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T0806

ID: 1401991170 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 258 (256)
Sequences: 1208 (876.1)
Seq/Len: 4.719
Nf(neff/√len): 54.8

Jackhmmer Results: (2014_04_16)
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: 4.719).

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
30_N150_I4.1831.00
52_I56_L3.5371.00
142_D145_Q2.8511.00
60_N63_R2.7621.00
100_D223_R2.7571.00
241_D244_S2.6311.00
47_S54_D2.5841.00
17_L77_R2.4841.00
81_L101_F2.4481.00
92_Q95_T2.4451.00
168_I219_I2.4131.00
100_D221_E2.3771.00
4_L167_V2.3731.00
149_D153_N2.3551.00
104_A220_I2.2251.00
241_D253_K2.1461.00
187_E248_G2.1261.00
10_T84_K2.1131.00
3_I219_I2.0991.00
228_E231_T2.0951.00
217_R221_E2.0071.00
151_I178_S1.9701.00
96_F217_R1.9651.00
244_S253_K1.9281.00
226_K229_Q1.9211.00
137_N140_G1.8521.00
13_Y82_A1.8451.00
61_A65_H1.8151.00
194_L253_K1.8081.00
59_I63_R1.7551.00
246_S249_E1.7551.00
15_S77_R1.7531.00
196_E255_Y1.7170.99
38_A64_F1.7100.99
96_F101_F1.6790.99
5_I216_S1.6420.99
26_E158_A1.6320.99
31_S67_W1.6200.99
219_I224_L1.5990.99
231_T250_L1.5980.99
5_I87_V1.5980.99
219_I230_L1.5960.99
5_I108_L1.5890.99
192_V249_E1.5870.99
96_F104_A1.5850.99
46_I52_I1.5730.99
103_F107_H1.5710.99
58_G62_A1.5590.99
8_A11_L1.5560.99
26_E154_K1.5410.99
227_P250_L1.5330.99
105_Q121_L1.5300.99
97_S100_D1.5130.98
52_I57_A1.5100.98
109_R158_A1.5010.98
168_I230_L1.4960.98
141_K145_Q1.4910.98
100_D220_I1.4710.98
37_E135_L1.4630.98
103_F220_I1.4570.98
214_L236_E1.4550.98
151_I179_V1.4550.98
168_I191_P1.4470.98
96_F100_D1.4380.98
224_L229_Q1.4190.97
18_T81_L1.4080.97
76_A123_L1.3900.97
191_P250_L1.3870.97
31_S146_F1.3770.97
81_L96_F1.3690.97
104_A216_S1.3660.96
80_I91_L1.3440.96
34_L137_N1.3360.96
221_E235_S1.3310.96
4_L155_L1.3290.96
96_F221_E1.3120.95
86_D206_F1.2890.95
99_D223_R1.2870.95
47_S57_A1.2850.95
62_A66_D1.2830.94
195_D205_S1.2810.94
27_L154_K1.2770.94
240_F250_L1.2510.93
75_N125_Q1.2510.93
207_Y254_R1.2500.93
166_V187_E1.2440.93
84_K94_E1.2370.93
35_I114_L1.2330.93
13_Y124_M1.2310.93
216_S220_I1.2290.93
47_S52_I1.2250.92
35_I46_I1.2210.92
37_E41_L1.2180.92
229_Q232_G1.1980.91
225_T229_Q1.1790.90
30_N139_R1.1640.90
166_V227_P1.1600.89
201_F253_K1.1580.89
192_V203_I1.1570.89
148_G180_K1.1460.89
93_A96_F1.1440.89
103_F224_L1.1290.88
71_F75_N1.1260.88
31_S35_I1.1190.87
144_Y177_K1.1140.87
43_P61_A1.0920.85
12_D84_K1.0910.85
72_T75_N1.0870.85
38_A41_L1.0790.84
190_K249_E1.0670.83
195_D254_R1.0560.83
153_N183_K1.0540.82
93_A217_R1.0500.82
2_L165_N1.0470.82
117_V154_K1.0400.81
154_K157_E1.0340.81
10_T89_T1.0280.80
54_D58_G1.0250.80
28_L70_D1.0220.80
149_D180_K1.0190.79
239_F255_Y1.0100.79
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: (29May14)
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  
4a1qA20.259710.30.971Contact Map
3bbnB10.48458.20.972Contact Map
2vqeB10.472980.972Contact Map
3eyiA20.240380.972Contact Map
1r45A40.60086.10.974Contact Map
1wrdA10.26365.50.974Contact Map
2duyA10.24815.40.974Contact Map
4ou0A10.22875.20.974Contact Map
4glxA10.32565.10.975Contact Map
1wy3A10.13184.70.975Contact 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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