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DYSF-666-790

ID: 1474824837 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 125 (125)
Sequences: 334 (195.2)
Seq/Len: 2.672
Nf(neff/√len): 17.5

Jackhmmer Results: (2016_04)
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: 2.672).

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 > 50% 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
23_G47_L1.9000.99
13_L114_L1.7580.98
47_L54_G1.6310.97
48_T51_L1.6270.97
36_S39_D1.5950.97
81_H95_L1.5900.96
21_E115_R1.5900.96
49_D77_Q1.5810.96
5_H69_T1.5530.96
88_E92_A1.4830.94
13_L77_Q1.4650.94
86_I123_N1.4160.92
78_L117_L1.3960.91
67_S115_R1.3900.91
50_E81_H1.3830.91
27_V44_V1.3480.89
44_V53_A1.3020.87
85_Q89_A1.2920.87
47_L108_E1.2700.85
107_A125_L1.2680.85
41_D45_A1.2670.85
29_L32_K1.2550.84
3_I123_N1.2480.84
77_Q113_R1.2470.84
58_P83_L1.2230.82
10_Q17_A1.2190.82
50_E104_L1.2160.82
20_L111_L1.1990.80
69_T110_W1.1840.79
104_L117_L1.1830.79
100_L106_Q1.1790.79
36_S41_D1.1780.79
66_P70_H1.1760.79
79_R123_N1.1710.78
35_C38_E1.1580.77
13_L81_H1.1570.77
5_H8_E1.1540.77
6_R122_Q1.1370.75
86_I93_L1.1370.75
69_T119_E1.1320.75
114_L121_P1.1150.73
93_L103_A1.1030.72
16_I63_H1.0930.71
19_R54_G1.0930.71
15_G88_E1.0860.70
24_L48_T1.0780.70
3_I79_R1.0760.69
102_A109_D1.0760.69
18_D83_L1.0720.69
50_E117_L1.0700.69
79_R120_E1.0700.69
31_L53_A1.0680.69
22_A91_L1.0660.68
25_E101_P1.0600.68
40_V44_V1.0540.67
76_Y80_T1.0530.67
88_E107_A1.0510.67
16_I80_T1.0490.67
17_A21_E1.0460.66
32_K55_C1.0440.66
24_L115_R1.0410.66
43_L46_Q1.0390.65
15_G30_A1.0380.65
17_A119_E1.0250.64
2_D6_R1.0160.63
9_T51_L1.0150.63
23_G79_R1.0120.62
105_E117_L1.0110.62
12_Q50_E1.0080.62
14_L118_A1.0070.62
12_Q43_L1.0070.62
102_A106_Q1.0040.62
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: (06Aug15)
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  
5c0wL1023.30.923Contact Map
2a01A30.93617.50.927Contact Map
4i3hA20.87214.60.93Contact Map
2xcsB20.87214.20.93Contact Map
2yn7A20.72813.80.931Contact Map
3mudA20.38411.60.933Contact Map
2inrA10.87211.50.933Contact Map
2novA40.86410.30.935Contact Map
3vkgA20.9769.70.935Contact Map
4lunU10.49.60.935Contact 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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