TB Genome Annotation Portal

Rv1664 (pks9)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: polyketide synthase pks9
  • REFSEQ: polyketide synthase pks9
  • PATRIC: Polyketide synthase
  • TUBERCULIST: Probable polyketide synthase Pks9
  • NCBI: Probable polyketide synthase Pks9
  • updated information (H37Rv4):
    • gene name: pks9
    • function:
    • reference:
• Type: Not Target
• Start: 1888026
• End: 1891079
• Operon:


• Trans-membrane region:
  
• Role: I.I - Polyketide and non-ribosomal peptide synthesis
• GO terms:
  • GO:0031177 - phosphopantetheine binding (Uniprot)
  • GO:0016740 - transferase activity (Uniprot)
  • GO:0008152 - metabolic process (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
  6H0Q	45%	Mycobacterium ulcerans (strain Agy99)	B1-type ACP domain from module 7 of MLSB
  6IYO	44%	Streptomyces albus subsp. albus	Crystal Structure of the acyltransferase domain from the second module of the salinomycin polyketide synthase
  2JU2	43%	Saccharopolyspora erythraea	Minimized mean solution structure of the acyl carrier protein domain from module 2 of 6-deoxyerythronolide B synthase (DEBS)
  2JU1	43%	Saccharopolyspora erythraea	Solution structure of acyl carrier protein domain from module 2 of 6-deoxyerythronolide B synthase (DEBS)
  5HVC	43%	Mycobacterium ulcerans	Solution structure of the apo state of the acyl carrier protein from the MLSA2 subunit of the mycolactone polyketide synthase
  5HV8	43%	Mycobacterium ulcerans	Solution structure of an octanoyl- loaded acyl carrier protein domain from module MLSA2 of the mycolactone polyketide synthase.
  6H0J	43%	Mycobacterium ulcerans (strain Agy99)	A1-type ACP domain from module 5 of MLSA1
  4QYR	40%	Streptomyces platensis subsp. rosaceus	Streptomyces platensis isomigrastatin ketosynthase domain MgsE KS3
  4MZ0	40%	Moorea producens 3L	Structure of a ketosynthase-acyltransferase di-domain from module CurL of the curacin A polyketide synthase
  4RL1	39%	Streptomyces avermitilis	Structural and functional analysis of a loading acyltransferase from the avermectin modular polyketide synthase

• Links to additional information on pks9:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.857 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VQPTGIAIIGLACRFPTVVSPGDLWDLLRDGREAAGSIDNVADFDADFFNLSPREASAMDPRQRLALELTWELLEDAFVVPETLRGQPIAVYLGAMNDDY
AVLTLAADRVDHHAFAGTSRAIIANRVSFAFGLRGPSVTIDSGQSSSLVAVHLACESVRTGEAPLAIAGGVHLNLARETAMLEQEFGAVSPSGHTYAFDE
RADGYVPGDGGGLVLLKPVQAALDDGDRIHAIIRGSAVGNAGHSATGLTVPSVAGQVDVIRRAMSGAGVDCHQVHYVEAHGTGTKIGDPIEARALGEIFA
ARQRRPVSVGSVKTNIGHTGGAAGIAGLLKAVLAIENAVIPPSLNYVGAAIDLDSLGLRVDTALTPWPVADEPRRAGVSSFGMGGTNAHVILEQGPTQSP
EIVESVAAAGSNAPVAVPWVLAARSPQALTNQAGRLLAHLTADDGLTALDVGWSLVSTRSVFDHRAVVVGADRGRLMAGLAGLAAGEPGAGVVVGRARSV
GKTVFVFPGQGSQWLGMGRQLYGRYSVFARAFDEVVAVLDGQLRLSVRQVMWGADAGLLESTEFAQPALFVVQVALAALLQDWGVLPDLVMGHSVGEIAA
AYVAGALSLVDAARVVAARGRLMQALPAGGVMVAVAASEDEVAPLLTEGVCIAAVNAPESVVISGEQAAVGVVVDRLVGLGRRVRRLAVSHAFHSVLMDP
MVEEFSKVLADVCVRAPRIGLVSNVTGQLAGAGYGSPAYWVEHVRKPVRFFDGVGLAESLGARVFVEVGPGAGLEASVALLARDRPEVESVLAGVGRLFA
EGVAVDWSSVFAGLGGRRVELPTYGFARQRFWLGDNGELSVDQTGKDAGAIARLQSLAPPELQRQLVELVCFHAAIVLGRKSSHDIDPECAFQDLGFDSM
SGVELRNRLQMAIGLPGLSLPRTLIFDYPTASALAECLGQLLGGQHESSDDESIWQLLKNIPIHQLRRTGLLDKLLLLAGQPEESLAGRTVSDEVIDSLS
PEALIGLALDEDENDIR

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 (0.63)	1.86 (0.93)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link