RegulonDB RegulonDB 10.10: Gene Form
   

ybdK gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybdK ybdJ sokE LexA hokEp hokEp ybdKp3 ybdKp3 ybdJp3 ybdJp3 ybdJp2 ybdJp2 ybdJp5 ybdJp5 ybdJp4 ybdJp4 ybdFp5 ybdFp5

Gene      
Name: ybdK    Texpresso search in the literature
Synonym(s): ECK0573, G6326, b0581
Genome position(nucleotides): 606265 <-- 607383 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.92
External database links:  
ASAP:
 ABE-0001992
ECHOBASE:
 EB3408
ECOLIHUB:
 ybdK
OU-MICROARRAY:
 b0581
STRING:
 511145.b0581
COLOMBOS: ybdK


Product      
Name: carboxylate-amine ligase
Synonym(s): YbdK
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 41.688
Isoelectric point: 6.122
Motif(s):
 
Type Positions Sequence
14 -> 292 LGIELEMQVVNPPGYDLSQDSSMLIDAVKNKITAGEVKHDITESMLELATDVCRDINQAAGQFSAMQKVVLQAATDHHLEICGGGTHPFQKWQRQEVCDNERYQRTLENFGYLIQQATVFGQHVHVGCASGDDAIYLLHGLSRFVPHFIALSAASPYMQGTDTRFASSRPNIFSAFPDNGPMPWVSNWQQFEALFRCLSYTTMIDSIKDLHWDIRPSPHFGTVEVRVMDTPLTLSHAVNMAGLIQATAHWLLTERPFKHQEKDYLLYKFNRFQACRYGL

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003824 - catalytic activity
GO:0016874 - ligase activity
GO:0016879 - ligase activity, forming carbon-nitrogen bonds
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0004357 - glutamate-cysteine ligase activity
biological_process GO:0042398 - cellular modified amino acid biosynthetic process
External database links:  
ECOCYC:
 G6326-MONOMER
ECOLIWIKI:
 b0581
INTERPRO:
 IPR014746
INTERPRO:
 IPR011793
INTERPRO:
 IPR006336
PDB:
 1R8G
PFAM:
 PF04107
PRIDE:
 P77213
REFSEQ:
 NP_415113
SMR:
 P77213
UNIPROT:
 P77213


Operon      
Name: ybdK         
Operon arrangement:
Transcription unit        Promoter
ybdK


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 ybdFp5 606053 reverse nd [ICWHO] [1]
  promoter ybdJp4 606223 reverse nd [ICWHO] [1]
  promoter ybdJp5 606264 reverse nd [ICWHO] [1]
  promoter ybdJp2 606405 reverse nd [ICWHO] [1]
  promoter ybdJp3 606411 reverse nd [ICWHO] [1]
  promoter ybdKp3 607561 reverse nd [ICWHO] [1]


Evidence    

 [ICWHO] Inferred computationally without human oversight


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

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