RegulonDB RegulonDB 10.8: Gene Form
   

rlmI gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rlmI hspQ yccX tusE terminator yccXp4 yccXp4 rlmIp4 rlmIp4 yccXp7 yccXp7 yccXp5 yccXp5 TSS_1294 (cluster) TSS_1294 (cluster) TSS_1293 TSS_1293

Gene      
Name: rlmI    Texpresso search in the literature
Synonym(s): ECK0958, G6501, b0967, yccW
Genome position(nucleotides): 1028779 <-- 1029969 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.81
External database links:  
ASAP:
 ABE-0003272
ECHOBASE:
 EB3489
OU-MICROARRAY:
 b0967
PortEco:
 rlmI
STRING:
 511145.b0967
COLOMBOS: rlmI


Product      
Name: 23S rRNA m5C1962 methyltransferase
Synonym(s): RlmI, YccW
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 44.357
Isoelectric point: 7.819
Motif(s):
 
Type Positions Sequence
6 -> 68 VLAKGREKSLLRRHPWVFSGAVARMEGKASLGETIDIVDHQGKWLARGAYSPASQIRARVWTF
174 -> 371 VTGELPPALLPIEEHGMKLLVDIQHGHKTGYYLDQRDSRLATRRYVENKRVLNCFSYTGGFAVSALMGGCSQVVSVDTSQEALDIARQNVELNKLDLSKAEFVRDDVFKLLRTYRDRGEKFDVIVMDPPKFVENKSQLMGACRGYKDINMLAIQLLNEGGILLTFSCSGLMTSDLFQKIIADAAIDAGRDVQFIEQFR
2 -> 81 SVRLVLAKGREKSLLRRHPWVFSGAVARMEGKASLGETIDIVDHQGKWLARGAYSPASQIRARVWTFDPSESIDIAFFSR

 
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:0008649 - rRNA methyltransferase activity
GO:0016434 - rRNA (cytosine) methyltransferase activity
GO:0003723 - RNA binding
GO:0042803 - protein homodimerization activity
GO:0009383 - rRNA (cytosine-C5-)-methyltransferase activity
biological_process GO:0031167 - rRNA methylation
GO:0006364 - rRNA processing
GO:0032259 - methylation
GO:0044010 - single-species biofilm formation
GO:0070475 - rRNA base methylation
Note(s): Note(s): ...[more].
External database links:  
DIP:
 DIP-11501N
ECOCYC:
 G6501-MONOMER
ECOLIWIKI:
 b0967
INTERPRO:
 IPR019614
INTERPRO:
 IPR041532
INTERPRO:
 IPR036974
INTERPRO:
 IPR029063
INTERPRO:
 IPR023542
INTERPRO:
 IPR015947
INTERPRO:
 IPR002478
MODBASE:
 P75876
PDB:
 3C0K
PFAM:
 PF10672
PFAM:
 PF17785
PRIDE:
 P75876
PRODB:
 PRO_000023771
PROSITE:
 PS50890
REFSEQ:
 NP_415487
SMART:
 SM00359
SMR:
 P75876
UNIPROT:
 P75876


Operon      
Name: rlmI         
Operon arrangement:
Transcription unit        Promoter
 


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 TSS_1293 1028531 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1294 (cluster) 1028744 reverse For this promoter, there
Read more > 		[RS-EPT-CBR] [1]
  promoter yccXp5 1029980 forward Similarity to the consensus
Read more > 		[ICWHO] [2]
  promoter yccXp7 1029994 forward Similarity to the consensus
Read more > 		[ICWHO] [2]
  promoter rlmIp4 1030001 reverse Similarity to the consensus
Read more > 		[ICWHO] [2]
  promoter yccXp4 1030061 forward Similarity to the consensus
Read more > 		[ICWHO] [2]


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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