-nusA-infB-rbfA-truB-rpsO-pnp         
Operon arrangement:
Transcription unit        Promoter
pnp
rpsO
rpsO-pnp
infB
nusA-infB
rimP-nusA-infB
metY
metY-yhbC-nusA-infB
metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp
metY
metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp


Transcriptional Regulation      
Display Regulation             
Activated by: Fis
Repressed by: CRP, ArgR


RNA cis-regulatory element    
Attenuation: Transcriptional


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_3453 3312149 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3454 3312155 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3455 3314593 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3456 3315518 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3457 3315522 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3458 3315577 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3459 3315601 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3460 3315649 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3461 3315652 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3462 3315673 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3463 3315804 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3464 (cluster) 3315809 reverse For this promoter, there
Read more > 		[RS-EPT-CBR] [3]
  promoter TSS_3465 3315884 reverse nd [RS-EPT-CBR] [3]


Evidence    

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


Reference(s)    

 [1] Bylund GO., Wipemo LC., Lundberg LA., Wikstrom PM., 1998, RimM and RbfA are essential for efficient processing of 16S rRNA in Escherichia coli., J Bacteriol 180(1):73-82

 [2] Leong V., Kent M., Jomaa A., Ortega J., 2013, Escherichia coli rimM and yjeQ null strains accumulate immature 30S subunits of similar structure and protein complement., RNA 19(6):789-802

 [3] 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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