Homework 4

Kevin Lyu, a graduate student in our department, got a cDNA that encode a protein from rice. Here is the sequence:

CGGCACGAGCAGCAACTTAACTTGATCTTCGTGTGACCGATCGATGGCTCGCGCGGGACATAATAAGTAT

GTGGCGCGCGTGATGGTGGTGGCGCTGCTGTTGGCCGCGCGGGCACCCGTGACATGCGGGCAGGTGGTGA

GCACTTGGGCGCCGTGCATCATGTACGCCGACGGGGAGGGTGTCGCCCCCACCGGCGGCTGCTGCGACGG

GGTCAGGACCCTCAACTCCGCCGCCGCCACCACCGCCGACCGCCAGACCACCTGCGCCTGCCTCAAGCAG

CAGACCAAGGCCATGGGCCGGCTGAGGCCCGACCACGTCGCCGGCATCCCCTCCAAGTGCGGGGTCAACA

TCCCCTACGCTATCAGCCCTTCCACCGACTGCTCCAGGGTGCACTGAGTGGATCAACGTCAAGTGATGCC

ACAATAATAATGGAGAGATGGATCCATCGATCTGCGGCTCTCATTTTGCGGTTGCTATCTGCAATATTCG

TCGTCGTCGGAGAGATCGAGCTAGAAATGCATGTTACTCCTCCGTTCTGTTACTATCTGCTTACCTGTTG

CTTCGTGCGGTTTGATAGTGTCGTTATAGCTAGTGTAAGAGTGTGAGGGTTGATTTTGATCTGTCTCCTT

TACGGGACGAGGGGCACGGCGAATCATGCATGAATCTTAGAGGACCTGCTTGCATTGTACCTTACTCAGT

GCATGCTTCAATATATATCCATCAAATGAAGATCTTTTAATGAAAAAAAAAAAAAAAAAAAAAAAA

Unfortunately, he doesn't know how to use the sequence analysis tools availabled in the internet since he did not take Bioinformatics course before. Could you help him to do the following analysis?

(1) Find its corresponding polypeptide sequence (DNA -> Protein translation).

(Blastx¬d¸ß)maraghnkyvarvmvvalllaarapvtcgqvvstwapcimyadgegvaptggccdgvrtlnsaaattadr qttcaclkqqtkamgrlrpdhvagipskcgvnipyaispstdcsrvh

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(2) Identify this protein. Is it a new protein? If not, what's the name of this protein?

ANSWER: NONSPECIFIC LIPID-TRANSFER PROTEIN

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(3) Report the total number of negatively charged residues and positively charged residues.

ANSWER: Total number of negatively charged residues : 6

Total number of positively charged residues : 15

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(4) Draw the hydrophobicity map for this protein using Eisenberg hydrophobicity scale with window size 7. The relative weight of the window edges compared to the window center should set to 40%.

ANSWER:

hk4-3.gif (10093 bytes)

(5) Is there any hydrophobic region in this protein?

ANSWER:Yes

Can you explain the possible role for this region?

ANSWER:Hydrophobic region may be the transmembrane domain of the protein.

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(6) Please help him to use Prosite scanning tool to find out possible functions or pattern of this protein.

Answer

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(7) Color the protein by the hydrophobicity of the amino acids. 

        10        20        30        40        50        60        70
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MARAGHNKYVARVMVVALLLAARAPVTCGQVVSTWAPCIMYADGEGVAPTGGCCDGVRTLNSAAATTADR
QTTCACLKQQTKAMGRLRPDHVAGIPSKCGVNIPYAISPSTDCSRVH