David Liu, a student in department of Life Sciences, got bit 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.
This is not a new toxin.
From NCBI , We know that it is
(2) Can you find proteins that share sequence homology with this toxin?
Show them in multiple alignment form. H3NJ3F - cytotoxin 3 - Chinese cobra
yellow : consensus
(3) Please predict its secondary structure.
Garnier plot of cytotoxin 3 - Chinese cobra
Residue totals: H: 8 E: 29 T: 21 C: 2
percent: H: 18.2 E: 65.9 T: 47.7 C: 4.5 (4) Please show its charge distribution.
Charge distributional analysis of cytotoxin 3 - Chinese cobra : From the first amino acid to the last (1--60)
1 0+00+00000 0+00000+00 00+0000000 +000++000- 000+00000+ 000000-+00
Homology protein
Secondary stucture
Charge distribution
H3NJ2I - cytotoxin 2 - Naja naja
JS0028 - cytotoxin II - monocled cobra
H3NJ5F - cytotoxin 5 - Chinese cobra
JC2469 - cardiotoxin - Chinese cobra
H3NJ2R - cytotoxin 2 - Asian cobra
H3NJ2F - cytotoxin 2 - Chinese cobra
H3NJ2K - cytotoxin 2 - monocled cobra
H3NJ4F - cytotoxin 4 - Chinese cobra
H3NJ3K - cytotoxin 3 - monocled cobra
green : conserve
blue : amino acid carry the same charge in the same coloum
60 aa; DCH = 0, DCS = 0
. 10 . 20 . 30 . 40 . 50 . 60
LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN
helix H HHH HHHH
sheet EEEEEEEEE EEEEE E E EEEEE EEEEEEEE
turns TTT TTTT T T TT TTTT TTTTTT
coil C C