8.2 Expasy proteomics tools  (Page 3/5)

View the results for Sequence 1. The first column of the results table identifieswhether or not the match is of type "family" or of type "domain".The family and domain names appear at the top of each box in the second column of the resultspage, the same column that contains the diagrams which show the localization of thesection of sequence that has been identified with the referenced family or domain.

View the results for Sequence 2.

View the results for Sequence 3.

Return to the ExPASy Proteomics Tools server . Now, scroll down to the section entitled "post-translational modification prediction".Use NetPhos (4) to predict possible sites for serine, threonine and tyrosine phosphorylation on the three sequences above (all 3 sequences can be enteredas one query). Accept the default values and select "submit". For help interpreting the results, view the NetPhos output format .

Once a protein sequence has been determined through proteomics techniques, bioinformatics can be used to predict certaintypes of topology. Topology is the sequence of secondary structure elements within a protein. The most basic secondary structure elements within proteins are the alpha helix, the beta sheet and the random coil. However, somealgorithms will predict topological features that are closely related to in vivo localization, such as signal sequences and transmembrane helices.

At the ExPASy Proteomics Tools server , scroll down on the ExPASy tools webpage to the section entitled "topology prediction". This sectioncontains tools that predict localization and sorting signals, as well as transmembrane regions within proteins. PSORT (5) is a computer programfor the prediction of protein localization. It requires input of an amino acid sequence and its source organism; and it searches for known,organism-specific protein sorting signals. It returns a list of candidate localization sites, accompanied by a score indicating the probability theprotein encoded by the input sequence would be localized to that site. To explore the use of PSORT, click on the PSORT link on the ExPASy tool page.Choose the "PSORT II" for eukaryotic sequences, and select the PSORT II Prediction. Cut and paste the following sequence for diacylglycerol kinase from Rattus norvegicus into the query box and click "Submit".