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Protein Analysis Subcellular Localization Prediction
Protein (or in general, proteome) Analysis Subcellular Localization Prediction is a process (usually through the use of web-based software) of predicting the location or destination of a protein within the cell using only the protein sequence as its inputs.
Additional recommended knowledge
Sample run of the tool
For our particular purpose, we will use the PA-Subcellular Localization Prediction server found at the University of Alberta. To do a sample run of the tool, let us consider the Oxalate oxidase (OxO) enzyme from rice (NCBI). To give you an introduction, OxO are involved in plant defence to pathogen infection such as powdery mildew of barley and wheat. It catalyzes the following reaction:
Oxalate + O2 + 2H+ = 2 CO2 + H2O2.
The hydrogen peroxide, H2O2, produced may play an important role in several aspects of defense mechanisms. In rice, this enzyme has been mapped at chromosome 3.
1. enter an Analysis ID, like, "OxO".
>gi|108710532|gb|ABF98327.1| Oxalate oxidase 2 precursor, putative, expressed [Oryza sativa (japonica cultivar-group)] MEHSFKTIAAGVVIVVLLLQQAPVLIRATDADPLQDFCVADLDSKVTVNGHACKPASAAGDEFLFSSKIA TGGDVNANPNGSNVTELDVAEWPGVNTLGVSMNRVDFAPGGTNPPHVHPRATEVGIVLRGELLVGIIGTL DTGNRYYSKVVRAGETFVIPRGLMHFQFNVGKTEATMVVSFNSQNPGIVFVPLTLFGSNPPIPTPVLVKA LRVDAGVVELLKSKFTGGY
3. Click the "Plant" radio button on the "Organism Type" table. Click the "Begin Analysis" button. An intermediate page will show up. You may view the file by clicking the appropriate hyperlink or you may download it in *.csv file.
A screenshot of the result of our sample run is shown at the right pane. It contains statistics on the protein we submitted, along with BLAST results and a Subcellular Prediction.
The positive prediction gives as the most probable location of the protein sequence, in this cae, the protein OxO is secreted extracellularly (100%), probably on the cell wall, or transported to vacuole (90.346%).
For references on interpreting the results, click any of the following   
Perform the same procedure as above but use the following sequence as an entry. This amino acid sequence is Ribulose bisphosphate carboxylase (RUBISCO) large unit. From this information, we can already predict its possible location.
>gi|476752|gb|AAB02583.1| rubisco large subunit MSPQTETKASVGFKAGVKDYKLTYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESSTGTWTTVW TDGLTSLDRYKGRCYHIEPVVGEDNQYIAYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRI PPTYSKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRACYECLAGGLDFTKDDENVNSQP FMRWRGRFVFCAEAIYKSQAETGEIKGHYLNATAGTCEEMIKRAVFARELGVPIVMHDYLTGGFTANTSL AHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRMSGGDHIHAGTVVGKLEGIFFFFFFFFFFFL RKELYVCVIIQNKHVVQGVAVHACRISSSLWYTYPSKRSKTYETNTQEEES
Other Subcellular Localization Servers
|This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "Protein_Analysis_Subcellular_Localization_Prediction". A list of authors is available in Wikipedia.|