TB Genome Annotation Portal

Rv2913c (-)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: deacetylase
  • REFSEQ: D-amino acid aminohydrolase
  • PATRIC: N-acyl-D-glutamate amidohydrolase
  • TUBERCULIST: Possible D-amino acid aminohydrolase (D-amino acid hydrolase)
  • NCBI: Possible D-amino acid aminohydrolase (D-amino acid hydrolase)
  • updated information (H37Rv4):
    • gene name: -
    • function:
    • reference:
• Coordinates in H37Rv: 3219863 - 3221698
• Gene length: 1836 bp (with stop codon), 611 aa (without stop codon)
• Operon:


• Trans-membrane region:
  
• Role: I.A.2 - Amino acids and amines
• GO terms:
  • GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (Uniprot)
  • GO:0016787 - hydrolase activity (Uniprot)
  • GO:0005829 - cytosol (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 Latest Homologs in PDB
• Top 10 Homologs in PDB (as of Apr 2026):
  

  PDB	aa ident	species	PDB title
  9KB4	38%	Pseudoalteromonas prydzensis ACAM 620	The structure of the PpOngB-citrate
  9KB3	38%	Pseudoalteromonas prydzensis ACAM 620	The structure of the carbohydrate deacetylase inactive mutant PpOngB in complex with GlcNAc1A.
  9KB1	38%	Pseudoalteromonas prydzensis ACAM 620	The Structure of the Carbohydrate Deacetylase PpOngB from Pseudoalteromonas prydzensis ACAM 620.
  3GIQ	37%	Bordetella bronchiseptica	Crystal structure of N-acyl-D-Glutamate Deacylase from Bordetella Bronchiseptica complexed with zinc and phosphonate inhibitor, a mimic of the reaction tetrahedral intermediate.
  3GIP	37%	Bordetella bronchiseptica	Crystal structure of N-acyl-D-Glutamate Deacylase from Bordetella Bronchiseptica complexed with zinc, acetate and formate ions.

• Links to additional information on Rv2913c:
  • KEGG - nucleotide and amino acid sequences of gene
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.877 (from Jeremy Rock's lab)
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MLAWRQLNDLEETVTYDVIIRDGLWFDGTGNAPLTRTLGIRDGVVATVAAGALDETGCPEVVDAAGKWVVPGFIDVHTHYDAEVLLDPGLRESVRHGVTT
VLLGNCSLSTVYANSEDAADLFSRVEAVPREFVLGALRDNQTWSTPAEYIEAIDALPLGPNVSSLLGHSDLRTAVLGLDRATDDTVRPTEAELAKMAKLL
DEALEAGMLGMSGMDAAIDKLDGDRFRSRALPSTFATWRERRKLISVLRHRGRILQSAPDVDNPVSALLFFLASSRIFNRRKGVRMSMLVSADAKSMPLA
VHVFGLGTRVLNKLLGSQVRFQHLPVPFELYSDGIDLPVFEEFGAGTAALHLRDQLQRNELLADRSYRRSFRREFDRIKLGPSLWHRDFHDAVIVECPDK
SLIGKSFGAIADERGLHPLDAFLDVLVDNGERNVRWTTIVANHRPNQLNKLAAEPSVHMGFSDAGAHLRNMAFYNFGLRLLKRARDADRAGQPFLSIERA
VYRLTGELAEWFGIGAGTLRQGDRADFAVIDPTHLDESVDGYHEEAVPYYGGLRRMVNRNDATVVATGVGGTVVFRGGQFGGQFRDGYGQNVKSGRYLRA
GELGAALSRSA

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 Rv2913c: 0.577002367
  • lineage-specific pN/pS in L1: 0.579755616
  • lineage-specific pN/pS in L2: 0.67782373
  • lineage-specific pN/pS in L3: 0.58408215
  • lineage-specific pN/pS in L4: 0.547347424

• 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)	1.84 (0.58)
codons under selection
omega plots
genetic variants*	link