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T0824

ID: 1403210945 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 110 (107)
Sequences: 263 (231)
Seq/Len: 2.458
Nf(neff/√len): 22.3

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: 2.458).

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
24_D78_R3.9351.00
45_R66_A2.9331.00
59_D86_R2.8771.00
34_C63_W2.3881.00
15_Y87_G1.9810.99
21_H76_S1.9780.99
67_M96_L1.8690.99
25_A63_W1.8630.99
18_T80_V1.8010.98
49_L60_R1.7840.98
68_C105_I1.7050.98
92_V107_F1.6980.97
63_W107_F1.6280.96
12_A23_S1.5430.95
72_G75_A1.5120.94
85_N88_A1.4880.93
12_A19_G1.4710.93
59_D85_N1.3860.90
80_V84_D1.3850.90
42_D53_P1.3850.90
60_R79_Y1.3570.88
59_D90_S1.3140.86
65_M68_C1.2890.85
17_E84_D1.2780.84
23_S79_Y1.2440.82
50_K56_P1.2190.80
86_R90_S1.1810.77
18_T88_A1.1740.76
18_T84_D1.1740.76
67_M92_V1.1700.76
33_V70_E1.1580.75
106_L109_V1.1410.73
28_A78_R1.1270.72
25_A89_G1.1260.72
80_V88_A1.1210.71
48_S75_A1.1080.70
34_C65_M1.1020.70
11_P23_S1.0730.67
24_D28_A1.0660.66
20_A24_D1.0650.66
10_F68_C1.0450.64
60_R65_M1.0240.61
94_N109_V1.0220.61
87_G90_S1.0060.59
37_E44_R1.0050.59
32_D106_L1.0040.59
58_F79_Y1.0000.59
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: (14Jun14)
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  
2cmyB10.19097.60.93Contact Map
4iykA10.37274.60.936Contact Map
4l0kA40.68183.40.94Contact Map
1q2fA10.27273.40.941Contact Map
2plxB10.236430.942Contact Map
2xuvA40.37272.80.943Contact Map
3bdlA10.20912.40.945Contact Map
3vgfA10.49092.40.945Contact Map
4nj5A10.33642.20.946Contact Map
1dj8A60.409120.947Contact 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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