TB Genome Annotation Portal

Rv2549c (vapC20)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: toxin
  • REFSEQ: hypothetical protein
  • PATRIC: hypothetical protein Rv2549c
  • TUBERCULIST: Possible toxin VapC20
  • NCBI: Possible toxin VapC20
  • updated information (H37Rv4):
    • gene name: vapC20
    • function:
    • reference:
• Type: Not Target
• Start: 2869727
• End: 2870122
• Operon:


• Trans-membrane region:
  
• Role: VI - Unknowns
• GO terms:
  • GO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic (Uniprot)
  • GO:0090501 - RNA phosphodiester bond hydrolysis (Uniprot)
  • GO:0090305 - nucleic acid phosphodiester bond hydrolysis (Uniprot)
  • GO:0046872 - metal ion binding (Uniprot)
  • GO:0045926 - negative regulation of growth (Uniprot)
  • GO:0016787 - hydrolase activity (Uniprot)
  • GO:0016075 - rRNA catabolic process (Uniprot)
  • GO:0005515 - protein binding (Uniprot)
  • GO:0004540 - ribonuclease activity (Uniprot)
  • GO:0004521 - endoribonuclease activity (Uniprot)
  • GO:0004519 - endonuclease activity (Uniprot)
  • GO:0004518 - nuclease 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
  5WZF	100%	Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)	Crystal structure of Mycobacterium tuberculosis VapC20 (Rv2549c), Sarcin-Ricin loop cleaving toxin
  5WZF	100%	Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)	Crystal structure of Mycobacterium tuberculosis VapC20 (Rv2549c), Sarcin-Ricin loop cleaving toxin
  5WZ4	99%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mycobacterium tuberculosis VapC20 (Rv2549c), Sarcin-Ricin loop cleaving toxin

• Links to additional information on vapC20:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.642 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MIFVDTSFWAALGNAGDARHGTAKRLWASKPPVVMTSNHVLGETWTLLNRRCGHRAAVAAAAIRLSTVVRVEHVTADLEEQAWEWLVRHDEREYSFVDAT
SFAVMRKKGIQNAYAFDGDFSAAGFVEVRPE

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)	1.44 (0.14)	2.01 (0.48)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link