TB Genome Annotation Portal

Rv2950c (fadD29)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: long chain fatty acid CoA FadD26
  • REFSEQ: acyl-CoA synthetase
  • PATRIC: Long-chain fatty-acid-AMP ligase Mycobacterial subgroup FadD29
  • TUBERCULIST: Fatty-acid-AMP ligase FadD29 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)
  • NCBI: Fatty-acid-AMP ligase FadD29 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)
  • updated information (H37Rv4):
    • gene name: fadD29
    • function:
    • reference:
• Type: Not Target
• Start: 3300596
• End: 3302455
• Operon:


• Trans-membrane region:
  
• Role: I.A.3 - Fatty acids
• GO terms:
  • GO:0097040 - phthiocerol biosynthetic process (Uniprot)
  • GO:0071766 - Actinobacterium-type cell wall biogenesis (Uniprot)
  • GO:0070566 - adenylyltransferase activity (Uniprot)
  • GO:0016878 - acid-thiol ligase activity (Uniprot)
  • GO:0016874 - ligase activity (Uniprot)
  • GO:0008610 - lipid biosynthetic process (Uniprot)
  • GO:0008152 - metabolic process (Uniprot)
  • GO:0006633 - fatty acid biosynthetic process (Uniprot)
  • GO:0006631 - fatty acid metabolic process (Uniprot)
  • GO:0006629 - lipid metabolic process (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0005524 - ATP binding (Uniprot)
  • GO:0003824 - catalytic activity (Uniprot)
  • GO:0000166 - nucleotide binding (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 Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  3E53	56%	Mycobacterium tuberculosis	Crystal structure of N-terminal domain of a Fatty Acyl AMP Ligase FAAL28 from Mycobacterium tuberculosis
  3T5A	56%	Mycobacterium tuberculosis	Crystal structure of N-terminal domain of FAAL28 G330W mutant from Mycobacterium tuberculosis
  5D6N	39%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Crystal structure of a mycobacterial protein
  5ICR	38%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	2.25 Angstrom Resolution Crystal Structure of Fatty-Acid-CoA Ligase (FadD32) from Mycobacterium smegmatis in complex with Inhibitor 5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine.
  5EY8	38%	Mycobacterium smegmatis	Structure of FadD32 from Mycobacterium smegmatis complexed to AMPC20
  5D6J	38%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Crystal structure of a mycobacterial protein
  5HM3	37%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	2.25 Angstrom Resolution Crystal Structure of Long-chain-fatty-acid-AMP Ligase FadD32 from Mycobacterium tuberculosis in complex with Inhibitor 5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine
  5EY9	36%	Mycobacterium marinum	Structure of FadD32 from Mycobacterium marinum complexed to AMPC12

• Links to additional information on fadD29:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.89 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MKTNSSFHAAGEVATQPAWGTGEQAAQPLNGSTSRFAMSESSLADLLQKAASQYPNRAAYKFIDYDTDPAGFTETVTWWQVHRRAMIVAEELWIYASSGD
RVAILAPQGLEYIIAFMGVLQAGLIAVPLPVPQFGIHDERISSALRDSAPSIILTTSSVIDEVTTYAPHACAAQGQSAPIVVAVDALDLSSSRALDPTRF
ERPSTAYLQYTSGSTRAPAGVVLSHKNVITNCVQLMSDYIGDSEKVPSTPVSWLPFYHDMGLMLGIILPMINQDTAVLMSPMAFLQRPARWMQLLAKHRA
QISSAPNFGFELAVRRTSDDDMAGLDLGHVRTIVTGAERVNVATLRRFTERFAPFNLSETAIRPSYGLAEATVYVATAGPGRAPKSVCFDYQQLSVGQAK
RAENGSEGANLVSYGAPRASTVRIVDPETRMENPAGTVGEIWVQGDNVGLGYWRNPQQTEATFRARLVTPSPGTSEGPWLRTGDLGVIFEGELFITGRIK
ELLVVDGANHYPEDIEATIQEITGGRVVAIAVPDDRTEKLVTIIELMKRGRTDEEEKNRLRTVKREVASAISRSHRLRVADVVMVAPGSIPVTTSGKVRR
SASVERYLHHEFSRLDAMA

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)	2.13 (0.49)	1.39 (0.69)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link