RegulonDB RegulonDB 10.7: Gene Form
   

ygbK 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: ygbK    Texpresso search in the literature
Synonym(s): ECK2732, G7418, b2737
Genome position(nucleotides): 2862335 --> 2863501 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
55.1
External database links:  
ASAP:
ABE-0008988
ECHOBASE:
EB2908
OU-MICROARRAY:
b2737
PORTECO:
ygbK
REGULONDB:
b2737
STRING:
511145.b2737
M3D: ygbK
COLOMBOS: ygbK
PortEco: b2737


Product      
Name: putative 3-oxo-tetronate kinase YgbK
Synonym(s): DUF1537 domain-containing protein YgbK, YgbK
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 41.339
Isoelectric point: 6.313
Motif(s):
 
Type Positions Sequence
253 -> 386 VVLSGSCSQMTNRQVAHYRQIAPAREVDVARCLSIETLAAYAHELAEWVLGQESVLAPLVFATASTDALAAIQQQYGAQKASQAVETLFSQLAARLAAEGVTRFIVAGGETSGVVTQSLGIKGFHIGPTISPAC
4 -> 227 IGVIADDFTGATDIASFLVENGLPTVQINGVPTGKMPEAIDALVISLKTRSCPVVEATQQSLAALSWLQQQGCKQIYFKYCSTFDSTAKGNIGPVTDALMDALDTPFTVFSPALPVNGRTVYQGYLFVMNQLLAESGMRHHPVNPMTDSYLPRLVEAQSTGRCGVVSAHVFEQGVDAVRQELARLQQEGYRYAVLDALTEHHLEIQGEALRDAPLVTGGSGLAI
360 -> 363 GGET

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
molecular_function GO:0016740 - transferase activity
GO:0016301 - kinase activity
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
biological_process GO:0005975 - carbohydrate metabolic process
GO:0016310 - phosphorylation
Note(s): Note(s): ...[more].
Reference(s): [1] Paradis-Bleau C., et al., 2014
[2] Zhang X., et al., 2016
External database links:  
DIP:
DIP-12112N
ECOCYC:
G7418-MONOMER
ECOLIWIKI:
b2737
INTERPRO:
IPR010737
INTERPRO:
IPR031475
INTERPRO:
IPR042213
INTERPRO:
IPR037051
MODBASE:
Q46889
PFAM:
PF07005
PFAM:
PF17042
PRIDE:
Q46889
PROTEINMODELPORTAL:
Q46889
REFSEQ:
NP_417217
SMR:
Q46889
SWISSMODEL:
Q46889
UNIPROT:
Q46889


Operon      
Name: ygbJK         
Operon arrangement:
Transcription unit        Promoter
ygbK
 


Transcriptional Regulation      
Display Regulation             
Activated by: FlhDC


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] [3]
  promoter ygbIp6 2861362 reverse Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter ygbIp5 2861441 reverse Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter ygbLp5 2863537 forward Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter ygbLp4 2863569 forward Similarity to the consensus
Read more >
[ICWHO] [4]


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] Paradis-Bleau C., Kritikos G., Orlova K., Typas A., Bernhardt TG., 2014, A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism., PLoS Genet 10(1):e1004056

 [2] 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

 [3] 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.

 [4] 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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