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T0808 330-418 -force run

ID: 1405035089 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 89 (87)
Sequences: 84 (72.7)
Seq/Len: 0.966
Nf(neff/√len): 7.8

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: 0.966).

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
34_A42_Y2.0920.97
24_T72_C2.0800.96
33_T70_F1.7150.87
22_R72_C1.6910.86
13_A77_K1.6040.82
5_E48_K1.5830.81
30_H66_M1.5720.80
8_F63_S1.5480.79
56_M60_F1.4810.74
44_G56_M1.4760.74
44_G60_F1.4280.71
8_F32_A1.4240.70
2_L53_Y1.4130.69
29_T34_A1.3870.67
8_F54_L1.3640.65
11_Q26_A1.3190.62
30_H34_A1.2980.60
33_T59_F1.2930.59
41_D59_F1.2880.59
33_T36_A1.2740.58
33_T44_G1.2560.56
36_A57_G1.2520.56
11_Q59_F1.2330.54
25_D71_Y1.2320.54
13_A64_V1.2280.54
3_S55_K1.2250.53
24_T76_G1.2190.53
8_F27_T1.2010.51
53_Y66_M1.1840.49
44_G59_F1.1710.48
33_T56_M1.1440.46
12_W20_W1.1320.45
31_D44_G1.1260.44
31_D54_L1.1240.44
12_W79_P1.1210.44
16_K28_F1.1090.43
14_R78_E1.1000.42
74_P77_K1.0900.41
6_V80_E1.0840.40
34_A60_F1.0770.40
81_I86_L1.0730.39
15_S21_S1.0500.37
33_T57_G1.0420.37
30_H43_Q1.0420.37
77_K82_D1.0360.36
64_V73_K1.0140.34
12_W24_T1.0130.34
25_D81_I1.0120.34
45_G53_Y1.0110.34
82_D85_A1.0070.34
59_F70_F1.0030.33
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  
4h2gA10.887610.60.929Contact Map
3owtC10.12368.40.932Contact Map
3zyqA10.29216.90.935Contact Map
4h62V10.08995.60.937Contact Map
2llzA10.70795.30.938Contact Map
3ztvA10.95514.90.939Contact Map
3cskA10.7644.20.941Contact Map
2bsgA30.30343.90.942Contact Map
1ojjA20.82023.60.943Contact Map
2ovwA40.82023.60.943Contact 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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