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T0812

ID: 1402427684 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 204 (194)
Sequences: 483 (277.2)
Seq/Len: 2.490
Nf(neff/√len): 19.9

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: 2.490).

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
101_I161_I3.6221.00
179_I182_I2.5371.00
199_A202_I2.0831.00
76_G185_E1.9090.99
73_A186_V1.8910.99
80_Y98_Q1.8840.99
62_L66_F1.8270.99
76_G80_Y1.7370.98
79_K128_E1.6960.97
62_L136_W1.6520.97
43_V46_M1.6510.97
152_E156_D1.6060.96
67_E161_I1.6000.96
196_T200_D1.5570.95
24_D28_Q1.5180.94
76_G151_R1.5150.94
94_T167_K1.4650.93
104_G159_Y1.4530.92
101_I193_T1.4520.92
98_Q167_K1.3720.89
77_K130_E1.3680.89
20_L24_D1.3450.88
127_H169_T1.3450.88
101_I129_I1.3420.88
169_T177_S1.3340.87
99_V182_I1.3050.86
101_I117_A1.3030.86
76_G84_F1.3000.86
62_L164_I1.2840.85
104_G154_F1.2810.84
118_A125_T1.2650.83
138_Y153_D1.2600.83
42_I45_H1.2570.83
75_G80_Y1.2470.82
188_E192_G1.2400.82
78_L184_M1.2400.82
16_E19_I1.2280.81
111_I154_F1.2120.80
76_G149_V1.2080.79
38_Q45_H1.2020.79
78_L182_I1.1920.78
14_K17_Q1.1920.78
7_I10_W1.1860.78
69_K131_M1.1810.77
19_I24_D1.1810.77
197_P200_D1.1750.77
131_M184_M1.1710.76
70_K179_I1.1640.76
166_I170_Y1.1590.75
60_W138_Y1.1510.75
159_Y164_I1.1500.74
156_D159_Y1.1490.74
71_L184_M1.1450.74
78_L99_V1.1350.73
135_E154_F1.1330.73
22_L169_T1.1310.73
11_V19_I1.1230.72
157_I185_E1.1220.72
6_L11_V1.1160.71
77_K128_E1.1070.70
132_T136_W1.1050.70
90_T101_I1.0980.70
60_W136_W1.0980.70
138_Y149_V1.0970.69
196_T199_A1.0950.69
117_A162_H1.0950.69
96_N101_I1.0910.69
113_V176_Q1.0910.69
101_I196_T1.0900.69
129_I192_G1.0770.67
113_V156_D1.0730.67
9_T14_K1.0650.66
59_Y178_R1.0640.66
58_F105_T1.0610.66
105_T160_D1.0590.65
46_M50_R1.0590.65
24_D27_L1.0580.65
66_F163_Y1.0510.65
62_L179_I1.0460.64
129_I136_W1.0390.63
97_P152_E1.0370.63
80_Y97_P1.0360.63
150_T153_D1.0350.63
99_V183_S1.0340.63
71_L151_R1.0330.63
18_T25_E1.0320.63
15_A18_T1.0300.62
97_P166_I1.0240.62
117_A161_I1.0230.62
93_S103_G1.0210.61
151_R155_L1.0180.61
80_Y152_E1.0160.61
98_Q170_Y1.0160.61
154_F157_I1.0150.61
111_I149_V1.0120.60
121_I170_Y1.0100.60
61_K69_K1.0080.60
62_L151_R1.0060.60
21_P30_T1.0040.59
69_K75_G1.0010.59
136_W149_V1.0010.59
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: (07Jun14)
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  
1fjjA10.6525.60.959Contact Map
2d7nA10.36274.80.96Contact Map
2dn7A10.54.20.961Contact Map
4hwbA10.47063.60.963Contact Map
1x5lA10.50983.20.963Contact Map
3n08A20.60782.70.965Contact Map
4goqA50.18142.50.966Contact Map
1owwA10.4022.40.966Contact Map
1eerB20.63732.30.966Contact Map
2djsA10.48532.20.966Contact 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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