RegulonDB RegulonDB 10.8: Gene Form
   

trmJ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

suhB trmJ iscR IscR IscR terminator anti-terminator anti-anti-terminator yfhRp2 yfhRp2 yfhRp4 yfhRp4 TSS_2834 TSS_2834 TSS_2833 (cluster) TSS_2833 (cluster) TSS_2832 TSS_2832 TSS_2831 TSS_2831 iscRp iscRp TSS_2830 TSS_2830

Gene      
Name: trmJ    Texpresso search in the literature
Synonym(s): ECK2529, G7327, b2532, yfhQ
Genome position(nucleotides): 2662583 <-- 2663323 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
55.47
External database links:  
ASAP:
ABE-0008332
ECHOBASE:
EB3225
OU-MICROARRAY:
b2532
PortEco:
trmJ
STRING:
511145.b2532
COLOMBOS: trmJ


Product      
Name: tRNA Cm32/Um32 methyltransferase
Synonym(s): TrMet(Xm32), TrmJ, YfhQ
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 27.048
Isoelectric point: 5.893
Motif(s):
 
Type Positions Sequence
23 -> 23 R
175 -> 175 T
214 -> 214 R
225 -> 225 E
5 -> 154 IRIVLVETSHTGNMGSVARAMKTMGLTNLWLVNPLVKPDSQAIALAAGASDVIGNAHIVDTLDEALAGCSLVVGTSARSRTLPWPMLDPRECGLKSVAEAANTPVALVFGRERVGLTNEELQKCHYHVAIAANPEYSSLNLAMAVQVIAY

 

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:0008168 - methyltransferase activity
GO:0016740 - transferase activity
GO:0008173 - RNA methyltransferase activity
GO:0003723 - RNA binding
GO:0042803 - protein homodimerization activity
GO:0052665 - tRNA (uracil-2'-O-)-methyltransferase activity
GO:0052666 - tRNA (cytosine-2'-O-)-methyltransferase activity
biological_process GO:0006396 - RNA processing
GO:0008033 - tRNA processing
GO:0032259 - methylation
GO:0002128 - tRNA nucleoside ribose methylation
Note(s): Note(s): ...[more].
Reference(s): [1] Liu RJ., et al., 2015
External database links:  
ECOCYC:
G7327-MONOMER
ECOLIWIKI:
b2532
INTERPRO:
IPR029028
INTERPRO:
IPR029026
INTERPRO:
IPR004384
INTERPRO:
IPR001537
MODBASE:
P0AE01
PANTHER:
PTHR42786
PDB:
4CNE
PDB:
4CND
PDB:
4XBO
PFAM:
PF00588
PRIDE:
P0AE01
PRODB:
PRO_000024116
REFSEQ:
NP_417027
SMR:
P0AE01
UNIPROT:
P0AE01


Operon      
Name: trmJ         
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 TSS_2830 2661996 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_2831 2662268 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_2832 2663305 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_2833 (cluster) 2663405 forward For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter TSS_2834 2663415 forward nd [RS-EPT-CBR] [2]
  promoter yfhRp4 2664204 forward Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter yfhRp2 2664244 forward Similarity to the consensus
Read more >
[ICWHO] [3]


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] Liu RJ., Long T., Zhou M., Zhou XL., Wang ED., 2015, tRNA recognition by a bacterial tRNA Xm32 modification enzyme from the SPOUT methyltransferase superfamily., Nucleic Acids Res 43(15):7489-503

 [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.

 [3] 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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