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OPENSEQ.org

10006_8

ID: 1433410372 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 66 (66)
Sequences: 135 (114.7)
Seq/Len: 2.045
Nf(neff/√len): 14.1

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: 2.045).

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
8_P34_R2.6251.00
35_R40_L2.2591.00
44_E50_Y2.0390.99
18_A22_L1.9880.99
12_M16_L1.7750.97
9_P34_R1.7730.97
12_M30_V1.7360.97
38_H42_R1.6460.95
40_L52_L1.6360.95
48_Y51_A1.3840.86
23_E28_L1.3640.85
49_R62_L1.3460.84
5_S33_V1.3110.82
14_R48_Y1.2720.79
41_A46_E1.2640.79
27_R65_E1.2630.79
23_E26_Q1.2520.78
15_I30_V1.1980.73
16_L28_L1.1720.71
29_L63_L1.1710.71
25_G37_I1.1660.70
2_V14_R1.1140.65
10_L35_R1.1010.64
13_Q42_R1.0970.64
6_W9_P1.0860.62
6_W12_M1.0860.62
17_E21_A1.0720.61
30_V42_R1.0630.60
39_L43_L1.0560.59
42_R46_E1.0400.57
27_R63_L1.0230.56
55_L59_R1.0100.54
30_V38_H1.0100.54
53_R62_L1.0100.54
2_V32_H1.0090.54
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: (31Jan15)
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  
1pavA1198.40.553Contact Map
1jdqA1198.40.556Contact Map
3lvjC2198.40.563Contact Map
3hz7A1198.30.568Contact Map
1je3A1198.10.59Contact Map
2lxrA10.969796.40.695Contact Map
1okgA10.666783.60.79Contact Map
3wx7A2134.70.85Contact Map
3grzA20.984816.60.871Contact Map
3pfgA1114.80.874Contact 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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