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ID: 1516142713 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 222 (194)
Sequences: 1195 (862.1)
Seq/Len: 6.160
Nf(neff/√len): 61.9

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: 6.160).

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
173_F190_Y3.6181.00
165_L189_L3.1791.00
133_E136_H3.0111.00
32_E52_L2.7191.00
101_A109_S2.6091.00
110_M137_W2.6051.00
24_H51_H2.5531.00
185_R188_D2.4451.00
118_D138_Y2.4161.00
55_A63_A2.4101.00
165_L196_A2.0371.00
30_Y116_A1.9491.00
193_A201_M1.9241.00
25_L60_E1.8861.00
47_S50_F1.8631.00
110_M144_M1.8371.00
56_A64_I1.7651.00
133_E137_W1.6561.00
176_G179_L1.6531.00
166_A204_R1.6461.00
27_M31_H1.6020.99
203_G206_A1.5240.99
72_S98_L1.5210.99
189_L192_Q1.5140.99
24_H58_L1.5020.99
95_F123_L1.5000.99
32_E66_G1.4910.99
51_H137_W1.4840.99
187_G209_Y1.4640.99
70_M116_A1.4460.99
139_N143_E1.4250.99
157_Q160_P1.3940.98
187_G205_L1.3760.98
64_I202_K1.3570.98
102_A194_A1.3560.98
137_W140_T1.3470.98
25_L166_A1.3460.98
194_A202_K1.3450.98
130_D133_E1.3420.98
30_Y36_F1.3370.98
34_G44_D1.3270.97
159_E162_Y1.3130.97
94_G98_L1.3020.97
93_K97_Y1.3020.97
56_A102_A1.2870.97
99_L133_E1.2830.97
169_A190_Y1.2780.97
114_A138_Y1.2750.97
28_V114_A1.2710.96
134_A138_Y1.2660.96
25_L63_A1.2560.96
167_R170_E1.2520.96
172_L185_R1.2510.96
93_K96_D1.2340.96
166_A198_M1.2330.96
201_M205_L1.2240.95
102_A110_M1.2170.95
64_I97_Y1.2090.95
49_V70_M1.1960.94
57_N103_E1.1880.94
113_V117_F1.1810.94
98_L112_L1.1800.94
199_E206_A1.1780.94
99_L103_E1.1760.94
189_L193_A1.1750.94
44_D182_D1.1670.93
168_E172_L1.1510.93
142_L194_A1.1490.93
55_A60_E1.1330.92
64_I104_A1.1220.92
117_F133_E1.1170.91
170_E190_Y1.1140.91
113_V137_W1.1140.91
114_A169_A1.0880.90
141_A149_E1.0870.90
19_I23_V1.0800.89
88_E180_E1.0770.89
115_R138_Y1.0760.89
53_E57_N1.0700.89
138_Y162_Y1.0650.89
16_G19_I1.0610.88
169_A189_L1.0590.88
101_A106_D1.0580.88
49_V53_E1.0530.88
157_Q162_Y1.0510.88
102_A142_L1.0470.87
111_I146_D1.0460.87
56_A194_A1.0370.87
51_H97_Y1.0330.86
140_T192_Q1.0250.86
66_G112_L1.0240.86
137_W144_M1.0220.86
81_D84_L1.0150.85
77_H80_A1.0130.85
186_S208_Q1.0100.85
95_F99_L1.0090.85
25_L66_G1.0060.84
67_L71_Y1.0020.84
182_D185_R1.0020.84
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  
4bwrA10.91441000.437Contact Map
1ouvA10.846899.90.486Contact Map
1klxA10.599199.80.591Contact Map
3e4bA40.833399.80.614Contact Map
3rjvA10.788399.60.684Contact Map
2pziA20.756898.50.802Contact Map
4ui9C2098.40.806Contact Map
4gpkA120.815398.30.81Contact Map
4gywA20.707298.30.81Contact Map
3ulqA10.810898.30.811Contact 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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