TB Genome Annotation Portal

Rv1027c (kdpE)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: two-component system OmpR family KDP operon response regulator KdpE
  • REFSEQ: transcriptional regulatory protein KdpE
  • PATRIC: DNA-binding response regulator KdpE
  • TUBERCULIST: Probable transcriptional regulatory protein KdpE
  • NCBI: Probable transcriptional regulatory protein KdpE
  • updated information (H37Rv4):
    • gene name: kdpE
    • function:
    • reference:
• Type: Not Target
• Start: 1148427
• End: 1149107
• Operon:


• Trans-membrane region:
  
• Role: I.J.2 - Two component systems
• GO terms:
  • GO:0040007 - growth (Uniprot)
  • GO:0006355 - regulation of transcription, DNA-templated (Uniprot)
  • GO:0006351 - transcription, DNA-templated (Uniprot)
  • GO:0005737 - cytoplasm (Uniprot)
  • GO:0005515 - protein binding (Uniprot)
  • GO:0003677 - DNA binding (Uniprot)
  • GO:0000160 - phosphorelay signal transduction system (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
• Gene Expression Profile (Transcriptional Responses to Drugs; Boshoff et al, 2004)
• Gene Modules extracted from cluster analysis of 249 transcriptomic datasets using ICA
• Orthologs among selected mycobacteria
• Protein structure:
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  1ZH4	54%	Escherichia coli	Crystal Structure Of The Mg+2/BeF3-Bound Receiver Domain Of Kdp Potassium Transport System Response Regulator KdpE
  1ZH2	54%	Escherichia coli	Crystal Structure Of The Calcium-Bound Receiver Domain Of Kdp Potassium Transport System Response Regulator KdpE
  4L85	52%	Escherichia coli	Crystal structure of receiver domain of KdpE D52A mutant from E. coli
  4KNY	49%	Escherichia coli	Crystal structure of the response regulator KdpE complexed to DNA in an active-like conformation
  4KFC	48%	Escherichia coli	Crystal structure of a hyperactive mutant of response regulator KdpE complexed to its promoter DNA
  3ZQ7	46%	ESCHERICHIA COLI	The Structure of DNA-binding domain of response regulator from Escherichia coli K-12
  1MVO	45%	Bacillus subtilis	Crystal structure of the PhoP receiver domain from Bacillus subtilis
  3NHZ	44%	Mycobacterium tuberculosis	Structure of N-terminal Domain of MtrA
  6EB7	43%	Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)	YycF homologue (SP1227) Receiver Domain Activated by BeF3
  3F6P	43%	Bacillus subtilis	Crystal Structure of unphosphorelated receiver domain of YycF

• Links to additional information on kdpE:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.964 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MTLVLVIDDEPQILRALRINLTVRGYQVITASTGAGALRAAAEHPPDVVILDLGLPDMSGIDVLGGLRGWLTAPVIVLSARTDSSDKVQALDAGADDYVT
KPFGMDEFLARLRAAVRRNTAAAELEQPVIETDSFTVDLAGKKVIKDGAEVHLTPTEWGMLEMLARNRGKLVGRGELLKEVWGPAYATETHYLRVYLAQL
RRKLEDDPSHPKHLLTESGMGYRFEA

Additional Information

Analysis of Positive Selection in Clinical Isolates *new*

• Analysis of dN/dS (omega) in two collections of Mtb clinical isolates using GenomegaMap (Window model) (see description of methods)
  • Moldova: 2,057 clinical isolates
  • global set: 5,195 clinical isolates from 15 other countries
• In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
• A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.

	Moldova (2,057)	global set (5,195)
under significant positive selection?	NO	NO
omega peak height (95%CI lower bound)	1.43 (0.27)	1.03 (0.46)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link