| << Chapter < Page | Chapter >> Page > |
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.
How many matches were of the type "family"?
How many were domains?
What are the names of the families identified with this sequence?
List any domains that were identified within Sequence 1.
View the results for Sequence 2.
How many families were returned as matches?
How many domains?
What families were identified with this sequence?
List any domains that were identified within Sequence 2.
View the results for Sequence 3.
How many families were returned as matches?
How many domains?
What families were identified with this sequence?
List any domains that were identified within 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 .
How many (a) serine, (b) threonine, and (c) tyrosine phosphorylation sites are predicted for Sequence 1?
How many (a) serine, (b) threonine, and (c) tyrosine phosphorylation sites are predicted for Sequence 2?
How many (a) serine, (b) threonine, and (c) tyrosine phosphorylation sites are predicted for Sequence 3?
Are there any serine, threonine and tyrosine in the sequence that were not listed as a potential phosphorylation site? If so, explain why some of the residues were not listed as predicted phosphorylation sites. (Those uncertain about the answer to this question should view the above link explaining the output.)
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
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".
Notification Switch
Would you like to follow the 'Bios 533 bioinformatics' conversation and receive update notifications?
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|