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bc1

ID: 1513229301 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 149 (118)
Sequences: 163 (67.1)
Seq/Len: 1.381
Nf(neff/√len): 6.2

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: 1.381).

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
113_F118_M1.9830.97
122_I126_M1.7650.94
95_E104_M1.7090.93
110_I149_V1.7070.93
90_F94_E1.5980.89
38_N41_G1.5840.88
76_M139_D1.5790.88
65_T68_P1.5570.87
52_E149_V1.5230.86
55_S62_L1.4250.80
32_M68_P1.3840.77
109_R137_I1.3750.77
117_D124_M1.3330.73
132_V135_I1.3230.73
36_Y78_P1.3180.72
88_F91_N1.3010.71
107_D114_R1.2830.69
79_Y89_D1.2800.69
134_D146_N1.2790.69
73_K133_I1.2750.69
89_D92_I1.2730.68
83_G129_E1.2680.68
133_I148_C1.2430.66
82_D107_D1.2240.64
82_D108_S1.2030.62
49_K92_I1.1870.61
66_R73_K1.1840.60
32_M65_T1.1840.60
56_I67_S1.1730.59
36_Y46_I1.1560.58
67_S93_L1.1550.57
37_N110_I1.1540.57
128_H133_I1.1470.57
101_L118_M1.1420.56
45_R114_R1.1410.56
128_H146_N1.1340.55
57_L147_V1.1320.55
37_N107_D1.1300.55
37_N66_R1.1210.54
61_E102_K1.1100.53
43_E71_A1.1070.53
113_F135_I1.1070.53
59_L126_M1.1070.53
59_L115_Q1.1020.52
145_T148_C1.1020.52
124_M149_V1.1000.52
34_I78_P1.0940.51
35_K43_E1.0930.51
52_E57_L1.0860.50
83_G130_A1.0750.49
106_K148_C1.0700.49
101_L104_M1.0580.48
52_E107_D1.0530.47
76_M115_Q1.0530.47
99_N102_K1.0500.47
110_I119_V1.0310.45
79_Y88_F1.0300.45
112_E117_D1.0290.45
114_R138_A1.0290.45
81_H129_E1.0220.44
52_E66_R1.0180.44
130_A141_Y1.0180.44
41_G44_F1.0100.43
143_V147_V1.0050.42
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  
1vbkA20.83897.20.966Contact Map
4eljA10.38936.70.967Contact Map
1vb3A10.6045.50.968Contact Map
1dj7B10.38934.80.969Contact Map
3drwA20.91284.60.969Contact Map
2bptB10.194640.97Contact Map
4ajyC10.51683.70.971Contact Map
2l7xA10.32892.80.973Contact Map
4ellA20.48992.70.973Contact Map
2vpkA10.73832.50.973Contact 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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