RegulonDB RegulonDB 11.1: Gene Form
   

ynfC gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ynfC speG ynfD ynfCp9 ynfCp9 TSS_1873 TSS_1873 TSS_1872 TSS_1872 ynfDp6 ynfDp6

Gene      
Name: ynfC    Texpresso search in the literature
Synonym(s): ECK1580, G6843, b1585
Genome position(nucleotides): 1656747 <-- 1657457
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 43.74
External database links:  
ASAP:
 ABE-0005288
ECHOBASE:
 EB3602
ECOLIHUB:
 ynfC
OU-MICROARRAY:
 b1585
STRING:
 511145.b1585
COLOMBOS: ynfC


Product      
Name: PF06788 family lipoprotein YnfC
Synonym(s): UPF0257 family lipoprotein YnfC, YnfC
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol,inner membrane
Molecular weight: 26.507
Isoelectric point: 4.38
Motif(s):
 
Type Positions Sequence Comment
1 -> 16 MKYKLLPCLLAIFLTG
2 -> 236 KYKLLPCLLAIFLTGCDRTEVTLSFTPEMASFSNEFDFDPLRGPVKDFTQTLMDEQGEVTKRVSGTLSEEGCFDSLELLDLENNTVVALVLDANYYRDAETLEKRVRLQGKCQLAELPSAGVSWETDDNGFVIKASSKQMQMEYRYDDQGYPLGKTTKSNDKTLSVSATPSTDPIKKLDYTAVTLLNNQRVGNVKQSCEYDSHANPVDCQLIIVDEGVKPAVERVYTIKNTIDYY
17 -> 236 CDRTEVTLSFTPEMASFSNEFDFDPLRGPVKDFTQTLMDEQGEVTKRVSGTLSEEGCFDSLELLDLENNTVVALVLDANYYRDAETLEKRVRLQGKCQLAELPSAGVSWETDDNGFVIKASSKQMQMEYRYDDQGYPLGKTTKSNDKTLSVSATPSTDPIKKLDYTAVTLLNNQRVGNVKQSCEYDSHANPVDCQLIIVDEGVKPAVERVYTIKNTIDYY UniProt: UPF0257 lipoprotein YnfC.

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0016020 - membrane
GO:0005886 - plasma membrane
Note(s): Note(s): ...[more].
Reference(s): [1] Berven FS., et al., 2004
[2] Brokx SJ., et al., 2004
[3] Gonnet P., et al., 2004
[4] Rao S., et al., 2020
External database links:  
ALPHAFOLD:
 P67553
ECOCYC:
 G6843-MONOMER
ECOLIWIKI:
 b1585
INTERPRO:
 IPR010646
PFAM:
 PF06788
PRIDE:
 P67553
PROSITE:
 PS51257
REFSEQ:
 NP_416102
SMR:
 P67553
UNIPROT:
 P67553


Operon      
Name: ynfC         
Operon arrangement:
Transcription unit        Promoter
ynfC


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 ynfDp6 1657414 forward nd [COMP-AINF] [5]
  promoter TSS_1872 1657482 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_1873 1657539 forward nd [RS-EPT-CBR] [6]
  promoter ynfCp9 1657547 reverse nd [COMP-AINF] [5]


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] Berven FS., Flikka K., Jensen HB., Eidhammer I., 2004, BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria., Nucleic Acids Res 32(Web Server issue):W394-9

 [2] Brokx SJ., Ellison M., Locke T., Bottorff D., Frost L., Weiner JH., 2004, Genome-wide analysis of lipoprotein expression in Escherichia coli MG1655., J Bacteriol 186(10):3254-8

 [3] Gonnet P., Rudd KE., Lisacek F., 2004, Fine-tuning the prediction of sequences cleaved by signal peptidase II: a curated set of proven and predicted lipoproteins of Escherichia coli K-12., Proteomics 4(6):1597-613

 [4] Rao S., Bates GT., Matthews CR., Newport TD., Vickery ON., Stansfeld PJ., 2020, Characterizing Membrane Association and Periplasmic Transfer of Bacterial Lipoproteins through Molecular Dynamics Simulations., Structure 28(4):475-487.e3

 [5] 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

 [6] 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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