RegulonDB RegulonDB 10.9: Gene Form
   

yhbY gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rlmE greA yhbY TSS_3488 TSS_3488 rlmEp1 rlmEp1 yhbYp yhbYp rlmEp2 rlmEp2 TSS_3487 TSS_3487 TSS_3486 (cluster) TSS_3486 (cluster) ftsHp1 ftsHp1

Gene      
Name: yhbY    Texpresso search in the literature
Synonym(s): ECK3169, EG12794, b3180
Genome position(nucleotides): 3327790 --> 3328083 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.64
External database links:  
ASAP:
ABE-0010452
ECHOBASE:
EB2646
ECOLIHUB:
yhbY
OU-MICROARRAY:
b3180
STRING:
511145.b3180
COLOMBOS: yhbY


Product      
Name: ribosome assembly factor YhbY
Synonym(s): YhbY
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 10.784
Isoelectric point: 10.072
Motif(s):
 
Type Positions Sequence
1 -> 97 MNLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKTLVLYRPTKERKISLPR
3 -> 86 LSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKTLVLYR

 

Classification:
Multifun Terms (GenProtEC)  
  6 - cell structure --> 6.6 - ribosomes
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0005515 - protein binding
GO:0003723 - RNA binding
GO:1990275 - preribosome binding
biological_process GO:0000027 - ribosomal large subunit assembly
GO:0000028 - ribosomal small subunit assembly
GO:0000967 - rRNA 5'-end processing
Note(s): Note(s): ...[more].
Evidence: [IGI] Inferred from genetic interaction
[IHBCE] Inferred by a human based on computational evidence
[IMP] Inferred from mutant phenotype
Reference(s): [1] Chen SS., et al., 2013
[2] Gagarinova A., et al., 2016
[3] Ostheimer GJ., et al., 2002
[4] Sharan M., et al., 2017
External database links:  
DIP:
DIP-47893N
ECOCYC:
EG12794-MONOMER
ECOLIWIKI:
b3180
INTERPRO:
IPR035920
INTERPRO:
IPR017924
INTERPRO:
IPR001890
MODBASE:
P0AGK4
PDB:
1LN4
PFAM:
PF01985
PRIDE:
P0AGK4
PROSITE:
PS51295
REFSEQ:
NP_417647
SMART:
SM01103
SMR:
P0AGK4
SWISSMODEL:
P0AGK4
UNIPROT:
P0AGK4


Operon      
Name: yhbY         
Operon arrangement:
Transcription unit        Promoter
yhbY


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 ftsHp1 3327102 reverse Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter TSS_3486 (cluster) 3327294 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [6]
  promoter TSS_3487 3327347 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_3488 3328043 forward nd [RS-EPT-CBR] [6]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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



Reference(s)    

 [1] Chen SS., Williamson JR., 2013, Characterization of the ribosome biogenesis landscape in E. coli using quantitative mass spectrometry., J Mol Biol 425(4):767-79

 [2] Gagarinova A., Stewart G., Samanfar B., Phanse S., White CA., Aoki H., Deineko V., Beloglazova N., Yakunin AF., Golshani A., Brown ED., Babu M., Emili A., 2016, Systematic Genetic Screens Reveal the Dynamic Global Functional Organization of the Bacterial Translation Machinery., Cell Rep 17(3):904-916

 [3] Ostheimer GJ., Barkan A., Matthews BW., 2002, Crystal structure of E. coli YhbY: a representative of a novel class of RNA binding proteins., Structure (Camb) 10(11):1593-601

 [4] Sharan M., Forstner KU., Eulalio A., Vogel J., 2017, APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins., Nucleic Acids Res 45(11):e96

 [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

 [6] 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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