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EB Split 2

ID: 1500938940 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 234 (227)
Sequences: 422 (364.5)
Seq/Len: 1.859
Nf(neff/√len): 24.2

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: 1.859).

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
170_L200_V2.9871.00
206_P209_D2.6811.00
45_R48_E2.3041.00
60_D63_T2.1260.99
207_V210_D2.0380.99
59_V64_V2.0260.99
35_R56_E2.0040.99
61_R65_E1.9380.98
109_I169_V1.7770.97
110_D209_D1.6630.95
20_H79_E1.6280.94
26_Y196_A1.6240.94
11_H14_D1.6020.93
3_I37_W1.5950.93
7_V18_L1.5840.93
101_K173_W1.5620.92
162_R167_S1.5570.92
157_C161_A1.5240.91
184_R219_P1.4540.88
17_V122_L1.4250.87
65_E69_R1.4220.86
105_D109_I1.4170.86
101_K177_Q1.4110.86
106_L153_A1.4060.86
170_L208_N1.3930.85
16_V34_S1.3830.84
37_W185_F1.3670.83
167_S209_D1.3660.83
23_T27_F1.3590.83
160_G166_R1.3510.82
51_D61_R1.3420.82
105_D169_V1.3350.81
201_E204_G1.3310.81
46_P50_V1.3200.80
136_S142_L1.3160.80
145_R178_G1.3160.80
185_F220_M1.3040.79
105_D172_M1.3040.79
168_L171_H1.2920.78
208_N223_P1.2920.78
33_G49_I1.2900.78
27_F99_I1.2630.76
162_R165_H1.2590.76
44_K49_I1.2540.75
15_E57_Y1.2520.75
48_E228_R1.2490.75
229_E233_D1.2460.75
107_I189_K1.2440.75
161_A170_L1.2390.74
91_L107_I1.2250.73
70_D73_R1.2140.72
20_H23_T1.2110.72
132_P137_R1.2100.72
70_D74_A1.2070.71
69_R73_R1.2060.71
173_W200_V1.1810.69
175_R225_R1.1790.69
51_D55_A1.1760.68
61_R150_I1.1730.68
91_L100_A1.1550.66
10_A17_V1.1480.66
55_A63_T1.1360.65
143_A180_P1.1360.65
186_G196_A1.1300.64
33_G36_I1.1270.64
230_A233_D1.1240.63
27_F149_R1.1230.63
23_T71_F1.1200.63
154_A161_A1.1130.62
2_K228_R1.1100.62
72_L81_L1.1100.62
1_M72_L1.1070.62
46_P72_L1.1030.61
80_L184_R1.1010.61
139_H142_L1.0970.61
150_I170_L1.0950.60
54_C73_R1.0930.60
49_I91_L1.0890.60
119_D123_I1.0880.60
35_R39_L1.0860.59
166_R213_S1.0840.59
162_R166_R1.0800.59
92_R95_D1.0800.59
184_R208_N1.0770.58
117_G120_P1.0670.57
10_A24_G1.0640.57
17_V33_G1.0630.57
147_A166_R1.0600.57
5_D79_E1.0590.57
54_C97_Q1.0530.56
228_R231_A1.0530.56
107_I110_D1.0530.56
15_E189_K1.0480.55
169_V200_V1.0460.55
165_H203_A1.0450.55
165_H189_K1.0430.55
24_G115_H1.0420.55
33_G71_F1.0340.54
26_Y187_V1.0300.53
167_S175_R1.0280.53
53_I68_L1.0270.53
17_V159_V1.0250.53
74_A77_N1.0220.53
40_L72_L1.0210.52
36_I49_I1.0120.51
196_A217_I1.0110.51
182_R224_R1.0080.51
8_V106_L1.0070.51
75_L184_R1.0030.50
184_R201_E1.0020.50
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  
3g2bA10.346299.50.729Contact Map
1x3zA10.747963.20.931Contact Map
4fgqA20.64160.50.932Contact Map
3deeA10.363253.80.935Contact Map
1l9mA20.8803490.937Contact Map
4ktyA20.837646.40.938Contact Map
2q3zA10.833339.90.94Contact Map
2hlyA10.40639.50.94Contact Map
3isrA40.871838.20.941Contact Map
2dk5A10.384638.10.941Contact 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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