TB Genome Annotation Portal

Rv3290c (lat)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: L-lysine 6-transaminase
  • REFSEQ: L-lysine aminotransferase
  • PATRIC: Probable L-lysine-epsilon aminotransferase (EC 2.6.1.36) (L-lysine aminotransferase) (Lysine 6-aminotransferase)
  • TUBERCULIST: Probable L-lysine-epsilon aminotransferase Lat (L-lysine aminotransferase) (lysine 6-aminotransferase)
  • NCBI: Probable L-lysine-epsilon aminotransferase Lat (L-lysine aminotransferase) (lysine 6-aminotransferase)
  • updated information (H37Rv4):
    • gene name: lat
    • function:
    • reference:
• Type: Not Target
• Start: 3670445
• End: 3671794
• Operon:


• Trans-membrane region:
  
• Role: IV.D - Antibiotic production and resistance
• GO terms:
  • GO:0045484 - L-lysine 6-transaminase activity (Uniprot)
  • GO:0030170 - pyridoxal phosphate binding (Uniprot)
  • GO:0017000 - antibiotic biosynthetic process (Uniprot)
  • GO:0016740 - transferase activity (Uniprot)
  • GO:0008483 - transaminase activity (Uniprot)
  • GO:0003824 - catalytic 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: 2cjd, 2cjg, 2jje, 2jjg, 2jjf, 2jjh, 2cjh, 2cin
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  2JJG	100%	MYCOBACTERIUM TUBERCULOSIS	Crystal structure of the M. tuberculosis Lysine-epsilon aminotransferase (Rv3290c) complexed to an inhibitor
  2CJH	100%	MYCOBACTERIUM TUBERCULOSIS	Lysine aminotransferase from M. tuberculosis in the internal aldimine form with bound substrate 2-ketoglutarate
  2CJG	100%	MYCOBACTERIUM TUBERCULOSIS	Lysine aminotransferase from M. tuberculosis in bound PMP form
  2CJD	100%	MYCOBACTERIUM TUBERCULOSIS	Lysine aminotransferase from M. tuberculosis in external aldimine form
  2CIN	100%	MYCOBACTERIUM TUBERCULOSIS	Lysine aminotransferase from M. tuberculosis in the internal aldimine form
  2JJH	99%	MYCOBACTERIUM TUBERCULOSIS	E243 mutant of M. tuberculosis Rv3290C
  2JJF	99%	MYCOBACTERIUM TUBERCULOSIS	N328A mutant of M. tuberculosis Rv3290c
  2JJE	99%	MYCOBACTERIUM TUBERCULOSIS	Crystal structure of T330S mutant of Rv3290c from M. tuberculosis

• Links to additional information on lat:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 1.387 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MAAVVKSVALAGRPTTPDRVHEVLGRSMLVDGLDIVLDLTRSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNSDVYS
VAMARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPALGTQVLHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPY
MRPGLDEPAMAALEAEALRQARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTGCGLTGTAWAYQQLDVAPDIVAFGK
KTQVCGVMAGRRVDEVADNVFAVPSRLNSTWGGNLTDMVRARRILEVIEAEGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLMCAFSLPTTADRD
ELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIAAVRSALPVVT

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)	1.73 (0.29)	1.57 (0.6)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link