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T0800 -force run

ID: 1401726898 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 247 (241)
Sequences: 64 (59)
Seq/Len: 0.266
Nf(neff/√len): 3.8

HHblits Results: (2013_03)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 0.266).

Sequences per length for each position, AFTER the coverage/gap filter was applied
Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

Trim query Generate MSA using: Filter MSA GREMLIN
Start: End: E-value: Iterations: Coverage: Remove gaps: Prior:

GREMLIN Results:
Residue pairs sorted by coevolution strength:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

ij Scaled score Prob
120_W160_G2.0790.74
130_T166_I1.9530.67
137_G158_G1.9200.65
160_G183_G1.8590.61
60_V138_T1.8250.59
120_W183_G1.7670.56
13_V17_F1.6620.49
120_W240_G1.6080.45
59_G158_G1.6010.45
61_G239_V1.5510.42
160_G240_G1.4940.38
167_S192_S1.4670.36
202_G238_G1.4600.36
52_T72_L1.4110.33
155_V239_V1.3790.31
194_G224_Y1.3740.31
161_K197_I1.3660.31
46_P173_N1.3640.31
164_L178_I1.3490.30
184_E217_N1.3370.29
139_G183_G1.3320.29
180_G204_G1.3300.29
124_L144_D1.3150.28
158_G238_G1.3140.28
210_G239_V1.3040.27
150_L202_G1.2980.27
76_K94_D1.2920.27
183_G240_G1.2860.26
134_L220_K1.2730.26
101_I132_I1.2710.26
159_V183_G1.2630.25
183_G239_V1.2470.24
159_V203_V1.2370.24
104_P184_E1.2360.24
149_N206_V1.2350.24
159_V167_S1.2350.24
210_G221_N1.2260.23
132_I246_Q1.2230.23
145_L166_I1.2180.23
9_I27_K1.2070.23
187_V216_E1.2010.22
143_A244_I1.1910.22
86_P149_N1.1780.21
49_A122_I1.1760.21
60_V180_G1.1760.21
144_D189_L1.1740.21
154_N217_N1.1730.21
143_A150_L1.1650.21
138_T167_S1.1620.21
222_S230_S1.1600.21
74_K152_E1.1570.20
59_G138_T1.1550.20
54_L132_I1.1490.20
107_K244_I1.1470.20
61_G66_S1.1470.20
122_I242_I1.1390.20
64_N173_N1.1370.20
15_L35_E1.1350.19
99_L208_A1.1340.19
8_S12_L1.1280.19
75_G196_K1.1280.19
62_K221_N1.1260.19
198_K202_G1.1260.19
189_L194_G1.1260.19
55_N162_V1.1240.19
197_I224_Y1.1190.19
104_P134_L1.1100.18
171_K200_E1.1060.18
72_L196_K1.1060.18
130_T240_G1.1050.18
125_N203_V1.1040.18
101_I129_P1.1040.18
142_K167_S1.1030.18
79_Y97_G1.1030.18
19_T25_S1.1010.18
12_L23_N1.1000.18
22_T25_S1.0940.18
12_L28_A1.0930.18
79_Y168_G1.0920.18
207_N223_Q1.0920.18
12_L27_K1.0910.18
39_E86_P1.0880.18
127_K166_I1.0870.18
132_I155_V1.0860.18
65_I238_G1.0820.17
100_E242_I1.0770.17
48_G185_A1.0740.17
9_I12_L1.0730.17
10_F29_T1.0730.17
114_N154_N1.0720.17
122_I125_N1.0710.17
138_T158_G1.0680.17
69_E120_W1.0670.17
28_A34_N1.0660.17
132_I241_A1.0660.17
52_T56_L1.0640.17
162_V208_A1.0620.17
124_L137_G1.0620.17
9_I22_T1.0580.17
86_P96_D1.0560.16
163_D176_V1.0560.16
27_K34_N1.0560.16
187_V197_I1.0500.16
61_G120_W1.0470.16
120_W130_T1.0450.16
50_E152_E1.0430.16
19_T32_D1.0400.16
124_L233_V1.0400.16
9_I30_V1.0360.16
86_P103_Q1.0350.16
131_E192_S1.0330.16
64_N221_N1.0320.16
77_F160_G1.0310.16
14_I29_T1.0310.16
18_A25_S1.0270.15
100_E221_N1.0250.15
176_V238_G1.0250.15
60_V159_V1.0200.15
159_V222_S1.0200.15
63_L150_L1.0180.15
6_L14_I1.0170.15
65_I191_K1.0160.15
115_N139_G1.0140.15
217_N237_A1.0130.15
14_I22_T1.0110.15
149_N204_G1.0050.15
82_N225_G1.0040.15
124_L130_T1.0040.15
54_L215_G1.0000.15
228_K244_I1.0000.15
Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
NEW Features
HHsearch Results: (06Aug15)
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
PDB M Cov P(%) HHΔ  
4qrkA10.85831000.469Contact Map
4yguA40.6761970.896Contact Map
3jx8A60.793595.50.91Contact Map
3petA20.769295.40.911Contact Map
3lycA160.7854950.913Contact Map
4opwA20.781494.40.916Contact Map
3glaA20.283428.50.955Contact Map
3l1eA10.33223.30.956Contact Map
3zbiC140.109322.20.957Contact Map
4mjhA20.255113.90.961Contact Map
M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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