RegulonDB RegulonDB 11.0: Gene Form
   

ybiY gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybiW ybiY fsaA TSS_981 TSS_981 fsaAp6 fsaAp6 ybiWp4 ybiWp4

Gene      
Name: ybiY    Texpresso search in the literature
Synonym(s): ECK0814, G6427, b0824, pflE
Genome position(nucleotides): 862612 <-- 863511
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.11
External database links:  
ASAP:
 ABE-0002812
ECHOBASE:
 EB3243
ECOLIHUB:
 ybiY
OU-MICROARRAY:
 b0824
STRING:
 511145.b0824
COLOMBOS: ybiY


Product      
Name: putative pyruvate formate-lyase activating enzyme YbiY
Synonym(s): PflE, YbiY
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 33.038
Isoelectric point: 6.275
Motif(s):
 
Type Positions Sequence Comment
11 -> 290 HDGPGIRTVVFLKGCSLGCRWCQNPESRARTQDLLYDARLCLEGCELCAKAAPEVIERALNGLLIHREKLTPEHLTALTDCCPTQALTVCGEVKSVEEIMTTVLRDKPFYDRSGGGLTLSGGEPFMQPEMAMALLQASHEAGIHTAVETCLHVPWKYIAPSLPYIDLFLADLKHVADAPFKQWTDGNAARVLDNLKKLAAAGKKIIIRVPLIQGFNADETSVKAITDFAADELHVGEIHFLPYHTLGINKYHLLNLPYDAPEKPLDAPELLDFAQQYACQ UniProt: Radical SAM core.
12 -> 153 DGPGIRTVVFLKGCSLGCRWCQNPESRARTQDLLYDARLCLEGCELCAKAAPEVIERALNGLLIHREKLTPEHLTALTDCCPTQALTVCGEVKSVEEIMTTVLRDKPFYDRSGGGLTLSGGEPFMQPEMAMALLQASHEAGI
19 -> 229 VVFLKGCSLGCRWCQNPESRARTQDLLYDARLCLEGCELCAKAAPEVIERALNGLLIHREKLTPEHLTALTDCCPTQALTVCGEVKSVEEIMTTVLRDKPFYDRSGGGLTLSGGEPFMQPEMAMALLQASHEAGIHTAVETCLHVPWKYIAPSLPYIDLFLADLKHVADAPFKQWTDGNAARVLDNLKKLAAAGKKIIIRVPLIQGFNADE
31 -> 33 WCQ UniProt: S-adenosyl-L-methionine binding; Sequence Annotation Type: region of interest.
181 -> 183 DLK UniProt: S-adenosyl-L-methionine binding; Sequence Annotation Type: region of interest.

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.7 - anaerobic respiration
  2 - information transfer --> 2.3 - protein related --> 2.3.3 - posttranslational modification
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.3 - inhibition / activation of enzymes
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003824 - catalytic activity
GO:0046872 - metal ion binding
GO:0016491 - oxidoreductase activity
GO:0051536 - iron-sulfur cluster binding
GO:0051539 - 4 iron, 4 sulfur cluster binding
GO:0043365 - [formate-C-acetyltransferase]-activating enzyme activity
Note(s): Note(s): ...[more].
External database links:  
ALPHAFOLD:
 P75794
DIP:
 DIP-11444N
ECOCYC:
 G6427-MONOMER
ECOLIWIKI:
 b0824
INTERPRO:
 IPR001989
INTERPRO:
 IPR007197
INTERPRO:
 IPR013785
INTERPRO:
 IPR034465
INTERPRO:
 IPR034457
INTERPRO:
 IPR012839
MODBASE:
 P75794
PANTHER:
 PTHR30352
PFAM:
 PF04055
PFAM:
 PF13353
PRIDE:
 P75794
PROSITE:
 PS51918
PROSITE:
 PS01087
REFSEQ:
 NP_415345
SMR:
 P75794
UNIPROT:
 P75794


Operon      
Name: ybiYW         
Operon arrangement:
Transcription unit        Promoter
ybiYW


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 ybiWp4 862783 reverse nd [ICWHO] [1]
  promoter fsaAp6 863530 forward nd [ICWHO] [1]
  promoter TSS_981 863614 forward nd [RS-EPT-CBR] [2]


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] 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

 [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.

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