TB Genome Annotation Portal

Rv1076 (lipU)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: lipase lipU
  • REFSEQ: lipase LipU
  • PATRIC: esterase
  • TUBERCULIST: Possible lipase LipU
  • NCBI: Possible lipase LipU
  • updated information (H37Rv4):
    • gene name: lipU
    • function:
    • reference:
• Coordinates in H37Rv: 1200767 - 1201660
• Gene length: 894 bp (with stop codon), 297 aa (without stop codon)
• Operon:


• Trans-membrane region:
  
• Role: II.B.5 - Esterases and lipases
• GO terms:
  • GO:0016787 - hydrolase activity (Uniprot)
  • GO:0008152 - metabolic process (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • PHOSPHATIDYLCHOLINE[c] -> DAG[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 Latest Homologs in PDB
• Top 10 Homologs in PDB (as of Apr 2026):
  

  PDB	aa ident	species	PDB title
  8YFZ	35%	Saccharolobus shibatae	CRYSTAL STRUCTURE OF THE EST1 H274E MUTANT AT PH 4.2
  8YFY	35%	Saccharolobus shibatae	CRYSTAL STRUCTURE OF THE EST1 H274D MUTANT AT PH 4.2
  4P9N	35%	Sulfolobus shibatae	Crystal structure of sshesti PE mutant
  3WJ1	35%	Sulfolobus shibatae	Crystal structure of SSHESTI

• Links to additional information on lipU:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.872 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • BioCyc
  • Systems Biology
  • Mycobrowser
  • PATRIC

Amino Acid Sequence

VAVRPVLAVGSYLPHAPWPWGVIDQAARVLLPASTTVRAAVSLPNASAQLVRASGVLPADGTRRAVLYLHGGAFLTCGANSHGRLVELLSKFADSPVLVV
DYRLIPKHSIGMALDDCHDGYRWLRLLGYEPEQIVLAGDSAGGYLALALAQRLQEVGEEPAALVAISPLLQLAKEHKQAHPNIKTDAMFPARAFDALDAL
VASAAARNQVDGEPEELYEPLEHITPGLPRTLIHVSGSEVLLHDAQLAAAKLAAAGVPAEVRVWPGQVHDFQVAASMLPEAIRSLRQIGEYIREATG

Additional Information

Analysis of Positive Selection in Clinical Isolates *new*

• data from Culviner et al (2025) (55,259 Mtb clinical isolates)
  • overall pN/pS for Rv1076: 0.829615132
  • lineage-specific pN/pS in L1: 0.655008564
  • lineage-specific pN/pS in L2: 1.132820074
  • lineage-specific pN/pS in L3: 0.761447455
  • lineage-specific pN/pS in L4: 0.849129284

• Analysis of dN/dS (omega) in a global collection of 10k Mtb clinical isolates using GenomegaMap (Window model)
• clinical isolates collection: global set of 10,626 Mtb genomes
• 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.

	global set of 10,626 Mtb clinical isolates
under significant positive selection?	NO
omega peak height (95%CI lower bound)	1.98 (0.97)
codons under selection
omega plots
genetic variants*	link