RegulonDB RegulonDB 10.8: Gene Form
   

ybdM 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: ybdM    Texpresso search in the literature
Synonym(s): ECK0595, G6330, b0601
Genome position(nucleotides): 634747 <-- 635376 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
46.83
External database links:  
ASAP:
ABE-0002071
ECHOBASE:
EB3303
OU-MICROARRAY:
b0601
PortEco:
ybdM
STRING:
511145.b0601
COLOMBOS: ybdM


Product      
Name: ParB-like nuclease domain-containing protein YbdM
Synonym(s): YbdM
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 23.943
Isoelectric point: 8.244
Motif(s):
 
Type Positions Sequence
52 -> 145 WVKNSQLMPNDYNPNNVAPPEKKLLQKSIEIDGFTQPIVVTHTDKNAMEIVDGFHRHEIGKGSSSLKLRLKGYLPVTCLEGTRNQRIAATIRHN

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
molecular_function GO:0005515 - protein binding
GO:0044212 - transcription regulatory region DNA binding
Note(s): Note(s): ...[more].
Reference(s): [1] Paradis-Bleau C., et al., 2014
External database links:  
ECOCYC:
G6330-MONOMER
ECOLIWIKI:
b0601
INTERPRO:
IPR036086
INTERPRO:
IPR003115
PFAM:
PF02195
PRIDE:
P77174
REFSEQ:
NP_415134
SMART:
SM00470
SMR:
P77174
UNIPROT:
P77174


Operon      
Name: ybdM         
Operon arrangement:
Transcription unit        Promoter
 


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] [2]
  promoter TSS_729 637288 forward nd [RS-EPT-CBR] [3]


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] Paradis-Bleau C., Kritikos G., Orlova K., Typas A., Bernhardt TG., 2014, A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism., PLoS Genet 10(1):e1004056

 [2] 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

 [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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