RegulonDB RegulonDB 10.9: Gene Form
   

ydcF gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

hrpA aldA ydcF ArcA ArcA ArcA DnaA FNR CRP ArcA ArcA SoxS Rob MarA anti-terminator terminator aldAp aldAp ydcFp4 ydcFp4 TSS_1802 TSS_1802 TSS_1801 TSS_1801 ydcFp3 ydcFp3

Gene      
Name: ydcF    Texpresso search in the literature
Synonym(s): ECK1407, EG12110, b1414
Genome position(nucleotides): 1487235 --> 1488035 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
51.19
External database links:  
ASAP:
ABE-0004722
ECHOBASE:
EB2033
ECOLIHUB:
ydcF
OU-MICROARRAY:
b1414
STRING:
511145.b1414
COLOMBOS: ydcF


Product      
Name: DUF218 domain-containing protein YdcF
Synonym(s): YdcF
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane,cytosol
Molecular weight: 29.706
Isoelectric point: 5.741
Motif(s):
 
Type Positions Sequence
40 -> 173 VILAGNAVMPTIDAACKIARDQQIPLLISGGIGHSTTFLYSAIAQHPHYNTIRTTGRAEATILADIAHQFWHIPHEKIWIEDQSTNCGENARFSIALLNQAVERVHTAIVVQDPTMQRRTMATFRRMTGDNPDA
217 -> 266 PRLRDDSDGYGPRGRDFIVHVDFPAEVIHAWQTLKHDAVLIEAMESRSLR
97 -> 97 A

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0005886 - plasma membrane
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-11642N
ECOCYC:
EG12110-MONOMER
ECOLIWIKI:
b1414
INTERPRO:
IPR014729
INTERPRO:
IPR003848
PDB:
3CA8
PFAM:
PF02698
PRIDE:
P34209
REFSEQ:
NP_415932
SMR:
P34209
UNIPROT:
P34209


Operon      
Name: ydcF         
Operon arrangement:
Transcription unit        Promoter
ydcF


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 ydcFp3 1487202 forward Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter TSS_1801 1487204 forward nd [RS-EPT-CBR] [2]
  promoter TSS_1802 1487218 forward nd [RS-EPT-CBR] [2]
  promoter ydcFp4 1487231 forward Similarity to the consensus
Read more >
[ICWHO] [1]


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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