TB Genome Annotation Portal

Rv3809c (glf)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: UDP-galactopyranose mutase
  • REFSEQ: UDP-galactopyranose mutase Glf
  • PATRIC: UDP-galactopyranose mutase (EC 5.4.99.9)
  • TUBERCULIST: UDP-galactopyranose mutase Glf (UDP-GALP mutase) (NAD+-flavin adenine dinucleotide-requiring enzyme)
  • NCBI: UDP-galactopyranose mutase Glf (UDP-GALP mutase) (NAD+-flavin adenine dinucleotide-requiring enzyme)
  • updated information (H37Rv4):
    • gene name: glf
    • function:
    • reference:
• Type: Not Target
• Start: 4272276
• End: 4273475
• Operon:


• Trans-membrane region:
  
• Role: II.C.3 - Murein sacculus and peptidoglycan
• GO terms:
  • GO:0071766 - Actinobacterium-type cell wall biogenesis (Uniprot)
  • GO:0071555 - cell wall organization (Uniprot)
  • GO:0045227 - capsule polysaccharide biosynthetic process (Uniprot)
  • GO:0016853 - isomerase activity (Uniprot)
  • GO:0008767 - UDP-galactopyranose mutase activity (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0005618 - cell wall (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • UDPGAL[c] -> UDPGALF[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: 1v0j
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  1V0J	100%	MYCOBACTERIUM TUBERCULOSIS	Udp-galactopyranose mutase from Mycobacterium tuberculosis
  4RPL	99%	Mycobacterium tuberculosis	Crystal structure of Micobacterium tuberculosis UDP-Galactopyranose mutase in complex with tetrafluorinated substrate analog UDP-F4-Galp
  4RPK	99%	Mycobacterium tuberculosis	Crystal structure of Micobacterium tuberculosis UDP-Galactopyranose mutase in complex with tetrafluorinated substrate analog UDP-F4-Galf
  4RPJ	99%	Mycobacterium tuberculosis	Crystal structure of Micobacterium tuberculosis UDP-Galactopyranose mutase in complex with UDP
  4RPH	99%	Mycobacterium tuberculosis	Crystal structure of Micobacterium tuberculosis UDP-Galactopyranose mutase in complex with substrate UDP-Galp (reduced)
  4RPG	99%	Mycobacterium tuberculosis	Crystal structure of Micobacterium tuberculosis UDP-Galactopyranose mutase in complex with substrate UDP-Galp
  5F3R	85%	Mycobacterium smegmatis	Structure of oxidized UDP-galactopyranose mutase from Mycobacterium smegmatis in complex with magnesium ion
  5ER9	85%	Mycobacterium smegmatis	Structure of oxidized UDP-galactopyranose mutase from Mycobacterium smegmatis in complex with UDP in mixed conformation and closed form
  5EQD	85%	Mycobacterium smegmatis	Structure of oxidized UDP-galactopyranose mutase from Mycobacterium smegmatis in complex with UDP in opened and closed form
  6D9E	76%	Corynebacterium diphtheriae	Crystal structure of Corynebacterium diphtheriae UDP-galactopyranose mutase in complex with UDP-GlcNAc (open, reduced)

• Links to additional information on glf:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -13.407 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MQPMTARFDLFVVGSGFFGLTIAERVATQLDKRVLVLERRPHIGGNAYSEAEPQTGIEVHKYGAHLFHTSNKRVWDYVRQFTDFTDYRHRVFAMHNGQAY
QFPMGLGLVSQFFGKYFTPEQARQLIAEQAAEIDTADAQNLEEKAISLIGRPLYEAFVKGYTAKQWQTDPKELPAANITRLPVRYTFDNRYFSDTYEGLP
TDGYTAWLQNMAADHRIEVRLNTDWFDVRGQLRPGSPAAPVVYTGPLDRYFDYAEGRLGWRTLDFEVEVLPIGDFQGTAVMNYNDLDVPYTRIHEFRHFH
PERDYPTDKTVIMREYSRFAEDDDEPYYPINTEADRALLATYRARAKSETASSKVLFGGRLGTYQYLDMHMAIASALNMYDNVLAPHLRDGVPLLQDGA

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)	1.46 (0.22)	1.55 (0.45)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link