System Biology BLAST Protein Network Cellular Signaling Genetics

1. Perform a BLASTn search with the following sequence but only use 30 of the 50 bases. What
was your best match?
5' ATGCT CTGGC CACGG CACTT GCGGA TCCCA TGATC TGTGC ACCTG CGATA 3'
3' TACGA CACCG GTGCC GTGAA CGCCT AGGGT ACTAG ACACG TGGAC GCTAT 5'
Look to the right at the "E value" and record this number. Comment on the significance
of the value.
Now submit all 50 bases and compare your results from the search with only 30 bases.
Why did the E value change even though the retrieved sequence was identical?
2. Search NCBI's Human Map Viewer using the term "obesity". You will get hits for every locus
that has obesity associated with it. How many loci do you see? Are they clustered on the genome
or distributed throughout?
3. Provide a working definition for "ortholog". Given that other species have orthologs of
99% of our genes, how can we be different from all other species?
4. Recall the discussion about the Japanese study on yeast origins (archae vs.
eubacteria). The following questions apply to that case study:
- Based on their findings, do you think Archaea transcription factors and DNA polymerases
more resemble Eubacterial or human orthologs? Test your prediction by using BLASTp and
the Archaea sequence. What type of protein is this? What species is it from? Are there any
human orthologs on the results page (perform a "find" function with your browser for the
word 'human').
- If you wanted to use an antibiotic to kill an Archaea but not a eukaryote, what cellular
processes would make the best targets? Which would be the worst? Explain your answers.
- Why does it make sense for proteins in the ER and protein translation to be among those
originating in Archaea, rather than the "cytoplasm" category, which has a less clear origin?