Version 2.0 

NCSA Computational Biology - SAPS Results

Statistical Analysis of Protein Sequences.

Algorithm Citation:
Brendel, V., Bucher, P., Nourbakhsh, I.R., Blaisdell, B.E. & Karlin, S. (1992) "Methods and algorithms for statistical analysis of protein sequences" Proc. Natl. Acad. Sci. U.S.A. 89, 2002-2006.
Program Citation:
Volker Brendel, Department of Mathematics,Stanford University, Stanford CA 94305, U.S.A., modified; any errors are due to the modification.

new protein

new protein

SAPS.  Version of January 7, 1995.
Date run: Sun Dec 14 20:14:59 1997



SWISS-PROT ANNOTATION:
ID   10831
DE   10831, 60 bases, 1E82 checksum.

number of residues:   60;   molecular weight:   6.8 kdal
 
       1  LKCNKLVPLF YKTCPAGKNI CYKMFMVATP KLPVKRGCID VCPKSSLLVR YVCCNTDKCN



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  :  2( 3.3%); 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  :  6(10.0%); 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  :   22 ( 36.7%); 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).


Copyright (C) 1997, Board of Trustees of the University of Illinois.