NCSA Computational Biology - SAPS
Results
Statistical Analysis of Protein Sequences.
----------------------------------------------------------------------------
toxin
----------------------------------------------------------------------------
toxin
SAPS. Version of January 7, 1995.
Date run: Mon Dec 9 07:46:12 1996
SWISS-PROT ANNOTATION:
ID 4143
DE 4143, 60 bases.
number of residues: 60; molecular weight: 6.7 kdal
1 LKCNKLVPLF YKTCPAGKNL CYKMFMVATP KVPVKRGCID VCPKSSLLVK YVCCNTDRCN
--------------------------------------------------------------------------------
COMPOSITIONAL ANALYSIS (extremes relative to: swp23s.q)
A : 2( 3.3%); C : 8(13.3%); D : 2( 3.3%); E : 0( 0.0%); F : 2( 3.3%)
G : 2( 3.3%); H : 0( 0.0%); I : 1( 1.7%); K : 9(15.0%); L : 6(10.0%)
M : 2( 3.3%); N : 4( 6.7%); P : 5( 8.3%); Q : 0( 0.0%); R : 2( 3.3%)
S : 2( 3.3%); T : 3( 5.0%); V : 7(11.7%); W : 0( 0.0%); Y : 3( 5.0%)
KR : 11 ( 18.3%); ED : 2 ( 3.3%); AGP : 9 ( 15.0%);
KRED : 13 ( 21.7%); KR-ED : 9 ( 15.0%); FIKMNY : 21 ( 35.0%);
LVIFM : 18 ( 30.0%); ST : 5 ( 8.3%).
--------------------------------------------------------------------------------
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
--------------------------------------------------------------------------------
DISTRIBUTION OF OTHER AMINO ACID TYPES
1. HIGH SCORING SEGMENTS.
__________________________________
High scoring hydrophobic segments:
2.00 (LVIFM) 1.00 (AGYCW) 0.00 (BZX) -2.00 (PH) -4.00 (STNQ)
-8.00 (KEDR)
Expected score/letter: -1.650
- now scoring for hydrophobic segments
........40........80.......120.......160.......200
******; Average information/letter: 0.452
Minimal length of displayed segments set to: 15
M_0.01= 23.51 (cv= 13.41, lambda= 0.30526, k= 0.21941, x= 10.10;
90% confidence interval for segment length: 23 +- 17)
M_0.05= 18.17 (x= 4.76)
# of segments (>=15 residues) exceeding M_0.05: none
____________________________________
High scoring transmembrane segments:
5.00 (LVIF) 2.00 (AGM) 0.00 (BZX) -1.00 (YCW) -2.00 (ST)
-6.00 (P) -8.00 (H) -10.00 (NQ) -16.00 (KR) -17.00 (ED)
Expected score/letter: -3.483
- now scoring for transmembrane segments
........40........80.......120.......160.......200
******; Average information/letter: 0.513
Minimal length of displayed segments set to: 15
M_0.01= 45.47 (cv= 26.27, lambda= 0.15585, k= 0.20016, x= 19.19;
90% confidence interval for segment length: 20 +- 16)
M_0.05= 35.01 (x= 8.74); M_0.30= 22.56 (x= -3.71)
# of segments (>=15 residues) exceeding M_0.30: none
2. SPACINGS OF C.
H2N-2-C-10-C-6-C-16-C-3-C-10
CC at 53
-4-C-1-COOH
--------------------------------------------------------------------------------
REPETITIVE STRUCTURES.
A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet.
Repeat core block length: 4
B. SEPARATED AND TANDEM REPEATS: 11-letter reduced alphabet.
(i= LVIF; += KR; -= ED; s= AG; o= ST; n= NQ; a= YW; p= P; h= H; m= M; c= C)
Repeat core block length: 8
--------------------------------------------------------------------------------
MULTIPLETS.
A. AMINO ACID ALPHABET.
1. Total number of amino acid multiplets: 3 (Expected range: 0-- 11)
2. Histogram of spacings between consecutive amino acid multiplets:
(1-5) 2 (6-10) 1 (11-20) 0 (>=21) 1
3. Clusters of amino acid multiplets (cmin = 10/30 or 12/45 or 15/60): none
B. CHARGE ALPHABET.
1. Total number of charge multiplets: 1 (Expected range: 0-- 6)
1 +plets (f+: 18.3%), 0 -plets (f-: 3.3%)
Total number of charge altplets: 1 (Critical number: 4)
2. Histogram of spacings between consecutive charge multiplets:
(1-5) 0 (6-10) 0 (11-20) 0 (>=21) 2
--------------------------------------------------------------------------------
PERIODICITY ANALYSIS.
A. AMINO ACID ALPHABET (core: 4; !-core: 4)
Location Period Element Copies Core Errors
There are no periodicities of the prescribed length.
B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 5)
and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 8)
Location Period Element Copies Core Errors
There are no periodicities of the prescribed length.
--------------------------------------------------------------------------------
SPACING ANALYSIS.
Not evaluated (sequence length < 100 aa, too short).
Back to homework 5
Mail to me:b821605@life.nthu.edu.tw