RegulonDB RegulonDB 10.9: Gene Form
   

hrpA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

hrpA ydcF azoR ArcA SoxS Rob MarA anti-terminator terminator terminator ydcFp4 ydcFp4 TSS_1802 TSS_1802 TSS_1801 TSS_1801 ydcFp3 ydcFp3 azoRp8 azoRp8 azoRp6 azoRp6 azoRp azoRp azoRp1 azoRp1 TSS_1800 TSS_1800

Gene      
Name: hrpA    Texpresso search in the literature
Synonym(s): ECK1406, G6732, b1413
Genome position(nucleotides): 1483061 --> 1486963 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.45
External database links:  
ASAP:
ABE-0004718
ECHOBASE:
EB2772
ECOLIHUB:
hrpA
OU-MICROARRAY:
b1413
STRING:
511145.b1413
COLOMBOS: hrpA


Product      
Name: ATP-dependent RNA helicase HrpA
Synonym(s): HrpA
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 149.027
Isoelectric point: 8.024
Motif(s):
 
Type Positions Sequence
466 -> 551 VRLLEELGAITTDEQASAYKLTPLGRQLSQLPVDPRLARMVLEAQKHGCVREAMIITSALSIQDPRERPMDKQQASDEKHRRFHDK
85 -> 233 DILEAIRDHQVVIVAGETGSGKTTQLPKICMELGRGIKGLIGHTQPRRLAARTVANRIAEELKTEPGGCIGYKVRFSDHVSDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFLLGYLKELLPRRPDLKIIITSATID
304 -> 304 R
681 -> 694 GRIAARIDPEWVEP
705 -> 705 S

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.3 - RNA modification
Gene Ontology Terms (GO)  
molecular_function GO:0003676 - nucleic acid binding
GO:0004386 - helicase activity
GO:0016787 - hydrolase activity
GO:0003723 - RNA binding
GO:0000166 - nucleotide binding
GO:0003724 - RNA helicase activity
GO:0005524 - ATP binding
biological_process GO:0009451 - RNA modification
GO:0006397 - mRNA processing
GO:0000462 - maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
Note(s): Note(s): ...[more].
Evidence: [APPP] Assay of partially-purified protein
[IMP] Inferred from mutant phenotype
Reference(s): [1] Jain C. 2006
[2] Koo JT., et al., 2004
External database links:  
DIP:
DIP-9937N
ECOCYC:
G6732-MONOMER
ECOLIWIKI:
b1413
INTERPRO:
IPR010222
INTERPRO:
IPR011545
INTERPRO:
IPR011709
INTERPRO:
IPR014001
INTERPRO:
IPR024590
INTERPRO:
IPR027417
INTERPRO:
IPR003593
INTERPRO:
IPR001650
INTERPRO:
IPR007502
MODBASE:
P43329
PFAM:
PF11898
PFAM:
PF07717
PFAM:
PF04408
PFAM:
PF00271
PFAM:
PF00270
PRIDE:
P43329
PRODB:
PRO_000022922
PROSITE:
PS51194
PROSITE:
PS51192
REFSEQ:
NP_415931
SMART:
SM00487
SMART:
SM00382
SMART:
SM00490
SMART:
SM00847
SMR:
P43329
UNIPROT:
P43329


Operon      
Name: hrpA         
Operon arrangement:
Transcription unit        Promoter
hrpA


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_1800 1482829 forward nd [RS-EPT-CBR] [3]
  promoter azoRp1 1482873 reverse Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter azoRp6 1482927 reverse Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter azoRp8 1482991 reverse Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter ydcFp3 1487202 forward Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter TSS_1801 1487204 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1802 1487218 forward nd [RS-EPT-CBR] [3]
  promoter ydcFp4 1487231 forward Similarity to the consensus
Read more >
[ICWHO] [4]


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] Jain C., 2006, Overexpression and purification of tagged Escherichia coli proteins using a chromosomal knock-in strategy., Protein Expr Purif 46(2):294-8

 [2] Koo JT., Choe J., Moseley SL., 2004, HrpA, a DEAH-box RNA helicase, is involved in mRNA processing of a fimbrial operon in Escherichia coli., Mol Microbiol 52(6):1813-26

 [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.

 [4] 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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