Protein Molecular Analysis

Updated 31 December '05

Objective

You have cloned a gene from a yeast DNA library that seems to be the site of an interesting mutation. Because of a limited laboratory budget and time you have obtained only a short sequence of this gene. You are interested in finding all the available molecular and biological information about the structure and function of this protein for use in the class discussion.

See an interesting introduction to this type of study, Bioinformatics and Comparative Genomics by Robert Jones.

Work through A Guide to Molecular Sequence Analysis for instructions on how make this project happen. Or see the resource guide in the SGD Tutorial. Keep a list of the questions you have as you work through the tutorial. Search for good answers for your questions so you can offer thorough explanations of your discoveries!

Procedure

• Obtain (copy) a partial amino acid sequence of unknown protein from the list below.
• Obtain complete sequence from SGD or other source on the Internet.
• Locate your sequence in the yeast genome map.
• Identify the closest ORF, obtain the base sequence, and translate it into protein.
• Explore information available about this protein (Follow the guide above).
• Find similar sequences in other databases.
• Do a global alignment of your sequence vs similar sequences.
• Look for evidence that this gene is part of a larger gene family.
• Look for specific patterns in your protein. Does it have known domains or modules.
• Determine the putative structure of your protein or show a published view, if available.
• Explore information about the function for this and related proteins.
• Collect information about genes with the same phenotype and the deletion phenotype.
• Find the expression pattern for this gene using Expression Connection or other sources.
• Explore connections to similar proteins in other species.
• View models of the protein.
• Check for information about interactions with other proteins.
• Write a short research report in web page format with links to appropriate information.
• Be ready to provide a summary computer demonstration for class in two weeks.

"Unknown" Protein Sequences

1. EEMKDTTYKRIAALDIKMPSNISQDAQ
2. RASCPSCTQECETHMKPVNIPHFKEVI
3. DILTISKDALDKYQLERDIAGTV
4. KLTDNVEALLALTNLASSETSDGEEV
5. KKNLPKPFKNKKKNGKEESKEDSSA
6. SENISIGYLMSAASDLPFEYNIQKDD
7. ALSSIKDVVPNLLNLLTRQNDPEDDD
8. ASSLVITALKEPPRDRKKDK
9. TRRRLLQLQKIGANKKCMDCGAPN
10. SSLMLKKWTPPDIESHGISDFKSKFS
11. GKEDLLVTKNMAPGESVYGEKRISVEE
12. QEDYDRLRPLSYPSTDVFLVCFSV
13. ELDGKTVKLQIWDTAGQERFRTITSS

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