RegulonDB RegulonDB 10.8: Gene Form
   

ycaL gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

aroA ycaL cmk DksA-ppGpp DksA-ppGpp DksA-ppGpp DksA-ppGpp terminator anti-terminator anti-anti-terminator rpsAp3 rpsAp3 TSS_1178 TSS_1178 rpsAp1 rpsAp1 cmkp cmkp ycaLp6 ycaLp6 ycaLp9 ycaLp9 ycaLp8 ycaLp8 ycaLp1 ycaLp1

Gene      
Name: ycaL    Texpresso search in the literature
Synonym(s): ECK0900, G6470, b0909
Genome position(nucleotides): 960264 --> 961028 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
49.93
External database links:  
ASAP:
ABE-0003098
ECHOBASE:
EB2932
OU-MICROARRAY:
b0909
PortEco:
ycaL
STRING:
511145.b0909
COLOMBOS: ycaL


Product      
Name: periplasmic protease YcaL
Synonym(s): YcaL
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane,periplasmic space,extracellular space
Molecular weight: 26.74
Isoelectric point: 7.6
Motif(s):
 
Type Positions Sequence
20 -> 254 CQNTHGIDTNMAISSGLNAYKAATLSDADAKAIANQGCAEMDSGNQVASKSSKYGKRLAKIAKALGNNINGTPVNYKVYMTSDVNAWAMANGCVRVYSGLMDMMNDNEIEGVLGHELGHVALGHSLAEMKASYAIVAARDAISATSGVASQLSRSQLGDIAEGAINAKYSRDKESEADDFSFDLLKKRGISTQGLVGSFETLASLDGGRTQSMFDSHPPSTERAQHIRDRIASGK
1 -> 19 MKNTKLLLAIATSAALLTG
77 -> 249 LAKIAKALGNNINGTPVNYKVYMTSDVNAWAMANGCVRVYSGLMDMMNDNEIEGVLGHELGHVALGHSLAEMKASYAIVAARDAISATSGVASQLSRSQLGDIAEGAINAKYSRDKESEADDFSFDLLKKRGISTQGLVGSFETLASLDGGRTQSMFDSHPPSTERAQHIRDR
241 -> 254 ERAQHIRDRIASGK

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.2 - degradation of macromolecules --> 1.2.3 - proteins/peptides/glycopeptides
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0030288 - outer membrane-bounded periplasmic space
GO:0005886 - plasma membrane
GO:0005576 - extracellular region
molecular_function GO:0005515 - protein binding
GO:0008233 - peptidase activity
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0004222 - metalloendopeptidase activity
GO:0008237 - metallopeptidase activity
biological_process GO:0006508 - proteolysis
GO:0051603 - proteolysis involved in cellular protein catabolic process
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-11467N
ECOCYC:
G6470-MONOMER
ECOLIWIKI:
b0909
INTERPRO:
IPR001915
PFAM:
PF01435
PRIDE:
P43674
PROSITE:
PS51257
REFSEQ:
NP_415429
SMR:
P43674
UNIPROT:
P43674


Operon      
Name: ycaL         
Operon arrangement:
Transcription unit        Promoter
 


RNA cis-regulatory element    
Attenuation: Transcriptional


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 ycaLp1 960132 forward Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter ycaLp8 960143 forward Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter ycaLp9 960238 forward Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter ycaLp6 960255 forward Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter TSS_1178 961718 forward nd [RS-EPT-CBR] [2]


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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