TB Genome Annotation Portal

Rv2589 (gabT)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: 4-aminobutyrate aminotransferase
  • REFSEQ: 4-aminobutyrate aminotransferase
  • PATRIC: Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
  • TUBERCULIST: 4-aminobutyrate aminotransferase GabT (gamma-amino-N-butyrate transaminase) (GABA transaminase) (glutamate:succinic semialdehyde transaminase) (GABA aminotransferase) (GABA-at)
  • NCBI: 4-aminobutyrate aminotransferase GabT (gamma-amino-N-butyrate transaminase) (GABA transaminase) (glutamate:succinic semialdehyde transaminase) (GABA aminotransferase) (GABA-at)
  • updated information (H37Rv4):
    • gene name: gabT
    • function:
    • reference:
• Type: Not Target
• Start: 2916360
• End: 2917709
• Operon:


• Trans-membrane region:
  
• Role: I.C.1 - General
• GO terms:
  • GO:0047298 - (S)-3-amino-2-methylpropionate transaminase activity (Uniprot)
  • GO:0034386 - 4-aminobutyrate:2-oxoglutarate transaminase activity (Uniprot)
  • GO:0030170 - pyridoxal phosphate binding (Uniprot)
  • GO:0016740 - transferase activity (Uniprot)
  • GO:0009450 - gamma-aminobutyric acid catabolic process (Uniprot)
  • GO:0009448 - gamma-aminobutyric acid metabolic process (Uniprot)
  • GO:0008483 - transaminase activity (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0003867 - 4-aminobutyrate transaminase activity (Uniprot)
  • GO:0003824 - catalytic activity (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • AKG[c] + GABA[c] <=> SUCCSAL[c] + GLU[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
  3R4T	83%	Mycobacterium marinum	Crystal structure of 4-aminobutyrate aminotransferase GabT from Mycobacterium marinum covalently bound to pyridoxal phosphate
  3OKS	78%	Mycobacterium smegmatis	Crystal structure of 4-aminobutyrate transaminase from mycobacterium smegmatis
  3Q8N	68%	Mycobacterium smegmatis	Crystal structure of 4-aminobutyrate transaminase from Mycobacterium smegmatis
  4FFC	64%	Mycobacterium abscessus	Crystal structure of a 4-aminobutyrate aminotransferase (GabT) from Mycobacterium abscessus
  4ATQ	62%	ARTHROBACTER AURESCENS	GABA-transaminase A1R958 in complex with external aldimine PLP-GABA adduct
  4ATP	62%	ARTHROBACTER AURESCENS	Structure of GABA-transaminase A1R958 from Arthrobacter aurescens in complex with PLP
  6J2V	60%	Corynebacterium glutamicum ATCC 13032	GABA aminotransferase from Corynebacterium glutamicum
  6WJ8	44%	Klebsiella pneumoniae subsp. pneumoniae SA1	Crystal structure of gamma-aminobutyrate aminotransferase PuuE from Klebsiella pneumoniae in complex with PLP
  7JH3	44%	Escherichia coli (strain K12)	Crystal structure of 4-aminobutyrate aminotransferase PuuE from Escherichia coli in complex with PLP
  6WOP	42%	Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)	Crystal structure of gamma-aminobutyrate aminotransferase PuuE from Acinetobacter baumannii

• Links to additional information on gabT:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 1.075 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VASLQQSRRLVTEIPGPASQALTHRRAAAVSSGVGVTLPVFVARAGGGIVEDVDGNRLIDLGSGIAVTTIGNSSPRVVDAVRTQVAEFTHTCFMVTPYEG
YVAVAEQLNRITPGSGPKRSVLFNSGAEAVENAVKIARSYTGKPAVVAFDHAYHGRTNLTMALTAKSMPYKSGFGPFAPEIYRAPLSYPYRDGLLDKQLA
TNGELAAARAIGVIDKQVGANNLAALVIEPIQGEGGFIVPAEGFLPALLDWCRKNHVVFIADEVQTGFARTGAMFACEHEGPDGLEPDLICTAKGIADGL
PLSAVTGRAEIMNAPHVGGLGGTFGGNPVACAAALATIATIESDGLIERARQIERLVTDRLTTLQAVDDRIGDVRGRGAMIAVELVKSGTTEPDAGLTER
LATAAHAAGVIILTCGMFGNIIRLLPPLTIGDELLSEGLDIVCAILADL

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)	1.67 (0.29)	1.74 (0.77)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link