How to compare gene sequences between species to examine functional differences using motif analysis?

Question

[luckilyduck]

I'm wondering how I could approach this. I am doing an undergraduate bioinformatics class project where I want to test the following hypothesis "Protein homolog are conserved motifs that mediate transport and other functions" on APOE in different organisms.

I am thinking to compare the gene sequences between the species to examine their differences on a functional level. Is this the correct approach? I'm not sure how to execute this.

Any help or guidance would be greatly appreciated!

[Emily]

Are you sure you don't mean "Protein homologues HAVE conserved motifs that mediate transport and other functions"?