RegulonDB RegulonDB 10.9: Gene Form
   

waaY gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

waaJ waaZ waaY SoxS MarA waaYp waaYp TSS_4209 TSS_4209 waaUp8 waaUp8 waaUp6 waaUp6 waaUp5 waaUp5 waaUp9 waaUp9

Gene      
Name: waaY    Texpresso search in the literature
Synonym(s): ECK3615, EG11425, b3625, rfaY
Genome position(nucleotides): 3800267 <-- 3800965 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
35.34
External database links:  
ASAP:
ABE-0011856
CGSC:
33828
ECHOBASE:
EB1395
ECOLIHUB:
rfaY
NCBI-GENE:
948145
OU-MICROARRAY:
b3625
STRING:
511145.b3625
COLOMBOS: waaY


Product      
Name: lipopolysaccharide core heptose (II) kinase
Synonym(s): L-glycero-D-manno-heptose (II) kinase, RfaY, WaaY
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 27.461
Isoelectric point: 10.218
Motif(s):
 
Type Positions Sequence
1 -> 229 MIQKSKIKDLVVFTDENNSKYLNVLNDFLSYNINIIKVFRSIDDTKVMLIDTDYGKLILKVFSPKVKRNERFFKSLLKGDYYERLFEQTQKVRNEGLNTLNDFYLLAERKTLRFVHTYIMIIEYIDGIELCDMPDIDDALKNKIQQSINALHQHGMVSGDPHRGNFIIKNGEVRIIDLSGKRASAQRKAKDRIDLERHYGIKNEIRDLGYYLLVYRKKMRNFMRRLKGK
51 -> 52 DT
145 -> 146 QQ

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents) --> 1.6.3 - lipopolysaccharide --> 1.6.3.2 - core region
  6 - cell structure --> 6.3 - surface antigens (ECA, O antigen of LPS)
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0016740 - transferase activity
GO:0016301 - kinase activity
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
biological_process GO:0009103 - lipopolysaccharide biosynthetic process
GO:0009244 - lipopolysaccharide core region biosynthetic process
GO:0016310 - phosphorylation
GO:0046835 - carbohydrate phosphorylation
Note(s): Note(s): ...[more].
Reference(s): [1] Klena JD., et al., 1992
[2] Ren G., et al., 2016
[3] Roncero C., et al., 1992
[4] Wang Z., et al., 2015
External database links:  
ECOCYC:
EG11425-MONOMER
ECOLIWIKI:
b3625
INTERPRO:
IPR009330
INTERPRO:
IPR011009
PFAM:
PF06176
PRIDE:
P27240
PRODB:
PRO_000023727
REFSEQ:
NP_418082
UNIPROT:
P27240


Operon      
Name: rirA-waaQGPSBOJYZU         
Operon arrangement:
Transcription unit        Promoter
rfaYZ
rfaQGPSBIJYZ-waaU
rirA-rfaQGPSBIJYZ-waaU
rfaZ-waaU


Transcriptional Regulation      
Display Regulation             
Activated by: MarA, SoxS


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 waaUp9 3799398 reverse Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter waaUp5 3799424 reverse Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter waaUp6 3799496 reverse Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter waaUp8 3799498 reverse Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter TSS_4209 3800612 reverse nd [RS-EPT-CBR] [6]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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



Reference(s)    

 [1] Klena JD., Ashford RS., Schnaitman CA., 1992, Role of Escherichia coli K-12 rfa genes and the rfp gene of Shigella dysenteriae 1 in generation of lipopolysaccharide core heterogeneity and attachment of O antigen., J Bacteriol 174(22):7297-307

 [2] Ren G., Wang Z., Li Y., Hu X., Wang X., 2016, Effects of Lipopolysaccharide Core Sugar Deficiency on Colanic Acid Biosynthesis in Escherichia coli., J Bacteriol 198(11):1576-84

 [3] Roncero C., Casadaban MJ., 1992, Genetic analysis of the genes involved in synthesis of the lipopolysaccharide core in Escherichia coli K-12: three operons in the rfa locus., J Bacteriol 174(10):3250-60

 [4] Wang Z., Wang J., Ren G., Li Y., Wang X., 2015, Influence of Core Oligosaccharide of Lipopolysaccharide to Outer Membrane Behavior of Escherichia coli., Mar Drugs 13(6):3325-39

 [5] 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

 [6] 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.


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