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OPENSEQ.org

5J8Y_A

ID: 1474941941 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 78 (73)
Sequences: 472 (302.6)
Seq/Len: 6.466
Nf(neff/√len): 35.4

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: 6.466).

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
10_E31_R2.2141.00
13_I27_G2.0041.00
57_G61_K1.9571.00
66_V69_V1.7461.00
7_W12_V1.6071.00
33_H40_L1.4910.99
12_V15_Y1.4870.99
37_G43_L1.4460.99
20_D23_L1.4050.99
16_I20_D1.3280.98
46_E49_M1.2970.97
47_M63_C1.2970.97
41_L61_K1.2930.97
58_P61_K1.2730.97
8_T71_G1.2630.97
45_S48_M1.2550.96
34_E39_A1.2520.96
35_I52_M1.2390.96
40_L64_N1.2030.95
49_M63_C1.1700.94
9_I12_V1.1600.94
63_C67_N1.1470.93
35_I61_K1.1290.93
52_M59_A1.1210.92
52_M61_K1.0900.91
14_Q17_E1.0790.90
17_E28_D1.0780.90
48_M70_N1.0680.90
17_E44_N1.0680.90
37_G57_G1.0550.89
4_P7_W1.0380.88
5_I70_N1.0290.87
28_D46_E1.0250.87
68_K73_R1.0150.86
47_M51_Y1.0100.86
39_A42_L1.0040.85
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  
1pk1B20.897499.70.323Contact Map
4pzoA60.910399.70.329Contact Map
1kw4A10.884699.60.38Contact Map
2dkzA10.923199.50.387Contact Map
4z8lC2099.30.46Contact Map
3bs5A10.987299.30.461Contact Map
2e8oA10.961599.30.463Contact Map
2d8cA10.948799.30.473Contact Map
2eanA10.987299.30.477Contact Map
2f3nA30.820599.30.478Contact 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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