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.
Ans: It is a new protein. The result when compare to protein sequences in NCBI BLAST, there are no proteins 100% identical to this sequence.
(2) Can you find proteins that share sequence homology with this toxin? Show them in multiple alignment form.
Ans: Multi Sequence Align Results
10 proteins are selected.
Their SwissProt accession numbers
are
1.Q02454
2.P01444
3.P01440
4.P24779
5.P07525
6.P01441
7.P49124
8.P80245
9.P01442
10.P01445
.
(3) Please predict its secondary structure.
Ans: Its secondary structure predicted
by Garnier method. Osgusthorpe, and Robinson, J. Mol. Biol.,(1978) 120:97-120
Garnier plot of CARDIOTOXIN III (NMR, 13 STRUCTURES)
60 aa; DCH = 0, DCS =0
LKCNKLVPLFYKTCPAGKNICYKMFMVATPKLPVKRGCIDVCPKSSLLVRYVCCNTDKCN
helix H------------------------HHHH-------------------------------
sheet ---EEEEEEEEE------EEEEEEE-----------EEEEE----EEEEEEE--------
turns TTT----------TTTTT-----------T-TTTTT-----TTTT-------TTTTTTT-
coil ------------C-----------------C-----------------------------
H--helix E--sheet
T--turn C--coil
residue totals: H:
5 E: 28 T: 25 C: 2
percent: H: 11.4
E: 63.6 T: 56.8 C: 4.5
(4) Please show its charge distribution.
Ans: CHARGE DISTRIBUTIONAL ANALYSIS
1 0+00+00000 0+00000+00
00+0000000 +000++000- 000+00000+ 000000-+00
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 13/30
or 18/45 or 22/60): none
Negative charge clusters: not
evaluated (frequency of - < 5%, too low)
Mixed charge clusters (cmin = 15/30
or 20/45 or 25/60): none
B. HIGH SCORING (UN)CHARGED SEGMENTS.
High scoring positive charge segments:
score= 2.00 frequency=
0.183 ( KR )
score= 0.00 frequency=
0.000 ( BZX )
score= -1.00 frequency=
0.783 ( LAGSVTIPNFQYHMCW )
score= -2.00 frequency=
0.033 ( ED )
Expected score/letter: -0.483
- now scoring for positive charge segments;
Average information/letter: 0.430
Minimal length of displayed segments
set to: 20
M_0.01= 13.07 (cv= 7.77, lambda=
0.52686, k= 0.16371, x= 5.30;
90% confidence interval for segment length: 23 +- 25)
M_0.05= 9.97 (x= 2.20)
# of segments (>=20 residues) exceeding M_0.05:
none
High scoring negative charge segments:
score= 2.00 frequency=
0.033 ( ED )
score= 0.00 frequency=
0.000 ( BZX )
score= -1.00 frequency=
0.783 ( LAGSVTIPNFQYHMCW )
score= -2.00 frequency=
0.183 ( KR )
Expected score/letter: -1.083
- now scoring for negative charge segments;
Average information/letter: 3.490
Minimal length of displayed segments
set to: 20
M_0.01= 4.94 (cv= 2.54, lambda=
1.61122, k= 0.47671, x= 2.40;
90% confidence interval for segment length: 3 +-
3)
M_0.05= 3.92 (x= 1.38)
# of segments (>=20 residues) exceeding M_0.05:
none
High scoring mixed charge segments:
score= 1.00 frequency=
0.217 ( KEDR )
score= 0.00 frequency=
0.000 ( BZX )
score= -1.00 frequency=
0.783 ( LAGSVTIPNFQYHMCW )
Expected score/letter: -0.567
- now scoring for mixed charge segments;
Average information/letter: 1.051
Minimal length of displayed segments
set to: 20
M_0.01= 6.07 (cv= 3.19, lambda=
1.28520, k= 0.40993, x= 2.89;
90% confidence interval for segment length: 11 +- 9)
M_0.05= 4.80 (x= 1.62)
# of segments (>=20 residues) exceeding M_0.05:
none
High scoring uncharged segments:
score= 1.00 frequency=
0.783 ( LAGSVTIPNFQYHMCW )
score= 0.00 frequency=
0.000 ( BZX )
score= -8.00 frequency=
0.217 ( KEDR )
Expected score/letter: -0.950
- now scoring for uncharged segments;
Average information/letter: 0.173
Minimal length of displayed segments
set to: 20
M_0.01= 32.53 (cv= 20.56, lambda=
0.19916, k= 0.10900, x= 11.97;
90% confidence interval for segment length: 54 +- 44)
M_0.05= 24.34 (x= 3.79)
# 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 | 6 | 29 | 10 | 6 | 10 |
11 | 6 | 12 |
lmin1 6 |
4 | 7 | 36 | 12 | 7 | 12 |
14 | 8 | 14 |
lmin2 7 |
4 | 8 | 39 | 13 | 8 | 14 |
15 | 9 | 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 >= 20:
0