1. I NTRODUCTION TO DATABASES - P RACTICAL

2. Q UERY S EQUENCE >my weird new protein MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT PLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVC KPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVV HFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQG SNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA

3. 1. D O A I NTER P RO S CAN http://www.ebi.ac.uk/Tools/services/web/toolform. ebi?tool=iprscanhttp://www.ebi.ac.uk/Tools/services/web/toolform. ebi?tool=iprscan using the sequence of interest Clear all program options and then select only ‘FPrintscan’ and ‘PatternScan’ and then submit Copy the image that is returned as the result summary for inclusion in your report What is the putative function based on the patterns reported by Interpro?

4. N OW DO A PROTEIN BASED BLAST SEARCH (http://blast.ncbi.nlm.nih.gov/Blast.cgi) using the same sequence.http://blast.ncbi.nlm.nih.gov/Blast.cgi Discuss whether the results correspond with the pattern results in terms of predicted function. Explain why these small motifs are so evolutionarily conserved that they can be used to predict what a protein’s function is?

5. 3. E XPLORE E NTREZ Click through the ‘G’ link in the first BLAST result. Use as much information on the next page and links from it (HINT: Click the ‘OMIM’ link on the right hand side of the page) to answer the following, with a reasonable amount of detail: What is this protein’s function in terms of its cellular role? What disease(s) is it involved in when mutated? (HINT: there is more than one – look carefully)

6. 4. U SE THE MODEL ORGANISM DATABASES Use the Mouse Genome Database and check what physiological characteristics become apparent when the gene is experimentally disrupted: Go to http://www.informatics.jax.org/http://www.informatics.jax.org/ Click on ‘Genes’ and do a Gene & Markers query using the gene symbol with the default settings Scroll down to the ‘Alleles and Phenotype’ section and click on the linked number next to ‘All alleles’ Do the experimental phenotypes agree with the diseases you found in (3)? Explain. Would you have been able to get a good idea of the HUMAN gene’s cellular functions from the mouse information if you knew completely nothing about it? Explain.