25 Jun Find the ermB coding sequence of Streptococcus agalactiae in GenBank
Question
1) Find the ermB coding sequence of Streptococcus agalactiae in GenBank. Make sure you find the complete coding sequence (hint: pay attention to the bp length of your query result), in nucleotide format. Report the accession number.
2.Identify orthologs by BLAST. Choose the “blastn” and “highly similar” sequence option. Explain to me – from your own knowledge, or perusal of the literature what the following parameters mean: a) Max ident, b) Query Coverage, c) e-value.
3.What evidence, if any, can you find among your BLAST result list of putative orthologs, that would suggest sharing of ermB among lineages – especially between agricultural species (like S. agalactiae) and human pathogens? (Hint: this requires some detective work on your part – i.e. you need to find out something about the ecology/biology as well as the phylogenetic relatedness of your species on this list. Explain your answer with specific examples. Describe to me whether you think that you have evidence for extensive HGT, a mix of HGT and vertical evolution, or mostly vertical evolution. Describe the evidence you are using to make a decision on HGT. Based on our discussion in class, what other tools can you imagine using beyond a BLAST search that would ultimately help you solving the question of HGT, as well as directionality of transfer?
4. S. agalactiae is a gram positive bacterium. How would you modify your BLAST search to enrich your hit list for gram negative query results? Why would searching for connections of ermB to gram negative bacteria be interesting? If you do this BLAST how does it change your results?
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