TB Genome Annotation Portal

Rv1660 (pks10)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: chalcone synthase
  • REFSEQ: chalcone synthase
  • PATRIC: Chalcone synthase (EC 2.3.1.74)
  • TUBERCULIST: Chalcone synthase Pks10
  • NCBI: Chalcone synthase Pks10
  • updated information (H37Rv4):
    • gene name: pks10
    • function:
    • reference:
• Type: Not Target
• Start: 1874160
• End: 1875221
• Operon:


• Trans-membrane region:
  
• Role: I.I - Polyketide and non-ribosomal peptide synthesis
• GO terms:
  • GO:0071770 - DIM/DIP cell wall layer assembly (Uniprot)
  • GO:0034081 - polyketide synthase complex (Uniprot)
  • GO:0016747 - transferase activity, transferring acyl groups other than amino-acyl groups (Uniprot)
  • GO:0016746 - transferase activity, transferring acyl groups (Uniprot)
  • GO:0016740 - transferase activity (Uniprot)
  • GO:0009058 - biosynthetic process (Uniprot)
  • GO:0008610 - lipid biosynthetic process (Uniprot)
  • GO:0008152 - metabolic process (Uniprot)
  • GO:0006633 - fatty acid biosynthetic process (Uniprot)
  • GO:0006631 - fatty acid metabolic process (Uniprot)
  • GO:0006629 - lipid metabolic process (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0003824 - catalytic activity (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
  4JAR	73%	Mycobacterium tuberculosis	Crystal structure of mycobacterium tuberculosis pks11 in complex with polyketide intermediates and evidence that it synthesize ALKYLPYRONES
  4JAQ	73%	Mycobacterium tuberculosis	Crystal Structure of Mycobacterium tuberculosis PKS11 Reveals Intermediates in the Synthesis of Methyl-branched Alkylpyrones
  4JAP	73%	Mycobacterium tuberculosis	Crystal Structure of Mycobacterium tuberculosis PKS11 Reveals Intermediates in the Synthesis of Methyl-branched Alkylpyrones
  4JAO	73%	Mycobacterium tuberculosis	Crystal Structure of Mycobacterium tuberculosis PKS11 Reveals Intermediates in the Synthesis of Methyl-branched Alkylpyrones
  4JD3	73%	Mycobacterium tuberculosis	Crystal Structure of Mycobacterium tuberculosis PKS11 Reveals Intermediates in the Synthesis of Methyl-branched Alkylpyrones
  4JAT	73%	Mycobacterium tuberculosis	Crystal Structure of Mycobacterium tuberculosis PKS11 Reveals Intermediates in the Synthesis of Methyl-branched Alkylpyrones

• Links to additional information on pks10:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 1.046 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VSVIAGVFGALPPYRYSQRELTDSFVSIPDFEGYEDIVRQLHASAKVNSRHLVLPLEKYPKLTDFGEANKIFIEKAVDLGVQALAGALDESGLRPEDLDV
LITATVTGLAVPSLDARIAGRLGLRADVRRVPLFGLGCVAGAAGVARLHDYLRGAPDGVAALVSVELCSLTYPGYKPTLPGLVGSALFADGAAAVVAAGV
KRAQDIGADGPDILDSRSHLYPDSLRTMGYDVGSAGFELVLSRDLAAVVEQYLGNDVTTFLASHGLSTTDVGAWVTHPGGPKIINAITETLDLSPQALEL
TWRSLGEIGNLSSASVLHVLRDTIAKPPPSGSPGLMIAMGPGFCSELVLLRWH

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)	2.11 (0.45)	1.57 (0.85)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link