TB Genome Annotation Portal

Rv0867c (rpfA)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: resuscitation-promoting factor rpfA
  • REFSEQ: resuscitation-promoting factor RpfA
  • PATRIC: FIG00820555: hypothetical protein
  • TUBERCULIST: Possible resuscitation-promoting factor RpfA
  • NCBI: Possible resuscitation-promoting factor RpfA
  • updated information (H37Rv4):
    • gene name: rpfA
    • function:
    • reference:
• Type: Not Target
• Start: 964312
• End: 965535
• Operon:


• Trans-membrane region:
  
• Role: II.C.5 - Other membrane proteins
• GO terms:
  • GO:0040010 - positive regulation of growth rate (Uniprot)
  • GO:0016787 - hydrolase activity (Uniprot)
  • GO:0010629 - negative regulation of gene expression (Uniprot)
  • GO:0009405 - pathogenesis (Uniprot)
  • GO:0005576 - extracellular region (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
  4CGE	67%	MYCOBACTERIUM TUBERCULOSIS	Crystal structure of Mycobacterium tuberculosis Resuscitation promoting factor E
  4OW1	65%	Mycobacterium tuberculosis	Crystal Structure of Resuscitation Promoting Factor C
  2N5Z	65%	Mycobacterium tuberculosis	Mycobacterium tuberculosis: a dynamic view of the resuscitation promoting factor RpfC catalytic domain
  5E27	64%	Mycobacterium tuberculosis	The structure of Resuscitation Promoting Factor B from M. tuberculosis reveals unexpected ubiquitin-like domains
  4KPM	64%	Mycobacterium tuberculosis	Crystal structure of the catalytic domain of RpfB from Mycobacterium tuberculosis in complex with triNAG
  4KL7	64%	Mycobacterium tuberculosis	Crystal structure of the catalytic domain of RpfB from Mycobacterium tuberculosis
  4EMN	64%	Mycobacterium tuberculosis	Crystal structure of RpfB catalytic domain in complex with benzamidine
  3EO5	64%	Mycobacterium tuberculosis	Crystal structure of the resuscitation promoting factor RpfB
  1XSF	64%	Mycobacterium tuberculosis	Solution structure of a resuscitation promoting factor domain from Mycobacterium tuberculosis

• Links to additional information on rpfA:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -0.782 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MSGRHRKPTTSNVSVAKIAFTGAVLGGGGIAMAAQATAATDGEWDQVARCESGGNWSINTGNGYLGGLQFTQSTWAAHGGGEFAPSAQLASREQQIAVGE
RVLATQGRGAWPVCGRGLSNATPREVLPASAAMDAPLDAAAVNGEPAPLAPPPADPAPPVELAANDLPAPLGEPLPAAPADPAPPADLAPPAPADVAPPV
ELAVNDLPAPLGEPLPAAPADPAPPADLAPPAPADLAPPAPADLAPPAPADLAPPVELAVNDLPAPLGEPLPAAPAELAPPADLAPASADLAPPAPADLA
PPAPAELAPPAPADLAPPAAVNEQTAPGDQPATAPGGPVGLATDLELPEPDPQPADAPPPGDVTEAPAETPQVSNIAYTKKLWQAIRAQDVCGNDALDSL
AQPYVIG

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)	1.39 (0.54)	1.17 (0.63)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link