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2PSM

ID: 1515674841 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 117 (112)
Sequences: 154 (87.8)
Seq/Len: 1.375
Nf(neff/√len): 8.3

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: 1.375).

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_T50_L1.9620.97
49_E56_E1.8460.96
56_E92_E1.8080.95
66_V106_F1.7840.94
29_Y49_E1.6780.92
29_Y56_E1.6750.92
49_E92_E1.6510.91
88_C110_V1.6200.90
5_W12_L1.5770.88
30_T96_E1.4620.82
29_Y92_E1.4610.82
46_F106_F1.4510.82
89_K106_F1.4500.82
110_V113_F1.4260.80
17_S66_V1.3700.76
68_N77_L1.3590.75
36_P42_A1.3520.75
42_A111_Q1.3320.73
42_A109_I1.3140.72
30_T105_S1.3090.71
42_A90_E1.2850.69
38_C102_F1.2630.67
54_L98_T1.2540.67
65_T97_K1.2030.62
13_E17_S1.1960.61
59_N65_T1.1860.60
6_I13_E1.1820.60
28_L106_F1.1720.59
10_Y13_E1.1660.58
28_L97_K1.1600.58
25_D28_L1.1410.56
10_Y62_L1.1260.54
47_L74_N1.1200.54
113_F116_T1.1160.53
43_M110_V1.1110.53
7_D70_L1.1080.53
58_S116_T1.1040.52
36_P54_L1.1020.52
88_C106_F1.0840.50
8_V13_E1.0740.49
71_Y108_R1.0710.49
5_W11_D1.0670.48
5_W106_F1.0530.47
90_E94_L1.0410.46
95_E106_F1.0410.46
30_T92_E1.0260.44
44_N54_L1.0230.44
26_T109_I1.0220.44
25_D33_D1.0210.44
25_D112_M1.0210.44
44_N76_T1.0190.44
23_H93_E1.0120.43
32_S95_E1.0090.43
13_E116_T1.0080.43
7_D76_T1.0060.42
6_I18_L1.0020.42
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  
2z3qA211000.075Contact Map
2oqpA10.957399.90.219Contact Map
4yueC1095.10.813Contact Map
4nejA10.829194.80.815Contact Map
2d48A10.914521.40.908Contact Map
2ilkA10.90611.90.918Contact Map
1n1fA10.914510.50.92Contact Map
3mtuE20.42749.90.921Contact Map
1lqsL20.87189.10.922Contact Map
3obvE40.87188.40.924Contact 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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