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T0791 -force run

ID: 1400863155 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 300 (269)
Sequences: 211 (162.9)
Seq/Len: 0.784
Nf(neff/√len): 9.9

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: 0.784).

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
167_A252_I3.3161.00
246_D251_R2.7120.99
166_P274_T2.0220.93
32_E244_L1.8730.89
12_V150_I1.8630.89
150_I246_D1.7500.85
223_V244_L1.7090.83
43_S126_H1.6530.80
80_A149_S1.6370.79
127_W224_A1.6030.77
78_L139_V1.5900.76
150_I251_R1.5500.73
81_P84_E1.5390.73
231_R234_A1.4920.69
214_Q252_I1.4900.69
30_A154_V1.4680.68
37_P166_P1.4660.67
122_R229_Q1.4640.67
16_G59_Q1.4500.66
30_A86_V1.4330.65
86_V241_V1.4310.65
80_A242_L1.3680.59
121_A164_A1.3540.58
52_G71_V1.3500.58
252_I273_A1.3350.57
41_T59_Q1.3280.56
199_L285_V1.3250.56
167_A223_V1.3090.54
122_R294_W1.2940.53
12_V16_G1.2800.52
48_N224_A1.2800.52
293_E297_H1.2790.52
150_I163_H1.2780.52
58_E134_G1.2740.51
82_D161_I1.2740.51
73_A123_R1.2730.51
134_G280_V1.2710.51
68_N278_V1.2610.50
86_V226_Y1.2520.50
167_A273_A1.2510.49
88_L285_V1.2510.49
71_V128_V1.2480.49
32_E132_R1.2430.49
70_Q134_G1.2360.48
32_E88_L1.2280.47
25_D137_I1.2240.47
197_G206_A1.2200.47
72_A203_G1.2100.46
89_L162_H1.2060.46
30_A262_G1.2010.45
244_L273_A1.2010.45
166_P219_P1.1880.44
64_N128_V1.1810.43
128_V242_L1.1800.43
132_R252_I1.1760.43
57_R137_I1.1740.43
172_V263_S1.1720.43
167_A227_A1.1690.42
245_K254_L1.1660.42
43_S50_H1.1640.42
51_P55_V1.1630.42
243_S263_S1.1600.42
44_N120_L1.1550.41
39_V225_V1.1520.41
164_A283_K1.1520.41
16_G61_I1.1510.41
293_E298_S1.1430.40
63_V77_V1.1420.40
78_L135_N1.1370.40
176_M238_S1.1370.40
60_G121_A1.1270.39
121_A130_A1.1230.38
40_S85_V1.1230.38
13_N16_G1.1220.38
57_R282_V1.1190.38
33_L37_P1.1170.38
22_A139_V1.1040.37
36_R82_D1.1020.37
132_R244_L1.1020.37
43_S148_A1.1010.37
41_T172_V1.0880.36
27_R220_A1.0870.36
70_Q212_L1.0870.36
75_M155_M1.0870.36
118_V242_L1.0850.35
40_S43_S1.0830.35
32_E84_E1.0810.35
81_P154_V1.0800.35
57_R272_P1.0770.35
132_R273_A1.0770.35
166_P194_F1.0760.35
224_A285_V1.0760.35
30_A88_L1.0750.35
134_G287_D1.0750.35
33_L177_E1.0730.34
178_E228_R1.0720.34
292_G296_T1.0720.34
120_L182_A1.0690.34
30_A211_A1.0650.34
130_A209_V1.0650.34
146_D297_H1.0630.34
82_D123_R1.0620.34
72_A156_D1.0590.33
49_E52_G1.0550.33
31_P34_R1.0530.33
30_A244_L1.0510.33
31_P252_I1.0510.33
30_A268_L1.0500.33
217_S248_S1.0500.33
76_K126_H1.0490.33
166_P211_A1.0480.33
139_V213_G1.0470.32
137_I216_L1.0450.32
16_G52_G1.0430.32
30_A277_L1.0420.32
25_D221_A1.0420.32
18_W278_V1.0360.32
25_D281_G1.0350.32
215_A270_I1.0330.31
77_V155_M1.0320.31
88_L132_R1.0320.31
135_N248_S1.0320.31
146_D293_E1.0310.31
253_A273_A1.0300.31
231_R235_K1.0270.31
149_S205_S1.0230.31
123_R130_A1.0200.30
77_V225_V1.0200.30
27_R248_S1.0190.30
34_R265_E1.0170.30
194_F289_L1.0160.30
81_P288_T1.0110.30
27_R52_G1.0070.29
128_V142_V1.0070.29
17_F60_G1.0040.29
59_Q172_V1.0040.29
222_E227_A1.0020.29
15_D117_R1.0020.29
172_V233_D1.0010.29
281_G289_L1.0000.29
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  
4w4lC10.97671000.166Contact Map
4l4wA20.88671000.239Contact Map
4w4iA10.87331000.245Contact Map
3proC20.328.80.964Contact Map
2o0yA40.79337.10.966Contact Map
2gqbA10.2260.967Contact Map
2ia2A40.785.90.967Contact Map
3v39A10.25.60.967Contact Map
4lixA10.21335.10.968Contact Map
3a3dA20.2350.968Contact 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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