RegulonDB RegulonDB 10.8: Gene Form
   

ycbZ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ycbZ fabA matP FadR FabR ycbZp4 ycbZp4 matPp matPp TSS_1259 (cluster) TSS_1259 (cluster) TSS_1258 TSS_1258 TSS_1257 TSS_1257 TSS_1256 TSS_1256 TSS_1255 (cluster) TSS_1255 (cluster) TSS_1254 TSS_1254 TSS_1253 TSS_1253 TSS_1252 TSS_1252 fabAp fabAp TSS_1251 (cluster) TSS_1251 (cluster) TSS_1250 TSS_1250 TSS_1249 TSS_1249

Gene      
Name: ycbZ    Texpresso search in the literature
Synonym(s): ECK0946, G6493, b0955
Genome position(nucleotides): 1016539 <-- 1018299 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
51.79
External database links:  
ASAP:
ABE-0003233
ECHOBASE:
EB3482
OU-MICROARRAY:
b0955
PortEco:
ycbZ
STRING:
511145.b0955
COLOMBOS: ycbZ


Product      
Name: putative ATP-dependent protease YcbZ
Synonym(s): YcbZ
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 65.819
Isoelectric point: 4.418
Motif(s):
 
Type Positions Sequence
140 -> 297 TLQPGLVHQANGGILIISLRTLLAQPLLWMRLKNIVNRERFDWVAFDESRPLPVSVPSMPLKLKVILVGERESLADFQEMEPELSEQAIYSEFEDTLQIVDAESVTQWCRWVTFTARHNHLPAPGADAWPILIREAARYTGEQETLPLSPQWILRQCK
435 -> 538 DGDSASMAELCALISALADVPVNQSIAITGSVDQFGRAQPVGGLNEKIEGFFAICQQRELTGKQGVIIPTANVRHLSLHSELVKAVEEGKFTIWAVDDVTDALP
346 -> 543 GERIGQINALSVIEFPGHPRAFGEPSRISCVVHIGDGEFTDIERKAELGGNIHAKGMMIMQAFLMSELQLEQQIPFSASLTFEQSYSEVDGDSASMAELCALISALADVPVNQSIAITGSVDQFGRAQPVGGLNEKIEGFFAICQQRELTGKQGVIIPTANVRHLSLHSELVKAVEEGKFTIWAVDDVTDALPLLLNL

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.6 - turnover, degradation
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0008233 - peptidase activity
GO:0016787 - hydrolase activity
GO:0005524 - ATP binding
GO:0004176 - ATP-dependent peptidase activity
GO:0004252 - serine-type endopeptidase activity
GO:0008236 - serine-type peptidase activity
biological_process GO:0006508 - proteolysis
GO:0030163 - protein catabolic process
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-11487N
ECOCYC:
G6493-MONOMER
ECOLIWIKI:
b0955
INTERPRO:
IPR027065
INTERPRO:
IPR041699
INTERPRO:
IPR020568
INTERPRO:
IPR014721
INTERPRO:
IPR008269
MODBASE:
P75867
PANTHER:
PTHR10046
PFAM:
PF13654
PFAM:
PF05362
PRIDE:
P75867
PROSITE:
PS51786
REFSEQ:
NP_415475
SMR:
P75867
SWISSMODEL:
P75867
UNIPROT:
P75867


Operon      
Name: ycbZ         
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 TSS_1249 1016472 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1250 1016488 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1251 (cluster) 1016497 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_1252 1016859 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1253 1017045 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1254 1017052 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1255 (cluster) 1017834 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_1256 1017837 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1257 1017843 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1258 1018324 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1259 (cluster) 1018330 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter ycbZp4 1018460 reverse Similarity to the consensus
Read more >
[ICWHO] [2]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] 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.

 [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


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