TB Genome Annotation Portal

Rv2610c (pimA)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase
  • REFSEQ: alpha-mannosyltransferase PIMA
  • PATRIC: Phosphatidylinositol alpha-mannosyltransferase (EC 2.4.1.57)
  • TUBERCULIST: Alpha-mannosyltransferase PimA
  • NCBI: Alpha-mannosyltransferase PimA
  • updated information (H37Rv4):
    • gene name: pimA
    • function:
    • reference:
• Type: Not Target
• Start: 2937865
• End: 2939001
• Operon:


• Trans-membrane region:
  
• Role: IV.H - Miscellaneous transferases
• GO terms:
  • GO:0097502 - mannosylation (Uniprot)
  • GO:0046488 - phosphatidylinositol metabolic process (Uniprot)
  • GO:0043750 - phosphatidylinositol alpha-mannosyltransferase activity (Uniprot)
  • GO:0016757 - transferase activity, transferring glycosyl groups (Uniprot)
  • GO:0016740 - transferase activity (Uniprot)
  • GO:0016020 - membrane (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:0004377 - GDP-Man:Man3GlcNAc2-PP-Dol alpha-1,2-mannosyltransferase activity (Uniprot)
  • GO:0000287 - magnesium ion binding (Uniprot)
  • GO:0000030 - mannosyltransferase activity (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • GDPMAN[c] + PI_TBA[c] -> GDP[c] + AC1PIM1[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
  4NC9	82%	Mycobacterium smegmatis	Crystal structure of phosphatidyl mannosyltransferase PimA
  4N9W	82%	Mycobacterium smegmatis	Crystal structure of phosphatidyl mannosyltransferase PimA
  2GEK	82%	Mycobacterium smegmatis	Crystal Structure of phosphatidylinositol mannosyltransferase (PimA) from Mycobacterium smegmatis in complex with GDP
  2GEJ	82%	Mycobacterium smegmatis	Crystal Structure of phosphatidylinositol mannosyltransferase (PimA) from Mycobacterium smegmatis in complex with GDP-Man

• Links to additional information on pimA:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -5.252 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MRIGMICPYSFDVPGGVQSHVLQLAEVMRTRGHLVSVLAPASPHAALPDYFVSGGRAVPIPYNGSVARLRFGPATHRKVKKWLAHGDFDVLHLHEPNAPS
LSMLALNIAEGPIVATFHTSTTKSLTLTVFQGILRPMHEKIVGRIAVSDLARRWQMEALGSDAVEIPNGVDVDSFASAARLDGYPRQGKTVLFLGRYDEP
RKGMAVLLDALPKVVQRFPDVQLLIVGHGDADQLRGQAGRLAAHLRFLGQVDDAGKASAMRSADVYCAPNTGGESFGIVLVEAMAAGTAVVASDLDAFRR
VLRDGEVGHLVPVDPPDLQAAALADGLIAVLENDVLRERYVAAGNAAVRRYDWSVVASQIMRVYETVAGSGAKVQVAS

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)	1.38 (0.16)	1.83 (0.61)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link