RegulonDB RegulonDB 10.9: Gene Form
   

ppdD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

hofB nadC ppdD hofC CRP terminator TSS_232 TSS_232 ppdDp ppdDp

Gene      
Name: ppdD    Texpresso search in the literature
Synonym(s): ECK0107, EG12107, b0108
Genome position(nucleotides): 117109 <-- 117549 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.06
External database links:  
ASAP:
 ABE-0000372
ECHOBASE:
 EB2031
ECOLIHUB:
 ppdD
OU-MICROARRAY:
 b0108
STRING:
 511145.b0108
COLOMBOS: ppdD


Product      
Name: prepilin-type N-terminal cleavage/methylation domain-containing protein PpdD
Synonym(s): PpdD, prepilin peptidase dependent protein
Sequence: Get amino acid sequence Fasta Format
Cellular location: pilus,membrane
Molecular weight: 15.622
Isoelectric point: 4.393
Motif(s):
 
Type Positions Sequence
7 -> 146 FTLIELMVVIGIIAILSAIGIPAYQNYLRKAALTDMLQTFVPYRTAVELCALEHGGLDTCDGGSNGIPSPTTTRYVSAMSVAKGVVSLTGQESLNGLSVVMTPGWDNANGVTGWTRNCNIQSDSALQQACEDVFRFDDAN
1 -> 25 MDKQRGFTLIELMVVIGIIAILSAI
6 -> 30 GFTLIELMVVIGIIAILSAIGIPAY

 
Classification:
Multifun Terms (GenProtEC)  
  6 - cell structure --> 6.5 - pilus
Gene Ontology Terms (GO)  
cellular_component GO:0009289 - pilus
GO:0016020 - membrane
GO:0016021 - integral component of membrane
GO:0044096 - type IV pilus
biological_process GO:0043683 - type IV pilus biogenesis
GO:0043107 - type IV pilus-dependent motility
Note(s): Note(s): ...[more].
Reference(s): [1] Cisneros DA., et al., 2012
[2] Sauvonnet N., et al., 2000
External database links:  
ECOCYC:
 EG12107-MONOMER
ECOLIWIKI:
 b0108
INTERPRO:
 IPR012902
MODBASE:
 P36647
PFAM:
 PF07963
PRIDE:
 P36647
PROSITE:
 PS00409
REFSEQ:
 NP_414650
UNIPROT:
 P36647


Operon      
Name: ppdD-hofBC         
Operon arrangement:
Transcription unit        Promoter
ppdD-hofBC


Transcriptional Regulation      
Display Regulation             
Activated by: CRP


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_232 118078 reverse nd [RS-EPT-CBR] [3]


Evidence    

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


Reference(s)    

 [1] Cisneros DA., Pehau-Arnaudet G., Francetic O., 2012, Heterologous assembly of type IV pili by a type II secretion system reveals the role of minor pilins in assembly initiation., Mol Microbiol 86(4):805-18

 [2] Sauvonnet N., Vignon G., Pugsley AP., Gounon P., 2000, Pilus formation and protein secretion by the same machinery in Escherichia coli., EMBO J 19(10):2221-8

 [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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