To identify the protein
We imported the sequence to Workbench,and then performed BLASTP to identify This sequence. As a result, we found several sequences similiar but not equal to it.Alignment between sequences
We performed MSAto align nine similiar sequences to this protein. And then useed MSASHADE to color the pre-aligned result.
Predict secondary structure
There are four tools is available in Workbench to predict secondary structure of protein. Garnieris one of these and the following is the result predicted by it.
60 aa; DCH = 158, DCS = 0
. 10 . 20 . 30 . 40 . 50 . 60
LKCNKLVPLFYKTCPAGKNICYKMFMVATPKLPVKRGCIDVCPKSSLLVRYVCCNTDKCN
helix
sheet EEEEEEEEE EEEEEEEEE EEEEE EEEEEEE
turns TTTT TTTTT TT TTTTT TTTT TTTTTTT
coil C C C
helix
sheet
turns
coil
Residue totals: H: 0 E: 30 T: 27 C: 3
percent: H: 0.0 E: 68.2 T: 61.4 C: 6.8
Show charge distribution
The following is the analyzing results of charge distribution by SAPS:
SAPS. Version of January 7, 1995.
Date run: Tue Jan 6 04:15:33 1998
SWISS-PROT ANNOTATION:
ID 29018
DE 29018, 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).