Homework 4: Fill in the blank – 6 points each – capitalization does not matter. Students can take this assignment an unlimited number of times with the best score kept.
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Question 1 of 1
1. Question
Use NCBI’s Protein database to acquire the protein sequences for human, marmoset, gibbon, monkey, and chimp 40S ribosomal subunit (NCBI locus tags AAA16105, NP_001240703, XP_012365903, XP_012325771, and NP_001238922, respectively). Use PROMALS3D to perform a multiple sequence alignment on these sequences.
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From these PROMALS3D results, which sequence is not similar to the others? Provide your answer as an NCBI locus tag.
Re-run PROMALS3D using only the 4 sequences that were similar – in other words remove the beforementioned locus tag. Do your results change? Response Yes or No.
From this second set of PROMALS3D results, which sequence is the representative sequence? HINT: Locus tags with a magenta color are representative sequences. Provide your answer as an NCBI locus tag.
From this second set of PROMALS3D results, how many conserved alpha-helix secondary structures were predicted?
From this second set of PROMALS3D results, how many conserved beta-strand secondary structures were predicted?
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