TB Genome Annotation Portal

Rv0899 (ompA)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: OOP family OmpA-OmpF porin
  • REFSEQ: outer membrane protein A OMPA
  • PATRIC: Outer membrane protein
  • TUBERCULIST: Outer membrane protein A OmpA
  • NCBI: Outer membrane protein A OmpA
  • updated information (H37Rv4):
    • gene name: ompA
    • function:
    • reference:
• Type: Not Target
• Start: 1002812
• End: 1003792
• Operon:


• Trans-membrane region:
  
• Role: II.C.2 - Surface polysaccharides, lipopolysaccharides, proteins and antigens
• GO terms:
  • GO:0072488 - ammonium transmembrane transport (Uniprot)
  • GO:0046872 - metal ion binding (Uniprot)
  • GO:0044121 - growth of symbiont in host organelle (Uniprot)
  • GO:0042834 - peptidoglycan binding (Uniprot)
  • GO:0016021 - integral component of membrane (Uniprot)
  • GO:0016020 - membrane (Uniprot)
  • GO:0015288 - porin activity (Uniprot)
  • GO:0010447 - response to acidic pH (Uniprot)
  • GO:0009279 - cell outer membrane (Uniprot)
  • GO:0006811 - ion transport (Uniprot)
  • GO:0005887 - integral component of plasma membrane (Uniprot)
  • GO:0005829 - cytosol (Uniprot)
  • GO:0005618 - cell wall (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: 2lbt, 2kgs, 2l26, 2ksm, 2kgw, 2lca
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  2LCA	100%	Mycobacterium tuberculosis	Solution structure of the C domain of RV0899 from mycobacterium tuberculosis
  2L26	100%	Mycobacterium tuberculosis	Rv0899 from Mycobacterium tuberculosis contains two separated domains
  2KSM	100%	Mycobacterium tuberculosis	Central B domain of Rv0899 from Mycobacterium tuberculosis
  2KGW	100%	Mycobacterium tuberculosis	Solution Structure of the carboxy-terminal domain of OmpATb, a pore forming protein from Mycobacterium tuberculosis
  2KGS	100%	Mycobacterium tuberculosis	Solution structure of the amino-terminal domain of OmpATb, a pore forming protein from Mycobacterium tuberculosis
  2LBT	99%	Mycobacterium tuberculosis	Solution structure of the C domain of RV0899(D236A) from mycobacterium tuberculosis
  2N48	48%	Escherichia coli K-12	EC-NMR Structure of Escherichia coli YiaD Determined by Combining Evolutionary Couplings (EC) and Sparse NMR Data. Northeast Structural Genomics Consortium target ER553
  2K1S	48%	Escherichia coli	Solution NMR structure of the folded C-terminal fragment of YiaD from Escherichia coli. Northeast Structural Genomics Consortium target ER553.
  6JFW	45%	Pseudomonas aeruginosa PAO1	Crystal structure of PA0833 periplasmic domain from Pseudomonas aeruginosa reveals an unexpected enlarged peptidoglycan binding pocket
  4G88	45%	Acinetobacter baumannii	Crystal structure of OmpA peptidoglycan-binding domain from Acinetobacter baumannii

• Links to additional information on ompA:
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.491 (from Jeremy Rock's lab)

Amino Acid Sequence

VASKAGLGQTPATTDARRTQKFYRGSPGRPWLIGAVVIPLLIAAIGYGAFERPQSVTGPTGVLPTLTPTSTRGASALSLSLLSISRSGNTVTLIGDFPDE
AAKAALMTALNGLLAPGVNVIDQIHVDPVVRSLDFSSAEPVFTASVPIPDFGLKVERDTVTLTGTAPSSEHKDAVKRAATSTWPDMKIVNNIEVTGQAPP
GPPASGPCADLQSAINAVTGGPIAFGNDGASLIPADYEILNRVADKLKACPDARVTINGYTDNTGSEGINIPLSAQRAKIVADYLVARGVAGDHIATVGL
GSVNPIASNATPEGRAKNRRVEIVVN

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)	1.5 (0.19)	1.86 (0.77)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link