RegulonDB RegulonDB 10.10: Gene Form
   

ymfK gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ymfK ymfJ nc10 ymfT ymfI terminator terminator cohEp10 cohEp10 cohEp9 cohEp9 croEp5 croEp5 cohEp8 cohEp8 TSS_1497 TSS_1497 TSS_1496 TSS_1496 croEp4 croEp4 ymfJp9 ymfJp9 ymfJp6 ymfJp6 ymfJp8 ymfJp8 ymfJp10 ymfJp10

Gene      
Name: ymfK    Texpresso search in the literature
Synonym(s): ECK1131, G6589, b1145, cohE
Genome position(nucleotides): 1202259 <-- 1202933 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 44.44
External database links:  
ASAP:
 ABE-0003851
ECHOBASE:
 EB3997
ECOLIHUB:
 ymfK
OU-MICROARRAY:
 b1145
STRING:
 511145.b1145
COLOMBOS: ymfK


Product      
Name: e14 prophage; putative repressor protein YmfK
Synonym(s): CohE, YmfK
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 25.095
Isoelectric point: 6.664
Motif(s):
 
Type Positions Sequence
93 -> 212 PVISWVQAGAWKEVGYSEVDLSTAETYPCPVPCGEMTYILRVIGDSMIDEYRPGDMIFVDPEVPACHGDDVIALMHDTGETTFKRLIEDGTQRYLKALNPNWPEPYIKINGNCSIIGTVI

 
Classification:
Multifun Terms (GenProtEC)  
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
Note(s): Note(s): ...[more].
Reference(s): [1] Maguin E., et al., 1986
External database links:  
DIP:
 DIP-12721N
ECOCYC:
 G6589-MONOMER
ECOLIWIKI:
 b1145
INTERPRO:
 IPR015927
INTERPRO:
 IPR039418
INTERPRO:
 IPR036286
MODBASE:
 P75974
PFAM:
 PF00717
PRIDE:
 P75974
REFSEQ:
 NP_415663
SWISSMODEL:
 P75974
UNIPROT:
 P75974


Operon      
Name: ymfK         
Operon arrangement:
Transcription unit        Promoter
ymfK


RNA cis-regulatory element    
Attenuation: Translational


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 ymfJp10 1202184 reverse nd [ICWHO], [RS-EPT-CBR] [2], [3]
  promoter ymfJp8 1202185 reverse nd [ICWHO], [RS-EPT-CBR] [2], [3]
  promoter ymfJp6 1202213 reverse nd [ICWHO] [2]
  promoter ymfJp9 1202259 reverse nd [ICWHO] [2]
  promoter croEp4 1202883 forward nd [ICWHO] [2]
  promoter TSS_1496 1202924 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1497 1202933 reverse nd [RS-EPT-CBR] [3]
  promoter cohEp8 1202955 reverse nd [ICWHO] [2]
  promoter croEp5 1203006 forward nd [ICWHO] [2]
  promoter cohEp9 1203014 reverse nd [ICWHO] [2]
  promoter cohEp10 1203088 reverse nd [ICWHO] [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] Maguin E., Brody H., Hill CW., D'Ari R., 1986, SOS-associated division inhibition gene sfiC is part of excisable element e14 in Escherichia coli., J Bacteriol 168(1):464-6

 [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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