RegulonDB RegulonDB 10.8: Gene Form
   

ybjD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybjD macA ybjX aqpZ macB macBp2 macBp2 macBp1 macBp1 ybjXp ybjXp aqpZp2 aqpZp2 aqpZp3 aqpZp3

Gene      
Name: ybjD    Texpresso search in the literature
Synonym(s): ECK0867, G6459, b0876
Genome position(nucleotides): 916473 --> 918131 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.1
External database links:  
ASAP:
ABE-0002980
ECHOBASE:
EB3199
OU-MICROARRAY:
b0876
PortEco:
ybjD
STRING:
511145.b0876
COLOMBOS: ybjD


Product      
Name: DUF2813 domain-containing protein YbjD
Synonym(s): YbjD, conserved protein with a nucleotide triphosphate hydrolase domain YbjD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 63.589
Isoelectric point: 9.619
Motif(s):
 
Type Positions Sequence
29 -> 36 GENAWGKS
379 -> 469 RCWLLVEGETETWVINELARQCGHHFDAEGIKVIEFAQSGLKPLVKFARRMGIEWHVLVDGDEAGKKYAATVRSLLNNDREAEREHLTALP
1 -> 375 MILERVEIVGFRGINRLSLMLEQNNVLIGENAWGKSSLLDALTLLLSPESDLYHFERDDFWFPPGDINGREHHLHIILTFRESLPGRHRVRRYRPLEACWTPCTDGYHRIFYRLEGESAEDGSVMTLRSFLDKDGHPIDVEDINDQARHLVRLMPVLRLRDARFMRRIRNGTVPNVPNVEVTARQLDFLARELSSHPQNLSDGQIRQGLSAMVQLLEHYFSEQGAGQARYRLMRRRASNEQRSWRYLDIINRMIDRPGGRSYRVILLGLFATLLQAKGTLRLDKDARPLLLIEDPETRLHPIMLSVAWHLLNLLPLQRIATTNSGELLSLTPVEHVCRLVRESSRVAAWRLGPSGLSTEDSRRISFHIRFNRPSS

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
biological_process GO:0006302 - double-strand break repair
GO:0000731 - DNA synthesis involved in DNA repair
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-11446N
ECOCYC:
G6459-MONOMER
ECOLIWIKI:
b0876
INTERPRO:
IPR006171
INTERPRO:
IPR034139
INTERPRO:
IPR027417
INTERPRO:
IPR022602
MODBASE:
P75828
PFAM:
PF11398
PRIDE:
P75828
PROSITE:
PS50880
REFSEQ:
NP_415397
SMR:
P75828
UNIPROT:
P75828


Operon      
Name: ybjD         
Operon arrangement:
Transcription unit        Promoter
ybjD


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 aqpZp3 916133 reverse Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter aqpZp2 916212 reverse Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter macBp1 920094 forward The sigma factor was determined
Read more >
[AIPP] [2]
  promoter macBp2 920337 forward The sigma factor was determined
Read more >
[AIPP] [2]


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [AIPP] Automated inference of promoter position



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] Zhao K., Liu M., Burgess RR., 2005, The global transcriptional response of Escherichia coli to induced sigma 32 protein involves sigma 32 regulon activation followed by inactivation and degradation of sigma 32 in vivo., J Biol Chem 280(18):17758-68


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