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OPENSEQ.org

d2xgva_

ID: 1448773103 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 133 (132)
Sequences: 269 (67.4)
Seq/Len: 2.038
Nf(neff/√len): 5.9

HHblits Results: (2015_06)
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: 2.038).

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
41_G118_R1.7630.97
129_A132_R1.7200.97
48_S64_A1.6700.96
37_I126_M1.6540.95
17_R22_W1.6470.95
79_E82_A1.6350.95
17_R35_E1.5390.93
53_V63_Q1.5100.92
57_E67_D1.5050.92
51_E62_L1.4700.90
64_A68_M1.4690.90
74_E77_A1.4590.90
125_L132_R1.4370.89
29_K35_E1.4320.89
54_Q58_V1.3460.84
53_V62_L1.3260.83
38_T98_L1.3240.83
94_H100_G1.2970.81
53_V57_E1.2940.81
57_E63_Q1.2880.80
35_E42_L1.2860.80
55_L62_L1.2720.79
25_Q36_T1.2660.79
84_P89_P1.2570.78
4_N21_A1.2550.78
79_E83_Q1.2490.77
108_A117_F1.2320.76
58_V72_Y1.2160.75
20_A23_I1.2070.74
87_P107_S1.2030.74
53_V59_V1.1900.72
41_G122_T1.1900.72
128_L131_L1.1830.72
84_P88_L1.1770.71
33_S71_A1.1760.71
93_A99_T1.1730.71
20_A24_R1.1710.71
4_N10_A1.1590.70
57_E62_L1.1580.70
45_Q51_E1.1480.69
3_V103_A1.1390.68
100_G103_A1.1340.67
37_I61_G1.1330.67
93_A108_A1.1230.66
22_W27_G1.1190.66
3_V8_G1.1170.65
18_T24_R1.1140.65
91_T109_Q1.1110.65
116_V120_W1.1100.65
50_R54_Q1.1070.64
3_V7_Q1.1060.64
114_A124_G1.0980.64
79_E101_D1.0960.63
58_V64_A1.0940.63
29_K92_S1.0860.62
62_L65_D1.0810.62
17_R23_I1.0810.62
71_A81_D1.0770.61
18_T23_I1.0760.61
108_A113_A1.0710.61
52_Q56_L1.0540.59
120_W129_A1.0350.57
17_R20_A1.0330.57
57_E65_D1.0230.55
42_L47_L1.0140.54
82_A85_Q1.0120.54
31_L82_A1.0110.54
21_A39_Y1.0050.53
23_I27_G1.0050.53
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  
1l6nA10.99251000.015Contact Map
2xgvA111000.039Contact Map
2xdeA20.9851000.049Contact Map
2wlvA10.9851000.056Contact Map
2xguA20.99251000.074Contact Map
4u0cA10.97741000.181Contact Map
3gv2A60.99251000.211Contact Map
1eiaA10.88721000.263Contact Map
3tirA10.96991000.362Contact Map
1d1dA10.89471000.4Contact 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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