TB Genome Annotation Portal

Rv0516c (-)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: anti-anti-sigma factor
  • REFSEQ: hypothetical protein
  • PATRIC: Anti-sigma F factor antagonist (spoIIAA-2); Anti-sigma B factor antagonist RsbV
  • TUBERCULIST: Possible anti-anti-sigma factor
  • NCBI: Possible anti-anti-sigma factor
  • updated information (H37Rv4):
    • gene name: oprA
    • function: SigF anti-anti穆igma factor; phosphorylated by PknD; osmosensory signaling pathway
    • reference: Greenstein (2007) PMID: 17411339; Hatzios (2013) PMID: 24309377
• Type: Not Target
• Start: 608059
• End: 608535
• Operon:


• Trans-membrane region:
  
• Role: V - Conserved hypotheticals
• GO terms:
  • GO:0005515 - protein binding (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): (none with >35% aa id)
• Links to additional information on Rv0516c:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.475 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MTTTIPTSKSACSVTTRPGNAAVDYGGAQIRAYLHHLATVVTIRGEIDAANVEQISEHVRRFSLGTNPMVLDLSELSHFSGAGISLLCILDEDCRAAGVQ
WALVASPAVVEQLGGRCDQGEHESMFPMARSVHKALHDLADAIDRRRQLVLPLISRSA

Additional Information

Rv0516c - SigF anti-anti–sigma factor (renamed OprA)

phosphorylated by PknD

Greenstein et al (2007). M. tuberculosis Ser/Thr Protein Kinase D Phosphorylates an Anti-Anti–Sigma Factor Homolog. PLOS Pathogens.
https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.0030049

Hatzios et al renamed Rv0516c as OprA, due to its involvement in an
osmosensory signaling pathway including PknD and SigF, which regulates
peptidoglycan architecture:

Hatzios, S. K. et al. (2013). Osmosensory signaling in Mycobacterium tuberculosis
mediated by a eukaryotic-like Ser/Thr protein kinase. PNAS 110, E5069-5077.
https://www.pnas.org/content/110/52/E5069

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)	0.95 (0.09)	1.13 (0.48)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link