Homework 7

Sequence comparison / Homology search

due on 5/28

1. David Liu, a student in department of Life Sciences, was bitten by a snake in the backyard of life science building. He was so angry! Thus, he killed the snake and purified several toxins from its venoms. He sequenced one of the toxin, got this sequence: .

1 L K C N K L V P L F Y K T C P A G K N L C Y K M F M V A T P

31 K V P V K R G C I D V C P K S S L L V K Y V C C N T D R C N

(1) Is this a new toxin? Please help him to identify this toxin.

(2) Can you find proteins that share sequence homology with this toxin? Show them in multiple alignment form

(3) Please predict its secondary structure.

(4) Please show its charge distribution.

Ans:

(1) The query sequence was identified as the following three cytotoxins ferived from PDB with 100 % homology: The sp|Q02454|CX1, the sp|P01444|CX3, and the pir. The more detail collected data is shown here.

(2)

(3)The predicted secondary structure

10 20 30 40 50 60 ....:....x....:....x....:....x....:....x....:....x....:....x CCCCCEEEEEECCCCCCCCHCEHHCCECEEEECCCCCCCCCCCCCCCEEEEEEEEECCCC BPS CHHHHCEEEEECCCCCCCHCCCCCEEECCCCCCCCCCCEEECCCCEEEEEEEEECCCCCC GAS HHHCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCC GOR CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCC H_K CCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCC Q_S CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCC JOI

(4)Charge Distribution Assay :

1 0+00+00000 0+00000+00 00+0000000 +000++000- 000+00000+ 000000-+00

Another references can link here.