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T0789 -force run

ID: 1400779296 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 295 (269)
Sequences: 225 (177.4)
Seq/Len: 0.836
Nf(neff/√len): 10.8

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: 0.836).

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
158_A240_V3.5411.00
144_L234_D2.2510.97
234_D239_R2.1520.96
14_N57_M2.1400.96
30_V232_I1.9270.92
105_V211_V1.7380.86
15_A101_L1.6480.81
77_V133_F1.5720.77
105_V158_A1.5600.76
158_A211_V1.5130.73
10_L144_L1.5070.72
39_D57_M1.4930.71
35_M270_T1.4670.69
80_P83_W1.4650.69
30_V126_R1.4490.68
14_N53_E1.4420.67
144_L239_R1.4300.66
124_A197_R1.4220.66
231_S249_D1.4090.65
105_V259_G1.4000.64
240_V259_G1.3880.63
157_P260_T1.3830.63
14_N59_L1.3620.61
211_V232_I1.3610.61
15_A174_D1.3420.59
28_P148_L1.3370.59
126_R232_I1.3270.58
212_E271_L1.3180.57
160_F240_V1.3020.56
202_S240_V1.2950.55
50_Q70_V1.2950.55
279_Q283_G1.2930.55
79_F143_A1.2910.55
14_N50_Q1.2870.54
76_V106_A1.2820.54
170_G177_L1.2810.54
218_N222_R1.2800.54
144_L154_H1.2790.54
56_R128_A1.2780.54
79_F230_L1.2700.53
16_W37_Y1.2610.52
25_G208_R1.2520.51
54_L148_L1.2470.51
158_A259_G1.2460.51
39_D123_V1.2380.50
160_F259_G1.2340.50
247_A267_A1.2320.50
19_A60_L1.2310.50
41_A120_N1.2310.50
44_G144_L1.2260.49
230_L254_S1.2230.49
74_I149_G1.2220.49
33_I44_G1.2200.49
19_A158_A1.2160.48
102_R271_L1.1940.46
16_W43_R1.1870.46
232_I259_G1.1820.45
211_V275_L1.1780.45
34_T37_Y1.1770.45
11_T14_N1.1770.45
45_A230_L1.1670.44
166_P219_R1.1630.44
52_D129_Q1.1580.43
45_A49_R1.1550.43
155_R269_Q1.1550.43
29_W32_A1.1520.43
57_M253_V1.1490.42
11_T213_I1.1480.42
153_A223_H1.1480.42
36_P173_A1.1420.42
166_P254_S1.1410.42
13_D173_A1.1320.41
78_C164_S1.1310.41
28_P232_I1.1290.41
67_N264_I1.1250.40
233_V253_V1.1250.40
191_G197_R1.1240.40
17_F47_V1.1240.40
212_E259_G1.1230.40
74_I103_G1.1230.40
71_A191_G1.1210.40
214_V259_G1.1200.40
69_A200_V1.1190.40
157_P207_P1.1180.40
170_G221_G1.1090.39
191_G255_T1.1070.39
74_I162_E1.1030.38
218_N221_G1.0990.38
22_I192_I1.0970.38
15_A19_A1.0950.38
16_W57_M1.0910.37
107_L280_W1.0850.37
167_T226_T1.0780.36
23_G131_V1.0740.36
215_A276_P1.0710.36
72_D268_I1.0680.36
254_S271_L1.0660.35
29_W83_W1.0620.35
71_A206_G1.0590.35
12_V126_R1.0570.35
217_C221_G1.0570.35
137_D144_L1.0560.35
30_V83_W1.0560.35
37_Y210_Y1.0520.34
45_A82_R1.0500.34
88_Y129_Q1.0490.34
102_R214_V1.0480.34
23_G209_S1.0460.34
101_L264_I1.0440.34
214_V235_T1.0370.33
278_G282_P1.0370.33
44_G156_P1.0310.33
70_V122_V1.0260.32
52_D55_T1.0250.32
56_R131_V1.0250.32
77_V124_A1.0250.32
31_L129_Q1.0240.32
58_G84_L1.0230.32
182_P237_A1.0220.32
41_A48_D1.0210.32
106_A146_P1.0180.32
85_D211_V1.0170.32
109_T195_S1.0140.31
11_T263_A1.0140.31
126_R240_V1.0120.31
129_Q236_S1.0110.31
106_A122_V1.0100.31
11_T208_R1.0100.31
37_Y43_R1.0090.31
134_T264_I1.0080.31
25_G50_Q1.0060.31
121_G212_E1.0050.31
173_A216_G1.0040.31
69_A128_A1.0010.30
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: (12Jul14)
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  
4l4wA20.90511000.186Contact Map
4kxrC10.8611000.251Contact Map
3s6mA10.189870.966Contact Map
1v9tA20.19666.40.967Contact Map
2g7uA40.83055.60.968Contact Map
2k7nA10.21025.30.968Contact Map
2fu0A10.18645.20.968Contact Map
3nn1A50.20685.10.968Contact Map
1ez0A40.18985.10.968Contact Map
2xrnA20.786450.968Contact 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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