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examplemyo

ID: 1518572404 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 153 (147)
Sequences: 3834 (2063.1)
Seq/Len: 26.082
Nf(neff/√len): 170.2

HHblits Results: (2016_02)
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: 26.082).

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
6_E133_K4.0351.00
11_L80_G2.7651.00
116_H128_Q2.7541.00
100_P103_Y2.5741.00
18_E77_K2.4781.00
27_D117_S2.4521.00
31_R113_H2.1101.00
3_S6_E2.0351.00
13_V131_M2.0291.00
32_L106_F2.0281.00
35_S113_H2.0121.00
4_E8_Q1.9591.00
35_S110_A1.9311.00
123_F128_Q1.8051.00
75_I138_F1.7651.00
14_W73_G1.7641.00
140_K144_A1.7281.00
108_S135_L1.7211.00
6_E129_G1.7011.00
22_A66_V1.7001.00
20_D23_G1.6991.00
5_G8_Q1.6851.00
129_G133_K1.6641.00
13_V127_A1.6561.00
124_G127_A1.6481.00
25_G69_L1.6351.00
108_S136_E1.6341.00
90_A145_K1.6181.00
128_Q132_N1.6031.00
29_L64_H1.6001.00
10_V134_A1.5711.00
9_L130_A1.5671.00
31_R110_A1.5531.00
90_A142_I1.5301.00
9_L127_A1.5151.00
16_K122_D1.5101.00
5_G126_D1.4771.00
27_D30_I1.4621.00
112_I132_N1.4571.00
7_W80_G1.4321.00
31_R117_S1.4261.00
33_F43_F1.4091.00
8_Q12_H1.3720.99
27_D31_R1.3230.99
116_H125_A1.2870.99
36_H110_A1.2470.99
71_A74_A1.2450.98
31_R35_S1.2270.98
3_S133_K1.2040.98
73_G77_K1.1790.98
132_N136_E1.1760.98
28_I111_I1.1720.98
64_H68_V1.1710.98
139_R143_A1.1640.97
92_S96_K1.1550.97
109_E113_H1.1450.97
36_H39_T1.1360.97
35_S109_E1.1300.97
112_I128_Q1.1260.97
43_F93_H1.1210.97
105_E143_A1.1050.96
123_F127_A1.0940.96
114_V118_R1.0890.96
26_Q65_G1.0830.96
135_L139_R1.0800.95
31_R114_V1.0700.95
66_V70_T1.0550.95
50_K57_A1.0540.95
4_E7_W1.0390.94
78_K81_H1.0380.94
136_E140_K1.0320.94
14_W17_V1.0090.93
29_L68_V1.0050.93
111_I135_L1.0010.92
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  
1a6mA10.98691000.057Contact Map
1lhsA111000.06Contact Map
2dc3A211000.073Contact Map
1v4xB20.94121000.094Contact Map
2r80B20.94121000.094Contact Map
2aa1B20.94771000.096Contact Map
1outB10.94121000.097Contact Map
3d1kB10.94121000.097Contact Map
3bomB20.94121000.1Contact Map
2w72B20.94771000.101Contact 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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