TB Genome Annotation Portal

Rv3541c (-)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: hypothetical protein
  • REFSEQ: hypothetical protein
  • PATRIC: Enoyl coenzyme A hydratase IgrE
  • TUBERCULIST: Conserved protein
  • NCBI: hypothetical protein
  • updated information (H37Rv4):
    • gene name: chsH1
    • function:
    • reference: Thomas (2013) PMID: 23560677
• Type: Conditional
• Start: 3980659
• End: 3981048
• Operon:


• Trans-membrane region:
  
• Role: VI - Unknowns
• GO terms:
  • No terms assigned.
• Reaction(s) (based on iSM810 metabolic model):
  • 3OXO23_24BISNORCHOL4_17DIEN22OYL_COA[c] -> 3OXO23_24BISNORCHOL4EN17OL22OYL_COA[c]
• 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
  4WNB	100%	Mycobacterium tuberculosis C	Crystal structure of the ChsH1-ChsH2 complex from Mycobacterium tuberculosis bound to 3-OPC-CoA
  4W78	100%	Mycobacterium tuberculosis SUMu008	Crystal structure of the ChsH1-ChsH2 complex from Mycobacterium tuberculosis

• Links to additional information on Rv3541c:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.129 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MTVVGAVLPELKLYGDPTFIVSTALATRDFQDVHHDRDKAVAQGSKDIFVNILTDTGLVQRYVTDWAGPSALIKSIGLRLGVPWYAYDTVTFSGEVTAVN
DGLITVKVVGRNTLGDHVTATVELSMRDS

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)	1.4 (0.09)	1.18 (0.32)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link