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.
Solution:
(1)
sp|Q02454|CX1_NAJSP CARDIOTOXIN PRECURSOR. pir||A44335 cardiotoxin -
¡@¡@¡@¡@ Naja naja gi|213375 (L04640) cardiotoxin [Naja naja]
¡@¡@¡@¡@ Length = 81
¡@
Score = 340 (163.9 bits), Expect = 1.0e-44, P = 1.0e-44
Identities = 60/60 (100%), Positives = 60/60 (100%)
Query:
1 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN
60LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN
Sbjct:
22 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 81
(2)
[Image]
Version 1.4
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Multi Sequence Align Results
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CARDIOTOXIN PRECURSOR.
CARDIOTOXIN III (NMR, 13 STRUCTURES)
CARDIOTOXIN II (NMR, MINIMIZED AVERAGE STRUCTURE)
CARDIOTOXIN CTX I (NMR, 11 STRUCTURES)
CARDIOTOXIN GAMMA (NMR, MINIMIZED AVERAGE STRUCTURE)
CARDIOTOXIN CTX IIB (NMR, 20 STRUCTURES)
CARDIOTOXIN V=4===/II$== (TOXIN /III$)
CARDIOTOXIN V (NMR, 2 STRUCTURES)
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(3)
81 aa; DCH = 0, DCS = 0
. 10 . 20 . 30 . 40 . 50 . 60
MKTLLLTTVVVTIVCLDLEYTLKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCI
helix HHHHHH HHHHHHH HHH HHHH
sheet EEEEEEEEEE EEEEEEEEE EEEEE E E EE
turns TT TTTT T T TT
coil C C
. 70 . 80
DVCPKSSLLVKYVCCNTDRCN
helix
sheet EEE EEEEEEEE
turns TTTT TTTTTT
coil
Residue totals: H: 20 E: 39 T: 20 C: 2
percent: H: 30.8 E: 60.0 T: 30.8 C: 3.1
(4) CHARGE DISTRIBUTIONAL ANALYSIS
1 0+00000000 000000-0-0 00+00+0000 00+00000+0 000+000000 0+000++000
61 -000+00000 +000000-+0 0
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 12/30 or 16/45 or 19/60): none
Negative charge clusters: not evaluated (frequency of - < 5%, too low)
Mixed charge clusters (cmin = 14/30 or 19/45 or 24/60): none
B. HIGH SCORING (UN)CHARGED SEGMENTS.
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High scoring positive charge segments:
score= 2.00 frequency= 0.148 ( KR )
score= 0.00 frequency= 0.000 ( BZX )
score= -1.00 frequency= 0.802 ( LAGSVTIPNFQYHMCW )
score= -2.00 frequency= 0.049 ( ED )
Expected score/letter: -0.605
- now scoring for positive charge segments; Average information/letter: 0.727
Minimal length of displayed segments set to: 20
M_0.01= 11.01 (cv= 6.42, lambda= 0.68489, k= 0.23341, x= 4.59;
90% confidence interval for segment length: 15 +- 15)
M_0.05= 8.63 (x= 2.21)
# of segments (>=20 residues) exceeding M_0.05: none
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High scoring negative charge segments:
score= 2.00 frequency= 0.049 ( ED )
score= 0.00 frequency= 0.000 ( BZX )
score= -1.00 frequency= 0.802 ( LAGSVTIPNFQYHMCW )
score= -2.00 frequency= 0.148 ( KR )
Expected score/letter: -100.00
- now scoring for negative charge segments; Average information/letter: 2.722
Minimal length of displayed segments set to: 20
M_0.01= 5.91 (cv= 3.17, lambda= 1.38629, k= 0.44580, x= 2.74;
90% confidence interval for segment length: 4 +- 4)
M_0.05= 4.73 (x= 1.56)
# of segments (>=20 residues) exceeding M_0.05: none
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High scoring mixed charge segments:
score= 1.00 frequency= 0.198 ( KEDR )
score= 0.00 frequency= 0.000 ( BZX )
score= -1.00 frequency= 0.802 ( LAGSVTIPNFQYHMCW )
Expected score/letter: -0.605
- now scoring for mixed charge segments; Average information/letter: 1.223
Minimal length of displayed segments set to: 20
M_0.01= 5.86 (cv= 3.13, lambda= 1.40180, k= 0.45603, x= 2.72;
90% confidence interval for segment length: 10 +- 8)
M_0.05= 4.69 (x= 1.56)
# of segments (>=20 residues) exceeding M_0.05: none
________________________________
High scoring uncharged segments:
score= 1.00 frequency= 0.802 ( LAGSVTIPNFQYHMCW )
score= 0.00 frequency= 0.000 ( BZX )
score= -8.00 frequency= 0.198 ( KEDR )
Expected score/letter: -0.778
- now scoring for uncharged segments; Average information/letter: 0.128
Minimal length of displayed segments set to: 20
M_0.01= 38.95 (cv= 26.39, lambda= 0.16653, k= 0.08143, x= 12.56;
90% confidence interval for segment length: 73 +- 63)
M_0.05= 29.16 (x= 2.78)
# of segments (>=20 residues) exceeding M_0.05: none
C. CHARGE RUNS AND PATTERNS.
pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)|
lmin0 5 | 3 | 5 | 34 | 9 | 6 | 10 | 11 | 7 | 12 |
lmin1 6 | 4 | 7 | 41 | 11 | 8 | 12 | 13 | 9 | 15 |
lmin2 7 | 5 | 8 | 45 | 12 | 9 | 14 | 15 | 10 | 16 |
There are no charge runs or patterns exceeding the given minimal lengths.
Run count statistics:
+ runs >= 3: 0
- runs >= 3: 0
* runs >= 4: 0
0 runs >= 22: 0