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:
- 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
Drosophilaspecies 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.
- Predicted Orthologs
A user can find a table of the best ortholog candidates for major model organisms based on DIOPT
ortholog prediction. 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
- Protein Abundance
Protein expression levels from a comprehensive study covering the completeDrosophila melanogaster
life cycle are plotted. On this tab, a user can view the stages of the Drosophila
life cycle during which a protein of interest is expressed.
- 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
- 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.
- Zhai B, Villen J, Beausoleil SA, Mintseris J, Gygi SP. 2008. Phosphoproteome analysis of Drosophila
melanogaster embryos. J Proteome Res 7:1675-1682.
- 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.
- 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.