RegulonDB RegulonDB 10.7: Gene Form
   

ygbJ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ygbK ygbJ ygbI ygbL ygbLp4 ygbLp4 ygbLp5 ygbLp5 ygbKp ygbKp ygbIp5 ygbIp5 ygbIp6 ygbIp6 TSS_3025 TSS_3025

Gene      
Name: ygbJ    Texpresso search in the literature
Synonym(s): ECK2731, G7417, b2736
Genome position(nucleotides): 2861430 --> 2862338 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.03
External database links:  
ASAP:
ABE-0008986
ECHOBASE:
EB2907
OU-MICROARRAY:
b2736
PORTECO:
ygbJ
REGULONDB:
b2736
STRING:
511145.b2736
M3D: ygbJ
COLOMBOS: ygbJ
PortEco: b2736


Product      
Name: putative L-threonate dehydrogenase
Synonym(s): YgbJ, putative dehydrogenase, with NAD(P)-binding Rossmann-fold domain
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 30.751
Isoelectric point: 4.914
Motif(s):
 
Type Positions Sequence
7 -> 35 FHVGIVGLGSMGMGAALSYVRAGLSTWGA
172 -> 291 GLGSTVKIIHQLLAGVHIAAGAEAMALAARAGIPLDVMYDVVTNAAGNSWMFENRMRHVVDGDYTPHSAVDIFVKDLGLVADTAKALHFPLPLASTALNMFTSASNAGYGKEDDSAVIKI
9 -> 166 VGIVGLGSMGMGAALSYVRAGLSTWGADLNSNACATLKEAGACGVSDNAATFAEKLDALLVLVVNAAQVKQVLFGETGVAQHLKPGTAVMVSSTIASADAQEIATALAGFDLEMLDAPVSGGAVKAANGEMTVMASGSDIAFERLAPVLEAVAGKVYR

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0016491 - oxidoreductase activity
GO:0050661 - NADP binding
GO:0051287 - NAD binding
biological_process GO:0005975 - carbohydrate metabolic process
GO:0055114 - oxidation-reduction process
Note(s): Note(s): ...[more].
Reference(s): [1] Zhang X., et al., 2016
External database links:  
ECOCYC:
G7417-MONOMER
ECOLIWIKI:
b2736
INTERPRO:
IPR006115
INTERPRO:
IPR002204
INTERPRO:
IPR036291
INTERPRO:
IPR008927
INTERPRO:
IPR013328
INTERPRO:
IPR015815
INTERPRO:
IPR029154
MODBASE:
Q46888
PANTHER:
PTHR22981
PFAM:
PF03446
PFAM:
PF14833
PRIDE:
Q46888
PROSITE:
PS00895
PROTEINMODELPORTAL:
Q46888
REFSEQ:
NP_417216
SMR:
Q46888
UNIPROT:
Q46888


Operon      
Name: ygbJK         
Operon arrangement:
Transcription unit        Promoter
ygbK
 


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_3025 2861256 reverse nd [RS-EPT-CBR] [2]
  promoter ygbIp6 2861362 reverse Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter ygbIp5 2861441 reverse Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter ygbLp5 2863537 forward Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter ygbLp4 2863569 forward Similarity to the consensus
Read more >
[ICWHO] [3]


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] Zhang X., Carter MS., Vetting MW., San Francisco B., Zhao S., Al-Obaidi NF., Solbiati JO., Thiaville JJ., de Crecy-Lagard V., Jacobson MP., Almo SC., Gerlt JA., 2016, Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars., Proc Natl Acad Sci U S A 113(29):E4161-9

 [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.

 [3] 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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