TB Genome Annotation Portal

Rv3343c (PPE54)

• 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 PPE54
  • NCBI: PPE family protein PPE54
  • updated information (H37Rv4):
    • gene name: PPE54
    • function:
    • reference:
• Type: Essential
• Start: 3729364
• End: 3736935
• Operon:


• Trans-membrane region:
  
• Role: IV.C.2 - PPE family
• GO terms:
  • GO:0052170 - negative regulation by symbiont of host innate immune response (Uniprot)
  • GO:0040007 - growth (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
  5XFS	52%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of PE8-PPE15 in complex with EspG5 from M. tuberculosis
  6VHR	41%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Structure of PE5-PPE4-EspG3 complex from the type VII (ESX-3) secretion system, space group I422
  6UUJ	41%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Structure of PE5-PPE4-EspG3 complex from the type VII (ESX-3) secretion system, space group P212121

• Links to additional information on PPE54:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.995 (from Jeremy Rock's lab)
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology
  • KEGG - nucleotide and amino acid sequences of gene

Amino Acid Sequence

MSFVVMPPEINSLLIYTGAGPGPLLAAAAAWDELAAELGSAAAAFGSVTSGLVGGIWQGPSSVAMAAAAAPYAGWLSAAAASAESAAGQARAVVGVFEAA
LAETVDPFVIAANRSRLVSLALSNLFGQNTPAIAAAEFDYELMWAQDVAAMLGYHTGASAAAEALAPFGSPLASLAAAAEPAKSLAVNLGLANVGLFNAG
SGNVGSYNVGAGNVGSYNVGGGNIGGNNVGLGNVGWGNFGLGNSGLTPGLMGLGNIGFGNAGSYNFGLANMGVGNIGFANTGSGNFGIGLTGDNLTGFGG
FNTGSGNVGLFNSGTGNVGFFNSGTGNWGVFNSGSYNTGIGNSGIASTGLFNAGGFNTGVVNAGSYNTGSFNAGEANTGGFNPGSVNTGWLNTGDINTGV
ANSGDVNTGAFISGNYSNGVLWRGDYQGLLGFSSGANVLPVIPLSLDINGGVGAITIEPIHILPDIPININETLYLGPLVVPPINVPAISLGVGIPNISI
GPIKINPITLWPAQNFNQTITLAWPVSSITIPQIQQVALSPSPIPTTLIGPIHINTGFSIPVTFSYSTPALTLFPVGLSIPTGGPLTLTLGVTAGTEAFT
IPGFSIPEQPLPLAINVIGHINALSTPAITIDNIPLNLHAIGGVGPVDIVGGNVPASPGFGNSTTAPSSGFFNTGAGGVSGFGNVGAHTSGWFNQSTQAM
QVLPGTVSGYFNSGTLMSGIGNVGTQLSGMLSGGALGGNNFGLGNIGFDNVGFGNAGSSNFGLANMGIGNIGLANTGNGNIGIGLSGDNLTGFGGFNSGS
ENVGLFNSGTGNVGFFNSGTGNLGVFNSGSHNTGFFLTGNNINVLAPFTPGTLFTISEIPIDLQVIGGIGPIHVQPIDIPAFDIQITGGFIGIREFTLPE
ITIPAIPIHVTGTVGLEGFHVNPAFVLFGQTAMAEITADPVVLPDPFITIDHYGPPLGPPGAKFPSGSFYLSISDLQINGPIIGSYGGPGTIPGPFGATF
NLSTSSLALFPAGLTVPDQTPVTVNLTGGLDSITLFPGGLAFPENPVVSLTNFSVGTGGFTVFPQGFTVDRIPVDLHTTLSIGPFPFRWDYIPPTPANGP
IPAVPGGFGLTSGLFPFHFTLNGGIGPISIPTTTVVDALNPLLTVTGNLEVGPFTVPDIPIPAINFGLDGNVNVSFNAPATTLLSGLGITGSIDISGIQI
TNIQTQPAQLFMSVGQTLFLFDFRDGIELNPIVIPGSSIPITMAGLSIPLPTVSESIPLNFSFGSPASTVKSMILHEILPIDVSINLEDAVFIPATVLPA
IPLNVDVTIPVGPINIPIITEPGSGNSTTTTSDPFSGLAVPGLGVGLLGLFDGSIANNLISGFNSAVGIVGPNVGLSNLGGGNVGLGNVGDFNLGAGNVG
GFNVGGGNIGGNNVGLGNVGFGNVGLANSGLTPGLMGLGNIGFGNAGSYNFGLANMGVGNIGFANTGSGNFGIGLTGDNLTGFGGFNTGSGNVGLFNSGT
GNVGFFNSGTGNWGVFNSGSYNTGIGNSGIASTGLFNAGGFNTGVVNAGSYNTGSFNAGQANTGGFNPGSVNTGWLNTGDINTGVANSGDVNTGAFISGN
YSNGAFWRGDYQGLLGFSYRPAVLPQTPFLDLTLTGGLGSVVIPAIDIPAIRPEFSANVAIDSFTVPSIPIPQIDLAATTVSVGLGPITVPHLDIPRVPV
TLNYLFGSQPGGPLKIGPITGLFNTPIGLTPLALSQIVIGASSSQGTITAFLANLPFSTPVVTIDEIPLLASITGHSEPVDIFPGGLTIPAMNPLSINLS
GGTGAVTIPAITIGEIPFDLVAHSTLGPVHILIDLPAVPGFGNTTGAPSSGFFNSGAGGVSGFGNVGAMVSGGWNQAPSALLGGGSGVFNAGTLHSGVLN
FGSGMSGLFNTSVLGLGAPALVSGLGSVGQQLSGLLASGTALHQGLVLNFGLADVGLGNVGLGNVGDFNLGAGNVGGFNVGGGNIGGNNVGLGNVGWGNF
GLGNSGLTPGLMGLGNIGFGNAGSYNFGLANMGVGNIGFANTGSGNFGIGLTGDNLTGFGGFNTGSGNVGLFNSGTGNVGFFNSGTGNWGVFNSGSYNTG
IGNSGIASTGLFNAGGFNTGVVNAGSYNTGSFNAGQANTGGFNPGSVNTGWLNTGDINTGVANSGDVNTGAFISGNYSNGAFWRGDYQGLLGFSYTSTII
PEFTVANIHASGGAGPIIVPSIQFPAIPLDLSATGHIGGFTIPPVSISPITVRIDPVFDLGPITVQDITIPALGLDPATGVTVGPIFSSGSIIDPFSLTL
LGFINVNVPAIQTAPSEILPFTVLLSSLGVTHLTPEITIPGFHIPVDPIHVELPLSVTIGPFVSPEITIPQLPLGLALSGATPAFAFPLEITIDRIPVVL
DVNALLGPINAGLVIPPVPGFGNTTAVPSSGFFNIGGGGGLSGFHNLGAGMSGVLNAISDPLLGSASGFANFGTQLSGILNRGADISGVYNTGALGLITS
ALVSGFGNVGQQLAGLIYTGTGP

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?	YES	YES
omega peak height (95%CI lower bound)	3.55 (1.89)	2.43 (1.13)
codons under selection	215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 1997, 1998, 1999	1419, 1420, 1421, 1422
omega plots
genetic variants*	link	link
statistics at each codon	link	link