HOMEWORK#9

Sequence comparison / model building

• due on 6/2

• Mac Lee, a student in the 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 I C Y K M F M V A T P

31 K L P V K R G C I D V C P K S S L L V R Y V C C N T D K 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 (at least 10 sequences) in multiple alignment form (in color).

(3) He would like to see 3D structure of this toxin. Please help him to make the model.
 
 

Ans:
(1)   Yes, it is a new toxin!!
        Definition: cytotoxin 3 - Chinese cobra
        Score = 329 (156.6 bits), Expect = 3.7e-39, P = 3.7e-39
        Identities = 56/60 (93%), Positives = 60/60 (100%)
        Features : Location/Qualifiers
         source          1..60
                     /organism="Naja atra"
                     /db_xref="taxon:8656"
         Protein         1..60
                     /note="cardiotoxin analog III"
                     /product="cytotoxin 3"
         Bond            bond(3,21)
                     /bond_type="disulfide"
         Bond            bond(14,38)
                     /bond_type="disulfide"
         Bond            bond(42,53)
                     /bond_type="disulfide"
         Bond            bond(54,59)
                     /bond_type="disulfide"

 Query:     1 LKCNKLVPLFYKTCPAGKNICYKMFMVATPKLPVKRGCIDVCPKSSLLVRYVCCNTDKCN 60
                     LKCNKLVPLFYKTCPAGKN+CYKMFMVATPK+PVKRGCIDVCPKSSLLV+YVCCNTD+CN
Sbjct:        1 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 60