TB Genome Annotation Portal

Rv3924c (rpmH)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: 50S ribosomal protein L34
  • REFSEQ: 50S ribosomal protein L34
  • TUBERCULIST: 50S ribosomal protein L34 RpmH
  • NCBI: 50S ribosomal protein L34 RpmH
  • updated information (H37Rv4):
    • gene name: rpmH
    • function:
    • reference:
• Type: Not Target
• Start: 4410786
• End: 4410929
• Operon:


• Trans-membrane region:
  
• Role: II.A.1 - Ribosomal protein synthesis and modification
• GO terms:
  • GO:0030529 - not-found (Uniprot)
  • GO:0006412 - translation (Uniprot)
  • GO:0005840 - ribosome (Uniprot)
  • GO:0005622 - intracellular (Uniprot)
  • GO:0003735 - structural constituent of ribosome (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
  5V93	100%	Mycobacterium tuberculosis	Cryo-EM structure of the 70S ribosome from Mycobacterium tuberculosis bound with Capreomycin
  5V7Q	97%	Mycobacterium tuberculosis	Cryo-EM structure of the large ribosomal subunit from Mycobacterium tuberculosis bound with a potent linezolid analog
  6DZI	86%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Cryo-EM Structure of Mycobacterium smegmatis 70S C(minus) ribosome 70S-MPY complex
  6DZP	82%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Cryo-EM Structure of Mycobacterium smegmatis C(minus) 50S ribosomal subunit
  5ZET	82%	Mycobacterium smegmatis str. MC2 155	M. smegmatis P/P state 50S ribosomal subunit
  5ZEP	82%	Mycobacterium smegmatis str. MC2 155	M. smegmatis hibernating state 70S ribosome structure
  5ZEB	82%	Mycobacterium smegmatis str. MC2 155	M. Smegmatis P/P state 70S ribosome structure
  5XYM	82%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Large subunit of Mycobacterium smegmatis
  5O61	82%	Mycobacterium smegmatis str. MC2 155	The complete structure of the Mycobacterium smegmatis 70S ribosome
  5O60	82%	Mycobacterium smegmatis str. MC2 155	Structure of the 50S large ribosomal subunit from Mycobacterium smegmatis

• Links to additional information on rpmH:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -11.992 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VTKGKRTFQPNNRRRARVHGFRLRMRTRAGRSIVSSRRRKGRRTLSA

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)	0.54 (0.05)	0.95 (0.36)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link