RegulonDB RegulonDB 11.1: Gene Form
   

rlhA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rlhA sutR yncJ terminator anti-terminator anti-anti-terminator anti-anti-terminator anti-terminator terminator TSS_1814 TSS_1814 TSS_1813 TSS_1813 ydcPp2 ydcPp2

Gene      
Name: rlhA    Texpresso search in the literature
Synonym(s): ECK1429, G6746, b1435, ydcP
Genome position(nucleotides): 1506781 --> 1508742
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.07
External database links:  
ASAP:
 ABE-0004786
ECHOBASE:
 EB3522
ECOLIHUB:
 ydcP
OU-MICROARRAY:
 b1435
STRING:
 511145.b1435
COLOMBOS: rlhA


Product      
Name: 23S rRNA 5-hydroxycytidine C2501 synthase
Synonym(s): RlhA, YdcP
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 72.702
Isoelectric point: 7.176
Motif(s):
 
Type Positions Sequence Comment
79 -> 305 EPAQRLITDLYQTGVDALIVQDMGILELDIPPIELHASTQCDIRTVEKAKFLSDVGFTQIVLARELNLDQIRAIHQATDATIEFFIHGALCVAYSGQCYISHAQTGRSANRGDCSQACRLPYTLKDDQGRVVSYEKHLLSMKDNDQTANLGALIDAGVRSFKIEGRYKDMSYVKNITAHYRQMLDAIIEERGDLARASSGRTEHFFVPSTEKTFHRGSTDYFVNARK
161 -> 161 E UniProt: Strong decrease in activity..
165 -> 165 H UniProt: No change in activity..
169 -> 169 C UniProt: Loss of activity..
175 -> 175 Q UniProt: No change in activity..

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.3 - RNA modification
  2 - information transfer --> 2.2 - RNA related --> 2.2.6 - rRNA, stable RNA
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0005515 - protein binding
biological_process GO:0000154 - rRNA modification
GO:0006364 - rRNA processing
Note(s): Note(s): ...[more].
Evidence: [EXP-IMP] Inferred from mutant phenotype
Reference(s): [1] Kimura S., et al., 2017
External database links:  
ALPHAFOLD:
 P76104
DIP:
 DIP-11650N
ECOCYC:
 G6746-MONOMER
ECOLIWIKI:
 b1435
INTERPRO:
 IPR020988
INTERPRO:
 IPR001539
MODBASE:
 P76104
PFAM:
 PF01136
PFAM:
 PF12392
PRIDE:
 P76104
PROSITE:
 PS01276
REFSEQ:
 NP_415952
SMR:
 P76104
UNIPROT:
 P76104


Operon      
Name: rlhA         
Operon arrangement:
Transcription unit        Promoter
rlhA


RNA cis-regulatory element    
Attenuation: Transcriptional


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 ydcPp2 1506754 forward nd [COMP-AINF] [2]
  promoter TSS_1813 1506757 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1814 1509035 reverse nd [RS-EPT-CBR] [3]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Kimura S., Sakai Y., Ishiguro K., Suzuki T., 2017, Biogenesis and iron-dependency of ribosomal RNA hydroxylation., Nucleic Acids Res 45(22):12974-12986

 [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

 [3] 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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