TB Genome Annotation Portal

Rv1566c (-)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: invasion-associated protein
  • REFSEQ: inv protein
  • PATRIC: Invasion protein
  • TUBERCULIST: Possible Inv protein
  • NCBI: Possible Inv protein
  • updated information (H37Rv4):
    • gene name: ripD
    • function:
    • reference:
• Type: Not Target
• Start: 1773928
• End: 1774620
• Operon:


• Trans-membrane region:
  
• Role: IV.A - Virulence
• GO terms:
  • 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
  4LJ1	99%	Mycobacterium tuberculosis	RipD (Rv1566c) from Mycobacterium tuberculosis: a non-catalytic NlpC/p60 domain protein with two penta-peptide repeat units (PVQQA-PVQPA)
  4JXB	99%	Mycobacterium tuberculosis	RipD (Rv1566c) from Mycobacterium tuberculosis: a non-catalytic NlpC/p60 domain protein, adaptation to peptidoglycan-binding function
  3GT2	86%	Mycobacterium avium subsp. paratuberculosis	Crystal Structure of the P60 Domain from M. avium paratuberculosis Antigen MAP1272c
  4Q4G	56%	Mycobacterium tuberculosis	Structure of the Resuscitation Promoting Factor Interacting protein RipA mutated at C383
  3S0Q	56%	Mycobacterium tuberculosis	Peptidase module of the peptidoglycan hydrolase RipA (Rv1477) from Mycobacterium tuberculosis, catalytic site mutant (Cys383Ala) at 1.45 resolution
  4Q4N	55%	Mycobacterium tuberculosis	Structure of the Resuscitation Promoting Factor Interacting protein RipA mutated at H432
  3PBC	55%	Mycobacterium tuberculosis	Peptidase module of the peptidoglycan hydrolase RipA (Rv1477) from Mycobacterium tuberculosis at 1.38 resolution
  3NE0	55%	Mycobacterium tuberculosis	Structure and functional regulation of RipA, a mycobacterial enzyme essential for daughter cell separation
  2XIV	55%	MYCOBACTERIUM TUBERCULOSIS	Structure of Rv1477, hypothetical invasion protein of Mycobacterium tuberculosis
  4Q4T	54%	Mycobacterium tuberculosis	Structure of the Resuscitation Promoting Factor Interacting protein RipA mutated at E444

• Links to additional information on Rv1566c:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 1.024 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MKRSMKSGSFAIGLAMMLAPMVAAPGLAAADPATRPVDYQQITDVVIARGLSQRGVPFSWAGGGISGPTRGTGTGINTVGFDASGLIQYAYAGAGLKLPR
SSGQMYKVGQKVLPQQARKGDLIFYGPEGTQSVALYLGKGQMLEVGDVVQVSPVRTNGMTPYLVRVLGTQPTPVQQAPVQPAPVQQAPVQQAPVQQAPVQ
QAPVQQAPVQQAPVQQAPVQPPPFGTARSR

Additional Information

ripD

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)	1.2 (0.23)	0.66 (0.29)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link