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T0814 300-424

ID: 1404854217 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 125 (119)
Sequences: 233 (214)
Seq/Len: 1.958
Nf(neff/√len): 19.6

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: 1.958).

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
49_N56_E6.3481.00
103_R110_D3.5371.00
97_S115_V2.6351.00
46_M57_K2.5541.00
99_Y112_L2.2401.00
28_S45_K2.1710.99
30_Y44_S1.9270.98
104_P107_A1.7700.97
41_D44_S1.6350.95
36_F44_S1.6240.94
35_L44_S1.6100.94
30_Y45_K1.5100.91
19_L85_I1.4760.90
63_Q110_D1.4090.87
61_L66_Y1.4080.87
31_L59_V1.3850.86
16_H66_Y1.3440.83
17_F61_L1.3170.81
67_N85_I1.3170.81
14_I58_A1.3090.81
44_S59_V1.2840.79
65_S85_I1.2490.76
52_T56_E1.2420.76
10_A35_L1.2400.76
93_Q120_N1.2330.75
108_R112_L1.2230.74
29_V85_I1.2010.72
32_N71_L1.1970.72
97_S109_Y1.1720.70
39_V88_N1.1700.69
23_P50_F1.1650.69
104_P111_R1.1450.67
86_E108_R1.1350.66
19_L92_T1.1320.66
65_S99_Y1.1300.66
36_F86_E1.1150.64
106_G109_Y1.1150.64
98_I113_I1.1130.64
83_G88_N1.1100.64
87_G94_N1.1020.63
66_Y106_G1.0940.62
13_Y116_T1.0710.59
5_D118_V1.0700.59
35_L65_S1.0430.56
67_N104_P1.0260.55
15_V50_F1.0190.54
23_P31_L1.0080.53
21_C24_L1.0080.53
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: (05Jul14)
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  
2qlvB20.68896.20.865Contact Map
4aeeA20.91294.90.878Contact Map
4aefA20.9294.80.879Contact Map
4pyhA10.9294.20.882Contact Map
2lu3A10.77694.10.883Contact Map
4cfeB20.76893.90.883Contact Map
1z0nA30.69693.60.885Contact Map
1gcyA10.01692.90.888Contact Map
1ac0A10.80892.60.889Contact Map
1vemA10.892.40.89Contact 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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