TB Genome Annotation Portal

Rv0234c (gabD1)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: succinate-semialdehyde dehydrogenase [NADP+] 1
  • REFSEQ: succinic semialdehyde dehydrogenase
  • PATRIC: Succinate-semialdehyde dehydrogenase [NAD] (EC 1.2.1.24); Succinate-semialdehyde dehydrogenase [NADP+] (EC 1.2.1.16)
  • TUBERCULIST: Succinate-semialdehyde dehydrogenase [NADP+] dependent (SSDH) GabD1
  • NCBI: Succinate-semialdehyde dehydrogenase [NADP+] dependent (SSDH) GabD1
  • updated information (H37Rv4):
    • gene name: gabD1
    • function:
    • reference:
• Type: Not Target
• Start: 279605
• End: 281140
• Operon:


• Trans-membrane region:
  
• Role: I.A.1 - Carbon compounds
• GO terms:
  • GO:0055114 - oxidation-reduction process (Uniprot)
  • GO:0016620 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (Uniprot)
  • GO:0016491 - oxidoreductase activity (Uniprot)
  • GO:0009013 - succinate-semialdehyde dehydrogenase [NAD(P)+] activity (Uniprot)
  • GO:0008152 - metabolic process (Uniprot)
  • GO:0006099 - tricarboxylic acid cycle (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • NADP[c] + SUCCSAL[c] -> NADPH[c] + SUCC[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
  4ITB	56%	Synechococcus sp.	Structure of bacterial enzyme in complex with cofactor and substrate
  4ITA	56%	Synechococcus sp.	Structure of bacterial enzyme in complex with cofactor
  4IT9	56%	Synechococcus sp.	Structure of Bacterial Enzyme
  3VZ1	56%	Synechococcus	Structural insights into substrate and cofactor selelction by sp2771
  3VZ3	56%	Synechococcus	Structural insights into substrate and cofactor selection by sp2771
  3VZ2	54%	Synechococcus	Structural insights into substrate and cofactor selection by sp2771
  3ETF	45%	Salmonella typhimurium	Crystal structure of a putative succinate-semialdehyde dehydrogenase from salmonella typhimurium lt2
  3EFV	45%	Salmonella typhimurium	Crystal Structure of a Putative Succinate-Semialdehyde Dehydrogenase from Salmonella typhimurium LT2 with bound NAD
  3VZ0	42%	Gluconobacter oxydans	Structural insights into cofactor and substrate selection by Gox0499
  3ROS	37%	Lactobacillus acidophilus	Crystal structure of NAD-dependent aldehyde dehydrogenase from Lactobacillus acidophilus

• Links to additional information on gabD1:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.808 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MRSVTCSATLVLPVIEPTPADRRPRHLLLGSAGHVSGRLDTGRFVQTHPAKDVSVPIATINPATGETVKTFTAATDDEVDAAIARAHRRFADYRQTSFAQ
RARWANATADLLEAEADQAAAMMTLEMGKTLAAAKAEALKCAKGFRYYAENAEALLADEPADAAKVGASAAYGRYQPLGVILAVMPWNFPLWQAVRFAAP
ALMAGNVGLLKHASNVPQCALYLADVIARGGFPDGCFQTLLVSSGAVEAILRDPRVAAATLTGSEPAGQSVGAIAGNEIKPTVLELGGSDPFIVMPSADL
DAAVSTAVTGRVQNNGQSCIAAKRFIVHADIYDDFVDKFVARMAALRVGDPTDPDTDVGPLATEQGRNEVAKQVEDAAAAGAVIRCGGKRLDRPGWFYPP
TVITDISKDMALYTEEVFGPVASVFRAANIDEAVEIANATTFGLGSNAWTRDETEQRRFIDDIVAGQVFINGMTVSYPELPFGGVKRSGYGRELSAHGIR
EFCNIKTVWIA

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)	1.68 (0.27)	1.49 (0.72)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link