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OPENSEQ.org

2l5f

ID: 1494491196 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 92 (81)
Sequences: 1440 (874.9)
Seq/Len: 17.778
Nf(neff/√len): 97.2

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: 17.778).

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
20_K26_T2.4141.00
15_M32_E2.3541.00
56_P73_Q2.2101.00
61_K67_T2.0761.00
12_A15_M2.0761.00
71_N74_T1.8091.00
61_K65_G1.7391.00
59_E67_T1.6371.00
83_K86_E1.6001.00
19_H60_Y1.5261.00
29_Y34_K1.4771.00
69_Y81_K1.4501.00
42_D45_K1.3800.99
25_R66_K1.3590.99
16_W28_Y1.3520.99
38_W41_P1.3360.99
18_E40_K1.3220.99
18_E26_T1.3040.99
53_S56_P1.2950.99
55_C85_L1.2900.99
81_K86_E1.2140.98
27_Y68_Y1.2090.98
68_Y79_W1.2090.98
39_E44_L1.2080.98
19_H29_Y1.1960.98
54_K88_L1.1930.98
29_Y70_Y1.1580.97
72_S75_K1.1370.97
80_A85_L1.1320.97
30_N33_T1.1300.97
24_G27_Y1.1270.97
27_Y38_W1.1020.96
25_R34_K1.0940.96
55_C84_E1.0600.95
36_S77_S1.0590.95
72_S77_S1.0530.95
28_Y40_K1.0480.94
58_K72_S1.0420.94
21_S62_S1.0380.94
30_N37_T1.0360.94
23_D62_S1.0320.94
46_T63_D1.0190.93
36_S41_P1.0100.93
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: (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  
2l5fA1199.80.115Contact Map
2jxwA10.815299.70.226Contact Map
4rohA10.826199.70.241Contact Map
1tk7A10.91399.70.241Contact Map
2kxqA10.923999.70.253Contact Map
1o6wA10.815299.70.26Contact Map
3l4hA10.815298.80.527Contact Map
2dk7A10.706598.80.53Contact Map
2ysbA10.532698.60.56Contact Map
2dwvA20.532698.60.562Contact 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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