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OPENSEQ.org

Q3YL5_full

ID: 1379493377 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 116 (102)
Sequences: 3603 (2460.8)
Seq/Len: 35.324
Nf(neff/√len): 243.7

HHblits Results: (2013_03)
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: 35.324).

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
65_D72_D2.9451.00
61_D66_G2.8311.00
91_D96_E2.6101.00
67_V97_Q2.4911.00
95_D102_E2.4701.00
23_D30_I2.2041.00
19_G24_W2.1771.00
91_D102_E2.1481.00
91_D94_D1.8491.00
91_D95_D1.8271.00
23_D27_S1.8161.00
93_N99_S1.7041.00
62_S75_H1.6631.00
61_D72_D1.6221.00
21_G30_I1.5931.00
93_N102_E1.5651.00
19_G22_G1.5381.00
73_I87_F1.5121.00
28_G31_S1.5101.00
63_N72_D1.5041.00
61_D65_D1.4971.00
58_M64_K1.4481.00
92_E105_D1.4481.00
100_T104_K1.4341.00
27_S30_I1.4331.00
70_H74_K1.4060.99
65_D69_T1.4000.99
54_P58_M1.3950.99
90_A98_I1.3480.99
19_G23_D1.3270.99
25_K67_V1.3070.99
61_D64_K1.2900.99
70_H73_I1.2850.99
20_R33_S1.2340.98
95_D99_S1.2180.98
19_G30_I1.2170.98
31_S57_L1.2060.98
18_I26_V1.1970.98
56_D59_S1.1760.98
92_E95_D1.1630.97
70_H87_F1.0830.96
13_E16_P1.0730.95
31_S103_F1.0680.95
99_S102_E1.0600.95
92_E102_E1.0600.95
28_G57_L1.0550.95
73_I90_A1.0530.95
15_K19_G1.0380.94
100_T103_F1.0340.94
60_Y76_I1.0190.93
84_E88_S1.0170.93
32_I36_K1.0120.93
28_G32_I1.0040.93
18_I34_W1.0030.93
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: (08Feb14)
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  
1alvA20.948399.30.367Contact Map
3sjsA10.948399.30.37Contact Map
3bowA10.991499.30.372Contact Map
3mwuA10.887999.30.379Contact Map
1y1xA20.948399.30.38Contact Map
3u0kA10.948399.30.386Contact Map
2ccmA20.948399.30.386Contact Map
4i2yA20.948399.30.387Contact Map
1qxpA20.836299.30.387Contact Map
2obhA20.922499.30.39Contact 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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