fragments G or A? Google \"NCBI BLAST pick the top entry, and choose: \"Protein
ID: 3165717 • Letter: F
Question
fragments G or A? Google "NCBI BLAST pick the top entry, and choose: "Protein BLAST. The resulting screen will look like Figure 2 to the left. Insert the 20aa sequence 1.f. If the promoter is to the left of G or to the right of A, what is the minimum number of exons that the 3.4knt mRNAinto the box could have? Make one change in BLAST a. Click on "Algorithm parameters" below "BLAST (red box). b. Under "General Parameters c. Change "Max target sequences" from 100 to 5000 Click BLAST and in a while (~2 min for me) you will get output. Scrolli down until you see what is in Figure 3, though I have blocked out some information. Answer these questions. Figure 2 1 Click on entry #7, which will take you down to a lower place in this file. Study the title. What is the "Query? 2. This entry was derived from an X-ray structure between a protein and an inhibitor. What is the inhibitor? 3. The X-ray structure did not contain all amino acids in the protein. How can you conclude that? K?GDFGLATEKSRwSGSHQF 4, Scroll back up and find Entry #11? Click on entry #11. what is the crucial difference between Entry 11 and Entry #7? S. How is Entry #11 different than #7 in the "Ident" column? What do you think "Ident" stands for? 6. Find Entry #10, what about the title of Entry ?10 don't you like, given what you know about this gene/protein? 7. In the table (below) two .Sbjet" have the same dent" (84%). (NOTE: BLAST only found 19 and not 20 amino acids of homology.) The E-values differ. (Review class notes about E-values.) Which Sbjct does BLAST rank to be more similar to your Query? 8. Study the amino acid differences between your Query and each Sbjct. Why is one Sbjct ranked more similar to your Query? You will have to look up the one-letter code for amino acids and look at amino acid structures Sequence KIGDEGLATEKSRWSGSHO Query Sbjet (Esox lucius) KIGorGLAN TARHTGSBQ 84% 2e-06 sbjct (Danio rerio) KIGDPGLATVKARWSGsoo 843e-06 Figure 3 Ident 10 E-valueExplanation / Answer
1- query is KIGDFGLATEKSRWSGSHQF
2- Inhibitor is Vemurafenib
3- Name of the protein is B-Raf which is a protein of 766 amino acids. When we click on the 30G7.A most of the amino acids are missing in the X-ray crystallography
4- Entry 11 is the wild-type B-Raf whose length is 3 amino acids.
In case entry 7, there is the mutation in which Valine present at 600 is mutated into E
In case of entry 11, the sequence is the wild-type B-Raf
5- In case of entry 7 the Ident is 100% whereas in case of entry 11 Ident is 95%.
Ident means the identity
6- In case of entry 10 there is the mutation in which Valine present at 599 is mutated into E
whereas In case entry 7, there is the mutation in which Valine present at 600 is mutated into E.
It means that in case of entry 10 there is the deletion of one amino acid in the B-Raf protein
7- Lesser the value of E, the protein is more homologous to the query sequence.
So Subject -Esox lucius is rank more similar to our query.
8- In case of Esox Lucius there in only one mutation that is also present in case of Danio Rerio. But in case of Danio rerio, Histinde is mutated into Glutamic acid. Or in other words, basic amino acid is mutated into acidic amino acid. So Exos Lucius subject is ranked more close to the query sequence.
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