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OPENSEQ.org

NepR_1

ID: 1487560911 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 68 (68)
Sequences: 375 (342.2)
Seq/Len: 5.515
Nf(neff/√len): 41.5

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: 5.515).

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
57_I61_A1.6100.99
11_H17_K1.5200.99
42_F57_I1.4880.99
34_I50_V1.4350.98
11_H22_A1.3510.97
20_G67_G1.3420.97
42_F61_A1.3130.96
61_A65_A1.2900.96
41_M46_V1.2820.96
26_E31_Q1.2610.95
51_P54_F1.2340.95
39_R48_E1.2250.94
28_R32_Q1.1950.93
7_D16_D1.1880.93
51_P61_A1.1710.92
15_E20_G1.1510.91
16_D19_K1.1500.91
59_R64_P1.1490.91
56_A60_K1.1470.91
38_L54_F1.1460.91
26_E30_R1.1120.89
42_F51_P1.1080.89
7_D11_H1.1060.89
33_A55_L1.0900.88
24_L28_R1.0860.88
55_L58_L1.0790.87
38_L57_I1.0660.87
9_I14_M1.0650.87
38_L58_L1.0640.87
48_E52_D1.0590.86
51_P57_I1.0580.86
1_M4_G1.0520.86
38_L51_P1.0520.86
38_L52_D1.0500.86
3_F12_V1.0390.85
55_L59_R1.0380.85
52_D56_A1.0370.85
36_V41_M1.0290.84
4_G8_M1.0270.84
38_L42_F1.0230.83
42_F50_V1.0090.82
41_M45_V1.0040.82
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  
3t0yB20.485310.533Contact Map
2lfwB10.91180.30.681Contact Map
3j2vC40.39710.20.757Contact Map
4qicB200.10.785Contact Map
4c7rA30.55880.10.804Contact Map
3j7y510.22060.10.804Contact Map
3j7yp100.10.812Contact Map
3wvzA20.36760.10.816Contact Map
3td7A100.10.82Contact Map
3d3lA20.250.10.824Contact 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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