RegulonDB RegulonDB 10.8: Gene Form
   

yfiC gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

nadB srmB yfiC rseD rpoE IHF GlrR NadR GlrR RcsB NtrC GlrR CRP CpxR DksA DksA-ppGpp DksA-ppGpp ppGpp terminator TSS_2874 (cluster) TSS_2874 (cluster) srmBp4 srmBp4 yfiCp3 yfiCp3 rpoEp1b rpoEp1b TSS_2873 TSS_2873 nadBp nadBp rpoEp2b rpoEp2b rpoEp4 rpoEp4 rpoEp1a rpoEp1a rpoEp5 rpoEp5 rpoEp2a rpoEp2a

Gene      
Name: yfiC    Texpresso search in the literature
Synonym(s): ECK2573, EG11538, b2575, trmM
Genome position(nucleotides): 2712027 <-- 2712764 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.44
External database links:  
ASAP:
ABE-0008473
ECHOBASE:
EB1500
OU-MICROARRAY:
b2575
PortEco:
yfiC
STRING:
511145.b2575
COLOMBOS: yfiC


Product      
Name: tRNA m6A37 methyltransferase
Synonym(s): TrmM, YfiC
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 27.27
Isoelectric point: 4.685
Motif(s):
 
Type Positions Sequence
46 -> 130 KRCLDIGAGSGLLALMLAQRTDDSVMIDAVELESEAAAQAQENINQSPWAERINVHTADIQQWITQQTVRFDLIISNPPYYQQGV
83 -> 83 A
211 -> 245 PQAGECFSDRLVIRGPDQNYSEAYTALTQAFYLFM

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.3 - RNA modification
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003676 - nucleic acid binding
GO:0008168 - methyltransferase activity
GO:0016740 - transferase activity
GO:0016430 - tRNA (adenine-N6-)-methyltransferase activity
biological_process GO:0030488 - tRNA methylation
GO:0008033 - tRNA processing
GO:0032259 - methylation
Note(s): Note(s): ...[more].
External database links:  
ECOCYC:
EG11538-MONOMER
ECOLIWIKI:
b2575
INTERPRO:
IPR022882
INTERPRO:
IPR029063
INTERPRO:
IPR007848
INTERPRO:
IPR002052
MODBASE:
P31825
PFAM:
PF05175
PRIDE:
P31825
PROSITE:
PS00092
REFSEQ:
NP_417070
SMR:
P31825
UNIPROT:
P31825


Operon      
Name: yfiC         
Operon arrangement:
Transcription unit        Promoter
yfiC


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_2873 2710392 forward nd [RS-EPT-CBR] [1]
  promoter yfiCp3 2712805 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter srmBp4 2712876 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_2874 (cluster) 2712878 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


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