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T0826 1-220

ID: 1403943237 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 220 (213)
Sequences: 513 (412.8)
Seq/Len: 2.408
Nf(neff/√len): 28.3

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: 2.408).

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
131_G135_A3.0261.00
62_N162_S2.7691.00
82_L138_Y2.6351.00
79_P139_I2.4761.00
52_T177_Y2.4351.00
87_A127_I2.1591.00
91_Q118_L2.1361.00
49_F177_Y2.1011.00
15_L138_Y2.0911.00
173_Q177_Y2.0841.00
79_P135_A1.9670.99
79_P138_Y1.9500.99
91_Q99_F1.8800.99
104_L203_K1.8620.99
92_E99_F1.8390.99
23_S65_F1.8370.99
22_Y27_L1.7500.98
103_M106_N1.7490.98
108_L203_K1.6770.97
59_F165_C1.6760.97
188_T198_G1.6380.96
31_F198_G1.5910.96
62_N158_L1.5690.95
151_E155_R1.5360.94
94_F138_Y1.5350.94
71_P75_K1.5070.94
152_L160_A1.4640.92
63_F163_F1.4550.92
174_Y178_A1.4440.92
19_L78_I1.4370.91
24_S58_F1.3730.89
49_F173_Q1.3620.88
86_A161_V1.3580.88
95_F153_L1.3530.88
63_F159_A1.3510.88
31_F185_K1.3500.88
170_A183_N1.3470.88
75_K79_P1.3370.87
161_V164_L1.3230.86
20_S27_L1.3220.86
99_F214_Y1.2760.83
76_V79_P1.2670.83
23_S81_I1.2630.83
140_A144_K1.2530.82
75_K81_I1.2510.82
63_F166_A1.2470.81
100_N103_M1.2430.81
132_V164_L1.2150.79
31_F192_V1.2120.79
31_F57_L1.1960.78
10_L18_F1.1930.77
23_S172_L1.1840.77
30_A93_I1.1720.76
19_L138_Y1.1680.75
91_Q214_Y1.1650.75
180_F195_N1.1510.74
128_V132_V1.1460.73
129_C136_L1.1450.73
23_S184_N1.1390.73
31_F35_V1.1350.72
190_L195_N1.1320.72
10_L14_A1.1310.72
21_L58_F1.1240.71
59_F169_I1.1140.70
145_Y151_E1.1130.70
86_A131_G1.1110.70
93_I192_V1.1020.69
68_I77_L1.1010.69
30_A89_S1.0930.68
92_E95_F1.0820.67
15_L78_I1.0770.66
99_F118_L1.0740.66
192_V198_G1.0730.66
179_S183_N1.0700.66
80_L84_I1.0520.64
16_I155_R1.0470.63
20_S64_V1.0470.63
63_F155_R1.0440.63
126_W130_L1.0400.62
174_Y191_I1.0300.61
54_P177_Y1.0300.61
99_F123_Y1.0300.61
119_I124_V1.0260.61
163_F167_L1.0240.61
156_L160_A1.0220.60
11_G84_I1.0220.60
137_A217_L1.0210.60
153_L206_D1.0190.60
204_Y208_K1.0120.59
136_L140_A1.0090.59
55_V125_L1.0090.59
52_T57_L1.0090.59
61_S82_L1.0060.59
95_F103_M1.0020.58
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: (21Jun14)
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  
3m73A10.74553.10.969Contact Map
1fmeA10.10452.60.97Contact Map
2hi2A10.30452.30.971Contact Map
3b5xA20.89552.20.971Contact Map
2yevB20.49552.10.971Contact Map
2ww9C10.09552.10.971Contact Map
4httA20.254520.972Contact Map
2wwbC10.16361.80.972Contact Map
4m48A10.651.70.973Contact Map
3ddlA20.47731.70.973Contact 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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