Background: Eukaryotic cells synthesize many thousands of different proteins that are distinct not only in their functional characteristics, but in their sub-cellular localization. The correct localization of protein products is just as important to the function of living cells as the synthesis of proteins with the correct amino acid sequences.  Although there are many factors that in?uence the localization of proteins (e.g. af?nity for lipid rafts, pH-dependent changes in conformation or interactions, posttranslational modi?cations, etc.) the most common principle underlying speci?c protein traf?cking is the existence of "targeting signals" - speci?c sequences within the primary structure of the proteins that are recognized by transporters and/or other cellular machinery, which then target the protein to the correct destination. 

Because many of these "shipping labels" are speci?ed by the primary sequence of the protein, various bioinformatic tools have been developed to predict the localization of unknown proteins on the basis of their [predicted] sequences.  Several programs have been developed to identify sorting signals in proteins; you can ?nd a list of them here: http://psort.org. 

Four you may ?nd particularly useful are: 1) SignalP (http://www.cbs.dtu.dk/services/SignalP/) 2) Minimotif Miner (http://mnm.engr.uconn.edu/MNM/SMSSearchServlet) (see Mi et al, 2012) (note: to use MmM for this assignment, you will have to ?lter for motifs involved in traf?cking) 3) PSORTII (http://psort.hgc.jp/form2.html) 4) YLoc (http://abi.inf.uni-tuebingen.de/Services/YLoc/webloc.cgi) (see Briesemeister et al. 2010). 

Part I Using the software referenced above, and your own understanding of cellular protein sorting mechanisms, predict where this protein will localize: 

Part II Below are listed 9 possible sub-cellular localizations (one of which can be subdivided into two). 

Pick any two of these, and use the NCBI protein database (http://www.ncbi.nlm.nih.gov/protein) to find an example of a protein that will localize to each of them. In your submission, include a FASTA format (https://en.wikipedia.org/wiki/FASTA_format) listing of each protein's amino acid sequence, its name and the organism it is from, and briefly justify your prediction by identifying the sequence features you expect play an important role in it's localization.

Localizations:

A) Cytosol (not associated with any particular organelle)

B) Nuclear

C) Plasma membrane

i) Apical plasma membrane

ii) Basolateral plasma membrane

D) Secreted

E) Endoplasmic reticulum (resident)

F) Lysosome

G) Peroxysome

H) Mitochondria

I) Plastid.

Attachment:- Assignment.rar