RegulonDB RegulonDB 10.10: Gene Form
   

rsmF gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yebT rsmF yebV yebS RyeB yebWp3 yebWp3 yebVp5 yebVp5 yebVp1 yebVp1 yebVp6 yebVp6 yebVp2 yebVp2 TSS_2183 TSS_2183 TSS_2182 TSS_2182

Gene      
Name: rsmF    Texpresso search in the literature
Synonym(s): ECK1834, G7008, b1835, yebU
Genome position(nucleotides): 1920223 --> 1921662 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.81
External database links:  
ASAP:
 ABE-0006106
ECHOBASE:
 EB3777
ECOLIHUB:
 rsmF
OU-MICROARRAY:
 b1835
STRING:
 511145.b1835
COLOMBOS: rsmF


Product      
Name: 16S rRNA m5C1407 methyltransferase
Synonym(s): RsmF, YebU, ribosomal RNA small subunit methyltransferase F
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 53.228
Isoelectric point: 5.359
Motif(s):
 
Type Positions Sequence
125 -> 131 AAAPGSK
9 -> 105 PDAFLTQMREAMPSTLSFDDFLAACQRPLRRSIRVNTLKISVADFLQLTAPYGWTLTPIPWCEEGFWIERDNEDALPLGSTAEHLSGLFYIQEASSM
421 -> 470 AEEWYRGRDVYPQAAPVADDVLVTFQHQPIGLAKRIGSRLKNSYPRELVR
118 -> 309 PQRVMDVAAAPGSKTTQISARMNNEGAILANEFSASRVKVLHANISRCGISNVALTHFDGRVFGAAVPEMFDAILLDAPCSGEGVVRKDPDALKNWSPESNQEIAATQRELIDSAFHALRPGGTLVYSTCTLNQEENEAVCLWLKETYPDAVEFLPLGDLFPGANKALTEEGFLHVFPQIYDCEGFFVARLR

 
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:0008757 - S-adenosylmethionine-dependent methyltransferase activity
GO:0008649 - rRNA methyltransferase activity
GO:0016434 - rRNA (cytosine) methyltransferase activity
GO:0003723 - RNA binding
GO:0009383 - rRNA (cytosine-C5-)-methyltransferase activity
biological_process GO:0001510 - RNA methylation
GO:0031167 - rRNA methylation
GO:0006396 - RNA processing
GO:0006364 - rRNA processing
GO:0032259 - methylation
GO:0070475 - rRNA base methylation
Note(s): Note(s): ...[more].
External database links:  
ECOCYC:
 G7008-MONOMER
ECOLIWIKI:
 b1835
INTERPRO:
 IPR023545
INTERPRO:
 IPR001678
INTERPRO:
 IPR011023
INTERPRO:
 IPR018314
INTERPRO:
 IPR023267
INTERPRO:
 IPR029063
INTERPRO:
 IPR031341
INTERPRO:
 IPR027391
MODBASE:
 P76273
PDB:
 2FRX
PFAM:
 PF17125
PFAM:
 PF13636
PFAM:
 PF01189
PRIDE:
 P76273
PRINTS:
 PR02008
PRODB:
 PRO_000023886
PROSITE:
 PS01153
PROSITE:
 PS51686
REFSEQ:
 NP_416349
SMR:
 P76273
UNIPROT:
 P76273


Operon      
Name: rsmF         
Operon arrangement:
Transcription unit        Promoter
rsmF


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_2182 1918414 forward nd [RS-EPT-CBR] [1]
  promoter TSS_2183 1920196 forward nd [RS-EPT-CBR] [1]
  promoter yebVp2 1921715 forward nd [ICWHO] [2]
  promoter yebVp6 1921725 forward nd [ICWHO] [2]
  promoter yebVp1 1921745 forward nd [ICWHO] [2]
  promoter yebVp5 1921753 forward nd [ICWHO] [2]
  promoter yebWp3 1921957 forward nd [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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