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Orthologues for the Schizosaccharomyces pombe mcm6 gene

(a) How many orthologues are predicted for the Schizosaccharomyces pombe mcm6 gene in Fungal Compara? What about in Pan-taxonomic Compara?

(b) How much sequence identity does the Giardia lamblia protein have to the one of Schizosaccharomyces pombe? Click on the View Sequence Alignments link in the Orthologue column to view a protein alignment in Clustal W format.

(a) Go to fungi.ensembl.org, choose Schizosaccharomyces pombe and search for mcm6. In the search results, click on the gene ID SPBC211.04c to open the Gene tab.

On the Gene tab, click on Orthologues under Fungal Compara in the left-hand menu to see all the orthologous genes.

There are 221 species with 1:1 orthologues and 11 with 1:many orthologues in Fungal Compara.

Click on Orthologues under Pan-taxonomic Compara.

There are 58 species with 1:1 orthologues, 23 species with 1:many orthologues and seven with many:many orthologues in Pan-taxonomic Compara.

(b) Find the the Giardia lamblia protein in the table

The percentage of identical amino acids in the Giardia lamblia protein (the orthologue) compared with the gene of interest i.e. Schizosaccharomyces pombe mcm6 (the target species/gene) is 26.52%. This is known as the Target %id.

The identity of the gene of interest (Schizosaccharomyces pombe mcm6) when compared with the orthologue (the Giardia lamblia gene, the query species/gene) is 28.36%. This is known as the Query %id.

Note that the difference in the values of the Target and Query %id reflects the different protein lengths for the Schizosaccharomyces pombe and Giardia lamblia mcm6 genes.

Click on View Sequence Alignments, then View Protein Alignment in the pop-up window, to view a protein alignment in Clustal W format.