RegulonDB RegulonDB 11.1: Gene Form
   

yafL gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yafL rayT dinJ DinJ-YafQ LexA terminator rayTp8 rayTp8 TSS_446 TSS_446 rayTp1 rayTp1 yafLp6 yafLp6 dinJp dinJp TSS_445 (cluster) TSS_445 (cluster)

Gene      
Name: yafL    Texpresso search in the literature
Synonym(s): ECK0228, G6111, b0227
Genome position(nucleotides): 246712 --> 247461
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.4
External database links:  
ASAP:
 ABE-0000775
ECHOBASE:
 EB2943
ECOLIHUB:
 yafL
OU-MICROARRAY:
 b0227
STRING:
 511145.b0227
COLOMBOS: yafL


Product      
Name: NlpC/P60 family protein YafL
Synonym(s): C40 family non-peptidase homologue, YafL
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 28.785
Isoelectric point: 9.955
Motif(s):
 
Type Positions Sequence Comment
1 -> 17 MSLPSIPSFVLSGLLLI
18 -> 249 CLPFSSFASATTSHISFSYAARQRMQNRARLLKQYQTHLKKQASYIVEGNAESKRALRQHNREQIKQHPEWFPAPLKASDRRWQALAENNHFLSSDHLHNITEVAIHRLEQQLGKPYVWGGTRPDKGFDCSGLVFYAYNKILEAKLPRTANEMYHYRRATIVANNDLRRGDLLFFHIHSREIADHMGVYLGDGQFIESPRTGETIRISRLAEPFWQDHFLGARRILTEETIL UniProt: Probable endopeptidase YafL.
116 -> 243 HNITEVAIHRLEQQLGKPYVWGGTRPDKGFDCSGLVFYAYNKILEAKLPRTANEMYHYRRATIVANNDLRRGDLLFFHIHSREIADHMGVYLGDGQFIESPRTGETIRISRLAEPFWQDHFLGARRIL UniProt: NlpC/P60.
131 -> 241 GKPYVWGGTRPDKGFDCSGLVFYAYNKILEAKLPRTANEMYHYRRATIVANNDLRRGDLLFFHIHSREIADHMGVYLGDGQFIESPRTGETIRISRLAEPFWQDHFLGARR

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
molecular_function GO:0008233 - peptidase activity
GO:0016787 - hydrolase activity
GO:0008234 - cysteine-type peptidase activity
biological_process GO:0006508 - proteolysis
Note(s): Note(s): ...[more].
Reference(s): [1] Paradis-Bleau C., et al., 2014
[2] Rao S., et al., 2020
External database links:  
ALPHAFOLD:
 Q47151
ECOCYC:
 G6111-MONOMER
ECOLIWIKI:
 b0227
INTERPRO:
 IPR000064
INTERPRO:
 IPR038765
PFAM:
 PF00877
PRIDE:
 Q47151
REFSEQ:
 NP_414762
SMR:
 Q47151
UNIPROT:
 Q47151


Operon      
Name: yafL         
Operon arrangement:
Transcription unit        Promoter
yafL


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_445 (cluster) 246533 reverse nd [RS-EPT-CBR] [3]
  promoter yafLp6 246641 forward nd [COMP-AINF] [4]
  promoter rayTp1 247544 forward nd [COMP-AINF] [4]
  promoter TSS_446 247622 forward nd [RS-EPT-CBR] [3]
  promoter rayTp8 247624 forward nd [COMP-AINF] [4]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Paradis-Bleau C., Kritikos G., Orlova K., Typas A., Bernhardt TG., 2014, A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism., PLoS Genet 10(1):e1004056

 [2] 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

 [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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