About

iProteinDB is an online protein database and resource tool for providing information on post-translational modifications (PTMs) in Drosophila species. The data of 6 Drosophila species was generated in the Perrimon lab, integrated with other high-throughput data sets from three studies[1, 2, 3] and annotation from UniProt and PhosphoSitePlus.

Users can query Drosophila genes of interest, and choose one isoform if there are multiple non-redundant isoforms for the gene of interest. There are three tabs from which to choose:

  1. Protein Details
    A user can view the protein sequence from any of the 6 Drosophila species in FASTA format. PTM sites are color-coded; the amino acid is displayed in red if the PTM is observed, or blue if it was not observed but is predicted to be phosphorylated based on the data from different Drosophila species. The amino acid is underlined if the phosphorylation event was observed in more than one Drosophila species. Protein domains are highlighted in green. A table summarizing all the PTM sites for a given protein, as well as the data sources from which the PTM information was extracted, is provided, along with detailed information from the original sources, i.e. the original scores and peptide sequences. A table summarizing all predicted sites based on data from closely-related Drosophila species is provided with a link to detailed information and multiple sequence alignments. Also indicated in this tab are sub-cellular localization annotation from UniProt for each phosphoprotein and kinase predicted to act on individual sites, as identified using ScanSite3.

  2. Predicted Orthologs
    A user can find a table of the best ortholog candidates for major model organisms based on DIOPT ortholog prediction[4]. Mulitple sequence alignments were performed based on the protein sequences of orthologous genes. The sequences of all aligned Drosophila phosphosites, over a sliding window of five residues, were compared to the corresponding sequences of each orthologous gene and a similarity score was calculated by pairwise comparison. For example, if 10 or the 11 amino acids (phosphorylation site plus five amino acids upstream and downstream) are identical between Drosophila and human sites, the similarity score was assigned as 0.9 (10 divided by 11). Then, an average similarity score was calculated based on all pairwise combinations at a given site. All phosphorylation sites with an average similarity score of >0.5 are listed and summarized as "conserved sites." Human disease-related variants annotated at UniProt are also listed, along with sub-cellular localization annotation of all orthologous proteins from UniProt. Multiple sequence alignment (MSA) across major model organisms is displayed. For MSAs, observed PTM sites for all orthologous genes are color-coded, domains are highlighted, and disease variants are underlined. Conserved sites are bolded. As we hope that iProteinDB will lead to new discoveries and hypotheses on previously uncharacterized phosphorylation events, we further integrated information on availability of corresponding antibodies from Cell Signaling Technology for proteins and sites that are homologous between Drosophila and human to help users with experimental designs.

  3. Protein Abundance
    Protein expression levels from a comprehensive study covering the complete Drosophila melanogaster life cycle[5] are plotted. On this tab, a user can view the stages of the Drosophila life cycle during which a protein of interest is expressed.

References

  1. Bodenmiller B, Campbell D, Gerrits B, Lam H, Jovanovic M, Picotti P, Schlapbach R, Aebersold R. 2008. PhosphoPep--a database of protein phosphorylation sites in model organisms. Nat Biotechnol 26:1339-1340.
  2. Hilger M, Bonaldi T, Gnad F, Mann M. 2009. Systems-wide analysis of a phosphatase knock-down by quantitative proteomics and phosphoproteomics. Mol Cell Proteomics 8:1908-1920.
  3. Zhai B, Villen J, Beausoleil SA, Mintseris J, Gygi SP. 2008. Phosphoproteome analysis of Drosophila melanogaster embryos. J Proteome Res 7:1675-1682.
  4. Hu Y, Flockhart I, Vinayagam A, Bergwitz C, Berger B, Perrimon N, Mohr SE. 2011. An integrative approach to ortholog prediction for disease-focused and other functional studies. BMC Bioinformatics 12:357.
  5. Casas-Vila N, Bluhm A, Sayols S, Dinges N, Dejung M, Altenhein T, Kappei D, Altenhein B, Roignant JY, Butter F. 2017. The developmental proteome of Drosophila melanogaster. Genome Res 27:1273-1285.