RegulonDB RegulonDB 10.9: Gene Form
   

ybdN gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybdN ybdL ybdO ybdM FNR CysB FNR ArcA TSS_729 TSS_729 ybdNp ybdNp ybdMp2 ybdMp2

Gene      
Name: ybdN    Texpresso search in the literature
Synonym(s): ECK0596, G6331, b0602
Genome position(nucleotides): 635349 <-- 636569 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
47.58
External database links:  
ASAP:
ABE-0002073
ECHOBASE:
EB3304
ECOLIHUB:
ybdN
OU-MICROARRAY:
b0602
STRING:
511145.b0602
COLOMBOS: ybdN


Product      
Name: putative PAPS reductase/DUF3440 domain-containing protein YbdN
Synonym(s): YbdN
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 47.827
Isoelectric point: 7.878
Motif(s):
 
Type Positions Sequence
237 -> 343 GVPLRHMRICEPFGPEQRQGLWLYHVIEPDRWAAMCARVSGVKSGGIYAGHDNHFYGHRKILKPEHLDWQEYALLLLNSMPEKTAEHYRNKIAIYLHWYQKKGIEVP
352 -> 384 AKDIPSWRRICKVLLNNDYWCRALSFSPTKSKN
30 -> 234 VCVSFSGGKDSGLMLHLTAELARQMGKKICVLFIDWEAQFSCTINYVQSLRELYTDVIEEFYWVALPLTTQNSLSQYQPEWQCWEPDVEWVRQPPQDAITDPDFFCFYQPGMTFEQFVREFAEWFSQKRPAAMMIGIRADESYNRFVAIASLNKQRFADDKPWTTAAPGGHSWYIYPIYDWKVADIWTWYANHQSLCNPLYNLMY

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
molecular_function GO:0003824 - catalytic activity
GO:0000976 - transcription regulatory region sequence-specific DNA binding
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-11352N
ECOCYC:
G6331-MONOMER
ECOLIWIKI:
b0602
INTERPRO:
IPR002500
INTERPRO:
IPR021845
INTERPRO:
IPR014729
MODBASE:
P77216
PFAM:
PF01507
PFAM:
PF11922
PRIDE:
P77216
REFSEQ:
NP_415135
UNIPROT:
P77216


Operon      
Name: ybdN         
Operon arrangement:
Transcription unit        Promoter
ybdN


Transcriptional Regulation      
Display Regulation             
Activated by: CysB, FNR, ArcA


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 ybdMp2 635555 reverse Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter TSS_729 637288 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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