TB Genome Annotation Portal

Rv0096 (PPE1)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: PPE family protein
  • REFSEQ: PPE family protein
  • PATRIC: PPE family protein
  • TUBERCULIST: PPE family protein PPE1
  • NCBI: PPE family protein PPE1
  • updated information (H37Rv4):
    • gene name: PPE1
    • function:
    • reference:
• Type: Conditional
• Start: 105324
• End: 106715
• Operon:


• Trans-membrane region:
  
• Role: IV.C.2 - PPE family
• GO terms:
  • GO:0016021 - integral component of membrane (Uniprot)
  • GO:0016020 - membrane (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0019563 - glycerol catabolic process (FLUTE) (FLUTE Assigned!)
• 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
  6VHR	64%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Structure of PE5-PPE4-EspG3 complex from the type VII (ESX-3) secretion system, space group I422
  6UUJ	64%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Structure of PE5-PPE4-EspG3 complex from the type VII (ESX-3) secretion system, space group P212121
  5XFS	38%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of PE8-PPE15 in complex with EspG5 from M. tuberculosis

• Links to additional information on PPE1:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.562 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MAIPPEVHSGLLSAGCGPGSLLVAAQQWQELSDQYALACAELGQLLGEVQASSWQGTAATQYVAAHGPYLAWLEQTAINSAVTAAQHVAAAAAYCSALAA
MPTPAELAANHAIHGVLIATNFFGINTVPIALNEADYVRMWLQAADTMAAYQAVADAATVAVPSTQPAPPIRAPGGDAADTRLDVLSSIGQLIRDILDFI
ANPYKYFLEFFEQFGFSPAVTVVLALVALQLYDFLWYPYYASYGLLLLPFFTPTLSALTALSALIHLLNLPPAGLLPIAAALGPGDQWGANLAVAVTPAT
AAVPGGSPPTSNPAPAAPSSNSVGSASAAPGISYAVPGLAPPGVSSGPKAGTKSPDTAADTLATAGAARPGLARAHRRKRSESGVGIRGYRDEFLDATAT
VDAATDVPAPANAAGSQGAGTLGFAGTAPTTSGAAAGMVQLSSHSTSTTVPLLPTTWTTDAEQ

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)	1.5 (0.34)	1.23 (0.63)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link