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.

 

Answer :

<1>

*I can find the cytotoxin 3 precursor and cardiotoxin precursor (identities = 93%) which are similar wth the snake toxin.

* sp|P01444|CX3_NAJAT
CYTOTOXIN 3 PRECURSOR
(CARDIOTOXIN ANALOGUE III) (CTX III) (CARDIOTOXIN C-10) (CYTOTOXIN IV).
 Length = 81
 
 Score =  132 bits (329), Expect = 6e-32
 Identities = 56/60 (93%), Positives = 60/60 (99%)

Query: 1  LKCNKLVPLFYKTCPAGKNICYKMFMVATPKLPVKRGCIDVCPKSSLLVRYVCCNTDKCN 60
                 LKCNKLVPLFYKTCPAGKN+CYKMFMVATPK+PVKRGCIDVCPKSSLLV+YVCCNTD+CN
Sbjct: 22  LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 81
 
 

* sp|Q02454|CX1_NAJSP
CARDIOTOXIN PRECURSOR.
Length = 81
 
 Score =  132 bits (329), Expect = 6e-32
 Identities = 56/60 (93%), Positives = 60/60 (99%)

Query: 1  LKCNKLVPLFYKTCPAGKNICYKMFMVATPKLPVKRGCIDVCPKSSLLVRYVCCNTDKCN 60
                LKCNKLVPLFYKTCPAGKN+CYKMFMVATPK+PVKRGCIDVCPKSSLLV+YVCCNTD+CN
Sbjct: 22  LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 81
 

<2>
        *  User Entered                                               snake toxin
 
         SWISSPROT:CX4_NAJAT                       OS NAJA ATRA (CHINESE COBRA).
 
         SWISSPROT:CX8_NAJAT                       OS NAJA ATRA (CHINESE COBRA).
 
         SWISSPROT:CX2_NAJKA                       OS NAJA NAJA KAOUTHIA (MONOCLED
                                                                                 COBRA) (NAJA NAJA SIAMENSIS).
 
         SWISSPROT:CX2_NAJAT                        OS NAJA ATRA (CHINESE COBRA).
 
         SWISSPROT:CX6_NAJAT                        OS NAJA ATRA (CHINESE COBRA).
 
         SWISSPROT:CXN_NAJAT                       OS NAJA ATRA (CHINESE COBRA).
 
         SWISSPROT:CX2_NAJOX                        OS NAJA OXIANA (CENTRAL ASIAN
                                                                                 COBRA) (OXUS COBRA).
 
         SWISSPROT:CX5_NAJAT                        OS NAJA ATRA (CHINESE COBRA).
 
         SWISSPROT:CX5_NAJKA                        OS NAJA NAJA KAOUTHIA (MONOCLED
                                                                                  COBRA) (NAJA NAJA SIAMENSIS).
 
         SWISSPROT:CX2_NAJNA                        OS NAJA NAJA (INDIAN COBRA).
 
         SWISSPROT:CX1_NAJSP                          OS NAJA SPUTATRIX (MALAYAN
                                                                                  SPITTING COBRA).
 
         SWISSPROT:CX3_NAJAT                         OS NAJA ATRA (CHINESE COBRA), AND
                                                                                   NAJA NAJA KAOUTHIA (MONOCLED
 
 
     * Sequence format is Pearson

• Sequence 1: 3331_   snake toxin                                60 aa
• Sequence 2: CX4_NA                                                 60 aa
• Sequence 3: CX8_NA                                                 81 aa
• Sequence 4: CX2_NA                                                 60 aa
• Sequence 5: CX2_NA                                                 81 aa
• Sequence 6: CX6_NA                                                 60 aa
• Sequence 7: CXN_NA                                                81 aa
• Sequence 8: CX2_NA                                                 60 aa
• Sequence 9: CX5_NA                                                 81 aa
• Sequence 10: CX5_NA                                               60 aa
• Sequence 11: CX2_N                                                  60 aa
• Sequence 12: CX1_N                                                  81 aa
• Sequence 13: CX3_N                                                  81 aa

 

 

<3>

*color green-----> 6 sheet
*color yellow-----> 1 helix

*sequence :
1 CNKLVPLFYKTCPAGKNICYKMFMVATPKLPVKRGCIDVCPKSSLLVRYVCCNTDKCN 58