TP11_fungal_protein_BLAST\TP11_fungal_protein_BLAST

Fungal Protein BLAST

BLAST is the most commonly used algorithm for comparing sequences. BLAST requires the database to be indexed (processed by BLAST), so BLAST is usually used in combination with a specific database such as Genbank or Saccharomyces genome database (SGD).

This document will demonstrate the capabilities of BLAST by using an example search of genes in different yeasts. The gene CaJEN2 in Candida albicans encodes a protein that is a membrane transporter for dicarboxylic acids such as malic and succinic acid and has biotechnological interest.

First we will find the sequence for this protein

Go to Candida Genome Database (http://www.candidagenome.org) and search for the gene JEN2 (Fig 1).

The JEN2 page looks like the

click on the tab called “Protein” (Fig 3)

Download the sequence in FASTA format by scrolling down and clicking the Download button (Fig 3).

You should now have a 513 aa sequence in FASTA format in your web browser or downloaded as a text file on your computer (Fig 5).

We call this sequence CaJEN2p (Candida albicans JEN2).

Question 1: What is the name of the gene that encodes the closest homolog of the CaJEN2p in the yeast Saccharmoyces cerevisiae? (Tip! Use the BLAST service of SGD).

Question 2: How many relevant homologs did you find?

Question 3: From which organism is the sequence below? Use the tool you think is the best.

>unknown

MDLDNLPAPDLSWKSIKHYLATRVTTLKPPKLSAEEKKHINPIPALRTLNKKQWLFVLCGLAGWTWDSFD

FFSVSLVASDIAKDLNVSVTDITWGITLVLMLRSVGAIIFGVASDRYGRKWPFIFNCVLFIVLELGTGFV

QTYKQFLGVRALFGIAMGGIYGNAAATALEDCPPEARGVISGLLQEGYALGYLLCVIFTRAIADTSPHGW

RALFWFGSGPPVLIIIFRFFLPETDTYIQSKQNAEALGVEKHFWLGIKTTFKTYWLMFIYLVVLMAGFNF

MSHGSQDLYPTMLKVQLGFSPDRSTVTNCVANLGAIAGGVIIGHFSSVLGRRLSIMISCILGGAMIYPWA

FVTNSGINAGVFFLQFFVQGAWGVIPIHLTELCPPALRSSLVGLAYQLGNLASSASSTIEAQIGTQFPIK

DDNGVDRPGVYNYSLVMCIFIACVFTFVFVVTFLGPENRMAEMVAHEHVEYTKEMSDDEEKGVQETVEVV

ERVDTNATK