RegulonDB RegulonDB 10.8: Gene Form
   

rsmA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

surA pdxA rsmA apaG TSS_93 TSS_93 TSS_92 TSS_92 TSS_91 TSS_91 TSS_90 TSS_90 rsmAp rsmAp TSS_89 TSS_89 TSS_88 TSS_88 TSS_87 (cluster) TSS_87 (cluster) TSS_86 TSS_86 apaGp apaGp TSS_84 TSS_84 apaHp4 apaHp4

Gene      
Name: rsmA    Texpresso search in the literature
Synonym(s): ECK0052, EG10523, b0051, ksgA
Genome position(nucleotides): 51609 <-- 52430 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.04
External database links:  
ASAP:
 ABE-0000175
CGSC:
 583
ECHOBASE:
 EB0518
OU-MICROARRAY:
 b0051
PortEco:
 ksgA
STRING:
 511145.b0051
COLOMBOS: rsmA


Shine dalgarno      
Sequence: aaaatgattgTTAACAcccAAT


Product      
Name: 16S rRNA m62A1518,m62A1519 dimethyltransferase
Synonym(s): KsgA, RsmA, rRNA small subunit methyltransferase A, ribosomal RNA small subunit methyltransferase A
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 30.42
Isoelectric point: 8.229
Motif(s):
 
Type Positions Sequence
9 -> 265 HLARKRFGQNFLNDQFVIDSIVSAINPQKGQAMVEIGPGLAALTEPVGERLDQLTVIELDRDLAARLQTHPFLGPKLTIYQQDAMTFNFGELAEKMGQPLRVFGNLPYNISTPLMFHLFSYTDAIADMHFMLQKEVVNRLVAGPNSKAYGRLSVMAQYYCNVIPVLEVPPSAFTPPPKVDSAVVRLVPHATMPHPVKDVRVLSRITTEAFNQRRKTIRNSLGNLFSVEVLTGMGIDPAMRAENISVAQYCQMANYLA
66 -> 66 E
2 -> 273 NNRVHQGHLARKRFGQNFLNDQFVIDSIVSAINPQKGQAMVEIGPGLAALTEPVGERLDQLTVIELDRDLAARLQTHPFLGPKLTIYQQDAMTFNFGELAEKMGQPLRVFGNLPYNISTPLMFHLFSYTDAIADMHFMLQKEVVNRLVAGPNSKAYGRLSVMAQYYCNVIPVLEVPPSAFTPPPKVDSAVVRLVPHATMPHPVKDVRVLSRITTEAFNQRRKTIRNSLGNLFSVEVLTGMGIDPAMRAENISVAQYCQMANYLAENAPLQES

 
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:0003723 - RNA binding
GO:0003729 - mRNA binding
GO:0019843 - rRNA binding
GO:0003690 - double-stranded DNA binding
GO:0016433 - rRNA (adenine) methyltransferase activity
GO:0000179 - rRNA (adenine-N6,N6-)-dimethyltransferase activity
GO:0052908 - 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity
biological_process GO:0000154 - rRNA modification
GO:0031167 - rRNA methylation
GO:0046677 - response to antibiotic
GO:0006364 - rRNA processing
GO:0032259 - methylation
GO:0000028 - ribosomal small subunit assembly
GO:0070475 - rRNA base methylation
Note(s): Note(s): ...[more].
External database links:  
DIP:
 DIP-10076N
ECOCYC:
 EG10523-MONOMER
ECOLIWIKI:
 b0051
INTERPRO:
 IPR023165
INTERPRO:
 IPR029063
INTERPRO:
 IPR020598
INTERPRO:
 IPR020596
INTERPRO:
 IPR011530
INTERPRO:
 IPR001737
MINT:
 MINT-1246440
MODBASE:
 P06992
PANTHER:
 PTHR11727
PDB:
 4ADV
PDB:
 3TPZ
PDB:
 1QYR
PFAM:
 PF00398
PRIDE:
 P06992
PRODB:
 PRO_000023881
PROSITE:
 PS01131
PROSITE:
 PS51689
REFSEQ:
 NP_414593
SMART:
 SM00650
SMR:
 P06992
UNIPROT:
 P06992


Operon      
Name: lptD-surA-pdxA-rsmA-apaGH         
Operon arrangement:
Transcription unit        Promoter
apaGH
rsmA-apaGH
imp
imp
imp-surA-pdxA
pdxA-rsmA
pdxA-rsmA-apaGH
surA-pdxA-rsmA-apaGH


Transcriptional Regulation      
Display Regulation             
Activated by: Fis


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 apaHp4 51293 reverse Similarity to the consensus
Read more > 		[ICWHO] [1]
  promoter TSS_84 51998 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_86 52194 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_87 (cluster) 52478 reverse For this promoter, there
Read more > 		[RS-EPT-CBR] [2]
  promoter TSS_88 52548 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_89 52587 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_90 53904 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_91 54275 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_92 54363 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_93 54605 reverse nd [RS-EPT-CBR] [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] 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

 [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.

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