TB Genome Annotation Portal

Rv1280c (oppA)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: peptide/nickel transporter substrate-binding protein
  • REFSEQ: periplasmic oligopeptide-binding lipoprotein OppA
  • PATRIC: Oligopeptide ABC transporter periplasmic oligopeptide-binding protein OppA (TC 3.A.1.5.1)
  • TUBERCULIST: Probable periplasmic oligopeptide-binding lipoprotein OppA
  • NCBI: Probable periplasmic oligopeptide-binding lipoprotein OppA
  • updated information (H37Rv4):
    • gene name: oppA
    • function:
    • reference:
• Type: Not Target
• Start: 1431665
• End: 1433440
• Operon:


• Trans-membrane region:
  
• Role: III.A.1 - Amino acids
• GO terms:
  • GO:0055085 - transmembrane transport (Uniprot)
  • GO:0052060 - evasion or tolerance by symbiont of host-produced nitric oxide (Uniprot)
  • GO:0043295 - glutathione binding (Uniprot)
  • GO:0043190 - ATP-binding cassette (ABC) transporter complex (Uniprot)
  • GO:0042597 - periplasmic space (Uniprot)
  • GO:0042277 - peptide binding (Uniprot)
  • GO:0030288 - outer membrane-bounded periplasmic space (Uniprot)
  • GO:0017038 - protein import (Uniprot)
  • GO:0016021 - integral component of membrane (Uniprot)
  • GO:0016020 - membrane (Uniprot)
  • GO:0015197 - not-found (Uniprot)
  • GO:0005887 - integral component of plasma membrane (Uniprot)
  • GO:0005886 - plasma membrane (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): (none with >35% aa id)
• Links to additional information on oppA:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 1.3 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VADRGQRRGCAPGIASALRASFQGKSRPWTQTRYWAFALLTPLVVAMVLTGCSASGTQLELAPTADRRAAVGTTSDINQQDPATLQDGGNLRLSLTDFPP
NFNILHIDGNNAEVAAMMKATLPRAFIIGPDGSTTVDTNYFTSIELTRTAPQVVTYTINPEAVWSDGTPITWRDIASQIHAISGADKAFEIASSSGAERV
ASVTRGVDDRQAVVTFAKPYAEWRGMFAGNGMLLPASMTATPEAFNKGQLDGPGPSAGPFVVSALDRTAQRIVLTRNPRWWGARPRLDSITYLVLDDAAR
LPALQNNTIDATGVGTLDQLTIAARTKGISIRRAPGPSWYHFTLNGAPGSILADKALRLAIAKGIDRYTIARVAQYGLTSDPVPLNNHVFVAGQDGYQDN
SGVVAYNPEQAKRELDALGWRRSGAFREKDGRQLVIRDLFYDAQSTRQFAQIAQHTLAQIGVKLELQAKSGSGFFSDYVNVGAFDIAQFGWVGDAFPLSS
LTQIYASDGESNFGKIGSPQIDAAIERTLAELDPGKARALANQVDELIWAEGFSLPLTQSPGTVAVRSTLANFGATGLADLDYTAIGFMRR

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)	2.04 (0.46)	1.26 (0.6)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link