Homework #7

Answer #1:

1.                                                                 Smallest
                                                                       Sum
                                                             High  Probability
Sequences producing High-scoring Segment Pairs:              Score  P(N)      N

sp|Q02454|CX1_NAJSP  CARDIOTOXIN PRECURSOR /pir||A44335 c...   340  1.2e-44   1
sp|P01444|CX3_NAJAT  CYTOTOXIN 3 PRECURSOR (CARDIOTOXIN A...   340  1.2e-44   1
pir||H3NJ3F          cytotoxin 3 - Chinese cobra /pir||JK...   340  1.6e-44   1
2.

3.

CHOFAS

Predict secondary protein structure (Chou-Fasman plot).
snake toxin
 60 aa
                .         .         .         .         .         .
       LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN
 helix <--------->        <------------->       <-------->         
 sheet     EEEEEEEEE      EEEEEEEEEE        EEEE     EEEEEEEEE     
 turns                  T           T     T       TT               

 Residue totals: H: 36   E: 32   T:  5
        percent: H: 60.0 E: 53.3 T:  8.3
4. 
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