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cwet_573

ID: 1513358396 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 116 (116)
Sequences: 389 (213.8)
Seq/Len: 3.353
Nf(neff/√len): 19.9

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: 3.353).

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
1_C7_G2.4041.00
3_E7_G2.2551.00
60_S67_I2.2551.00
2_W17_D2.1361.00
2_W8_Q2.0081.00
32_R53_S1.8010.99
4_T8_Q1.7220.99
73_I87_N1.6070.98
76_G81_P1.6040.98
2_W7_G1.5820.98
70_Q74_W1.5290.97
17_D90_R1.5190.97
77_S92_H1.4770.96
95_M98_Q1.4760.96
10_F16_S1.4530.96
76_G83_L1.4260.95
64_L70_Q1.3800.94
64_L74_W1.3770.94
78_F115_A1.3750.94
67_I113_F1.3610.93
1_C8_Q1.3330.92
89_L92_H1.3300.92
6_V85_G1.3080.91
33_A37_R1.2920.90
102_V105_C1.2860.90
8_Q17_D1.2850.90
66_L91_L1.2810.90
2_W9_E1.2760.90
59_I103_M1.2710.90
22_Y27_I1.2600.89
16_S111_R1.2500.88
29_D105_C1.2410.88
86_I94_S1.2190.87
57_F74_W1.2090.86
57_F70_Q1.2050.86
13_L17_D1.1980.85
63_V84_P1.1660.83
1_C9_E1.1480.82
79_F111_R1.1410.81
101_A112_V1.1380.81
59_I91_L1.1120.79
4_T114_K1.1060.79
61_G105_C1.1030.78
102_V111_R1.1030.78
28_G31_L1.0800.76
90_R94_S1.0750.76
56_E111_R1.0470.73
64_L84_P1.0320.71
61_G65_A1.0310.71
9_E12_R1.0310.71
92_H115_A1.0300.71
10_F111_R1.0130.69
102_V114_K1.0010.68
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  
4xxoA20110.934Contact Map
4wisA20.89667.10.939Contact Map
4bkfC20.086220.954Contact Map
1jb0M10.10341.40.958Contact Map
2wscI10.22411.10.96Contact Map
1tt5A20.33621.10.96Contact Map
4xk8I2010.962Contact Map
1wijA10.29310.90.962Contact Map
2vq5A20.33620.90.963Contact Map
3pp4P10.12070.80.964Contact 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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