RegulonDB RegulonDB 10.8: Gene Form
   

ybcL gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybcK ybcM ybcL TSS_683 TSS_683 ybcLp2 ybcLp2 ybcLp7 ybcLp7

Gene      
Name: ybcL    Texpresso search in the literature
Synonym(s): ECK0536, G6301, b0545
Genome position(nucleotides): 570893 --> 571444 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
42.39
External database links:  
ASAP:
ABE-0001869
ECHOBASE:
EB3393
OU-MICROARRAY:
b0545
PortEco:
ybcL
STRING:
511145.b0545
COLOMBOS: ybcL


Product      
Name: DLP12 prophage; periplasmic protein YbcL
Synonym(s): YbcL
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 19.476
Isoelectric point: 7.571
Motif(s):
 
Type Positions Sequence
22 -> 183 FQVTSNEIKTGEQLTTSHVFSGFGCEGGNTSPSLTWSGVPEGTKSFAVTVYDPDAPTGSGWWHWTVVNIPATVTYLPVDAGRRDGTKLPTGAVQGRNDFGYAGFGGACPPKGDKPHHYQFKVWALKTEKIPVDSNSSGALVGYMLNANKIATAEITPVYEIK
44 -> 180 FGCEGGNTSPSLTWSGVPEGTKSFAVTVYDPDAPTGSGWWHWTVVNIPATVTYLPVDAGRRDGTKLPTGAVQGRNDFGYAGFGGACPPKGDKPHHYQFKVWALKTEKIPVDSNSSGALVGYMLNANKIATAEITPVY
1 -> 21 MKTLIVSTVLAFITFSAQAAA

 

Classification:
Multifun Terms (GenProtEC)  
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.3 - inhibition / activation of enzymes
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
cellular_component GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
molecular_function GO:0004857 - enzyme inhibitor activity
biological_process GO:0043086 - negative regulation of catalytic activity
Note(s): Note(s): ...[more].
Evidence: [IHBCE] Inferred by a human based on computational evidence
Reference(s): [1] Serre L., et al., 2001
External database links:  
ECOCYC:
G6301-MONOMER
ECOLIWIKI:
b0545
INTERPRO:
IPR005247
INTERPRO:
IPR036610
INTERPRO:
IPR008914
MODBASE:
P77368
PANTHER:
PTHR30289
PDB:
1FUX
PFAM:
PF01161
PRIDE:
P77368
REFSEQ:
NP_415077
SMR:
P77368
UNIPROT:
P77368


Operon      
Name: ybcLM         
Operon arrangement:
Transcription unit        Promoter
 


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 ybcLp7 570845 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter ybcLp2 570847 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_683 571937 forward nd [RS-EPT-CBR] [3]


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] Serre L., Pereira de Jesus K., Zelwer C., Bureaud N., Schoentgen F., Benedetti H., 2001, Crystal structures of YBHB and YBCL from Escherichia coli, two bacterial homologues to a Raf kinase inhibitor protein., J Mol Biol 310(3):617-34

 [2] 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

 [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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