RegulonDB RegulonDB 10.8: Gene Form
   

yefM gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yeeZ yoeB yefM hisL YefM-YoeB YefM YefM-YoeB YefM DksA-ppGpp DksA-ppGpp Cis-reg; leader TSS_2331 (cluster) TSS_2331 (cluster) TSS_2330 (cluster) TSS_2330 (cluster) TSS_2329 TSS_2329 hisLp hisLp TSS_2327 TSS_2327 yefMp yefMp TSS_2325 TSS_2325 yeeZp5 yeeZp5 yeeZp7 yeeZp7 TSS_2324 TSS_2324 TSS_2323 TSS_2323

Gene      
Name: yefM    Texpresso search in the literature
Synonym(s): ECK2012, EG12844, b2017
Genome position(nucleotides): 2089462 <-- 2089713 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.41
External database links:  
ASAP:
ABE-0006705
ECHOBASE:
EB2693
OU-MICROARRAY:
b2017
PortEco:
yefM
STRING:
511145.b2017
COLOMBOS: yefM


Product      
Name: YefM antitoxin of the YoeB-YefM toxin-antitoxin pair and DNA binding transcriptional repressor
Synonym(s): YefM
Sequence: Get amino acid sequence Fasta Format
Regulator Family: YefM, YoeB/Txe_like
Molecular weight: 9.308
Isoelectric point: 4.8
Motif(s):
 
Type Positions Sequence
1 -> 73 MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKS
10 -> 10 R
31 -> 31 R

 

Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.10 - defense/survival
Gene Ontology Terms (GO)  
molecular_function GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0015643 - toxic substance binding
GO:0043565 - sequence-specific DNA binding
GO:0042803 - protein homodimerization activity
biological_process GO:0045892 - negative regulation of transcription, DNA-templated
GO:0044010 - single-species biofilm formation
External database links:  
DISPROT:
DP01488
ECOCYC:
EG12844-MONOMER
ECOLIWIKI:
b2017
INTERPRO:
IPR006442
INTERPRO:
IPR036165
MINT:
P69346
PDB:
2A6Q
PFAM:
PF02604
PRIDE:
P69346
REFSEQ:
NP_416521
SMR:
P69346
UNIPROT:
P69346


Operon      
Name: yefM-yoeB         
Operon arrangement:
Transcription unit        Promoter
yefM-yoeB


Transcriptional Regulation      
Display Regulation             
Repressed by: YefM-YoeB, YefM


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_2323 2089152 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2324 2089158 reverse nd [RS-EPT-CBR] [1]
  promoter yeeZp7 2089176 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter yeeZp5 2089211 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_2325 2089731 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2327 2089902 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2329 2089980 forward nd [RS-EPT-CBR] [1]
  promoter TSS_2330 (cluster) 2089990 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_2331 (cluster) 2089999 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] 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.

 [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


RegulonDB