TB Genome Annotation Portal

Rv2833c (ugpB)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: sn-glycerol 3-phosphate transporter substrate-binding protein
  • REFSEQ: sn-glycerol-3-phosphate-binding lipoprotein UGPB
  • PATRIC: Glycerol-3-phosphate ABC transporter periplasmic glycerol-3-phosphate-binding protein (TC 3.A.1.1.3)
  • TUBERCULIST: Probable Sn-glycerol-3-phosphate-binding lipoprotein UgpB
  • NCBI: Probable Sn-glycerol-3-phosphate-binding lipoprotein UgpB
  • updated information (H37Rv4):
    • gene name: ugpB
    • function:
    • reference:
• Type: Not Target
• Start: 3139174
• End: 3140484
• Operon:


• Trans-membrane region:
  
• Role: III.A.3 - Carbohydrates, organic acids and alcohols
• GO terms:
  • GO:0040007 - growth (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • PI[c] -> GL3P[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
  6R1B	100%	Mycobacterium tuberculosis	Crystal structure of UgpB from Mycobacterium tuberculosis in complex with glycerophosphocholine
  6R1B	100%	Mycobacterium tuberculosis	Crystal structure of UgpB from Mycobacterium tuberculosis in complex with glycerophosphocholine
  4MFI	100%	Mycobacterium tuberculosis	Crystal structure of Mycobacterium tuberculosis UgpB
  6R1B	96%	Mycobacterium tuberculosis	Crystal structure of UgpB from Mycobacterium tuberculosis in complex with glycerophosphocholine
  6R1B	96%	Mycobacterium tuberculosis	Crystal structure of UgpB from Mycobacterium tuberculosis in complex with glycerophosphocholine

• Links to additional information on ugpB:
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.997 (from Jeremy Rock's lab)

Amino Acid Sequence

MDPLNRRQFLALAAAAAGVTAGCAGMGGGGSVKSGSGPIDFWSSHPGQSSAAERELIGRFQDRFPTLSVKLIDAGKDYDEVAQKFNAALIGTDVPDVVLL
DDRWWFHFALSGVLTALDDLFGQVGVDTTDYVDSLLADYEFNGRHYAVPYARSTPLFYYNKAAWQQAGLPDRGPQSWSEFDEWGPELQRVVGAGRSAHGW
ANADLISWTFQGPNWAFGGAYSDKWTLTLTEPATIAAGNFYRNSIHGKGYAAVANDIANEFATGILASAVASTGSLAGITASARFDFGAAPLPTGPDAAP
ACPTGGAGLAIPAKLSEERKVNALKFIAFVTNPTNTAYFSQQTGYLPVRKSAVDDASERHYLADNPRARVALDQLPHTRTQDYARVFLPGGDRIISAGLE
SIGLRGADVTKTFTNIQKRLQVILDRQIMRKLAGHG

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)	1.96 (0.55)	1.9 (0.87)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link