GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
EB Split

ID: 1500916285 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 234 (232)
Sequences: 446 (389.9)
Seq/Len: 1.922
Nf(neff/√len): 25.6

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: 1.922).

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
16_V34_S1.9850.99
35_R56_E1.8800.98
75_L80_L1.8760.98
68_L80_L1.8250.98
216_G222_S1.8220.98
59_V64_V1.8110.97
68_L75_L1.7570.97
199_W209_D1.7330.96
196_A199_W1.7180.96
67_D80_L1.6830.96
45_R48_E1.6090.94
89_M92_R1.5770.93
219_P222_S1.5510.92
154_A157_C1.5350.92
197_H209_D1.5260.91
197_H200_V1.5180.91
194_L199_W1.5170.91
187_V198_A1.5150.91
61_R65_E1.5130.91
60_D63_T1.5080.91
187_V197_H1.4450.88
64_V68_L1.4230.87
217_I222_S1.3890.85
188_W197_H1.3840.85
63_T67_D1.3470.83
110_D113_L1.3330.82
161_A170_L1.3250.81
120_P128_E1.3080.80
187_V199_W1.3000.80
201_E208_N1.2950.79
189_K198_A1.2890.79
51_D61_R1.2880.79
92_R97_Q1.2730.78
75_L79_E1.2710.78
113_L116_E1.2640.77
110_D114_S1.2620.77
217_I220_M1.2540.76
10_A17_V1.2490.76
99_I114_S1.2410.75
194_L197_H1.2300.74
54_C73_R1.2290.74
117_G120_P1.2290.74
163_C186_G1.2280.74
185_F197_H1.2280.74
17_V26_Y1.2230.74
20_H79_E1.2230.74
57_Y64_V1.2210.74
199_W207_V1.2200.73
197_H201_E1.2130.73
106_L110_D1.2130.73
187_V190_A1.2000.72
188_W198_A1.1970.71
161_A165_H1.1920.71
216_G219_P1.1910.71
206_P211_R1.1850.70
163_C199_W1.1780.70
51_D55_A1.1720.69
170_L208_N1.1700.69
53_I68_L1.1670.69
189_K197_H1.1630.68
20_H30_D1.1610.68
186_G198_A1.1580.68
10_A24_G1.1580.68
9_S16_V1.1560.68
215_Q218_S1.1540.67
187_V196_A1.1490.67
163_C198_A1.1450.67
26_Y30_D1.1440.66
139_H142_L1.1400.66
67_D71_F1.1330.65
154_A158_P1.1330.65
133_Q138_E1.1310.65
71_F75_L1.1300.65
195_R198_A1.1290.65
189_K199_W1.1240.64
163_C167_S1.1210.64
67_D75_L1.1210.64
53_I56_E1.1180.64
198_A207_V1.1160.64
19_L29_L1.1130.63
183_L186_G1.1110.63
186_G196_A1.1090.63
26_Y36_I1.1050.62
168_L171_H1.1050.62
26_Y29_L1.1040.62
188_W199_W1.1020.62
184_R197_H1.1010.62
23_T27_F1.1000.62
158_P170_L1.0990.62
103_W119_D1.0990.62
12_I15_E1.0970.62
192_E197_H1.0960.62
17_V24_G1.0960.62
201_E204_G1.0950.61
114_S118_L1.0920.61
118_L121_I1.0880.61
200_V209_D1.0860.60
96_L104_S1.0850.60
188_W196_A1.0820.60
71_F80_L1.0760.59
184_R189_K1.0730.59
76_A80_L1.0580.57
40_L72_L1.0560.57
218_S222_S1.0560.57
44_K49_I1.0550.57
114_S117_G1.0530.57
67_D79_E1.0520.57
24_G53_I1.0510.57
15_E33_G1.0490.57
187_V195_R1.0490.57
28_G34_S1.0470.56
189_K195_R1.0450.56
167_S209_D1.0430.56
194_L198_A1.0430.56
186_G197_H1.0390.55
197_H207_V1.0380.55
23_T47_E1.0350.55
73_R77_N1.0350.55
215_Q219_P1.0320.55
215_Q222_S1.0310.55
64_V75_L1.0300.54
185_F189_K1.0250.54
69_R73_R1.0240.54
105_D112_R1.0220.54
7_V20_H1.0210.53
7_V18_L1.0180.53
226_V230_A1.0170.53
207_V210_D1.0170.53
11_H16_V1.0150.53
113_L121_I1.0120.52
198_A209_D1.0120.52
200_V207_V1.0110.52
184_R198_A1.0100.52
184_R188_W1.0100.52
199_W206_P1.0100.52
110_D117_G1.0070.52
24_G29_L1.0070.52
163_C166_R1.0040.52
226_V229_E1.0040.52
92_R95_D1.0030.51
36_I49_I1.0020.51
163_C197_H1.0000.51
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  
3g2bA10.346299.20.621Contact Map
3deeA10.350490.926Contact Map
2mvoA107.60.928Contact Map
3io5A20.25216.20.931Contact Map
1oyiA10.2656.20.931Contact Map
2dk5A10.384660.932Contact Map
4ou0A10.26925.60.933Contact Map
1d0qA20.28634.90.935Contact Map
2yu3A10.38034.90.935Contact Map
4trbA20.33764.40.936Contact 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.

Page generated in 0.0468 seconds.