TB Genome Annotation Portal

Rv2188c (pimB)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase
  • REFSEQ: hypothetical protein
  • PATRIC: Poly(glycerol-phosphate) alpha-glucosyltransferase (EC 2.4.1.52)
  • TUBERCULIST: Mannosyltransferase PimB
  • NCBI: Mannosyltransferase PimB
  • updated information (H37Rv4):
    • gene name: pimB
    • function:
    • reference:
• Type: Essential
• Start: 2449993
• End: 2451150
• Operon:


• Trans-membrane region:
  
• Role: V - Conserved hypotheticals
• GO terms:
  • GO:0097502 - mannosylation (Uniprot)
  • GO:0046488 - phosphatidylinositol metabolic process (Uniprot)
  • GO:0043750 - phosphatidylinositol alpha-mannosyltransferase activity (Uniprot)
  • GO:0040007 - growth (Uniprot)
  • GO:0033164 - glycolipid 6-alpha-mannosyltransferase activity (Uniprot)
  • GO:0016757 - transferase activity, transferring glycosyl groups (Uniprot)
  • GO:0016740 - transferase activity (Uniprot)
  • GO:0009405 - pathogenesis (Uniprot)
  • GO:0009247 - glycolipid biosynthetic process (Uniprot)
  • GO:0008654 - phospholipid biosynthetic process (Uniprot)
  • GO:0006629 - lipid metabolic process (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0000030 - mannosyltransferase 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
  3OKP	50%	Corynebacterium glutamicum	Crystal structure of Corynebacterium glutamicum PimB' bound to GDP-Man (orthorhombic crystal form)
  3OKC	50%	Corynebacterium glutamicum	Crystal structure of Corynebacterium glutamicum PimB' bound to GDP (orthorhombic crystal form)
  3OKA	50%	Corynebacterium glutamicum	Crystal structure of Corynebacterium glutamicum PimB' in complex with GDP-Man (triclinic crystal form)

• Links to additional information on pimB:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -2.75 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VSRVLLVTNDFPPRRGGIQSYLGEFVGRLVGSRAHAMTVYAPQWKGADAFDDAARAAGYRVVRHPSTVMLPGPTVDVRMRRLIAEHDIETVWFGAAAPLA
LLAPRARLAGASRVLASTHGHEVGWSMLPVARSVLRRIGDGTDVVTFVSSYTRSRFASAFGPAASLEYLPPGVDTDRFRPDPAARAELRKRYRLGERPTV
VCLSRLVPRKGQDTLVTALPSIRRRVDGAALVIVGGGPYLETLRKLAHDCGVADHVTFTGGVATDELPAHHALADVFAMPCRTRGAGMDVEGLGIVFLEA
SAAGVPVIAGNSGGAPETVQHNKTGLVVDGRSVDRVADAVAELLIDRDRAVAMGAAGREWVTAQWRWDTLAAKLADFLRGDDAAR

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	YES
omega peak height (95%CI lower bound)	1.64 (0.37)	3.21 (1.28)
codons under selection		381, 382, 383
omega plots
genetic variants*	link	link
statistics at each codon	link	link