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galectin 8

ID: 1501849120 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 317 (303)
Sequences: 500 (350.4)
Seq/Len: 1.650
Nf(neff/√len): 20.1

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: 1.650).

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
243_S290_Y3.6171.00
114_F135_I3.3341.00
64_F116_V3.1781.00
50_L107_I2.6331.00
65_H69_R2.4771.00
80_T126_Y2.3651.00
228_L280_V2.3091.00
48_V105_I2.2340.99
78_C124_L2.2300.99
11_I15_P2.1650.99
229_H233_R2.1470.99
12_I15_P2.1450.99
33_I50_L2.0980.99
49_D65_H2.0340.99
23_I26_Q2.0090.98
211_A263_P1.8900.97
76_I123_T1.8400.97
117_A122_H1.7720.96
23_I33_I1.7630.96
65_H77_V1.7170.95
233_R252_E1.7170.95
45_R71_K1.6890.94
242_N249_W1.6720.94
185_L309_I1.6500.93
63_A67_N1.6470.93
233_R242_N1.6100.92
205_G267_F1.5670.91
253_E260_P1.4920.88
236_I254_R1.4860.87
213_S235_N1.4840.87
229_H242_N1.4810.87
50_L64_F1.4700.87
69_R91_I1.4560.86
233_R254_R1.4550.86
241_R253_E1.4290.84
241_R259_F1.4220.84
63_A68_P1.4210.84
201_V218_L1.4090.83
281_A289_E1.3920.82
64_F78_C1.3770.81
72_R91_I1.3650.80
217_D304_E1.3620.80
86_W103_F1.3540.80
108_M117_A1.3510.80
278_F300_I1.3420.79
69_R77_V1.3260.78
65_H229_H1.3190.77
214_F232_P1.3170.77
227_A278_F1.3070.76
46_F61_D1.3000.76
218_L271_I1.3000.76
261_F282_V1.2970.76
30_G37_G1.2890.75
286_H289_E1.2810.74
259_F281_A1.2770.74
272_Y281_A1.2760.74
67_N77_V1.2740.74
311_L314_V1.2650.73
18_P30_G1.2590.72
229_H232_P1.2570.72
87_G103_F1.2510.72
271_I278_F1.2470.71
267_F283_N1.2440.71
140_I146_I1.2360.70
230_L287_S1.2270.70
144_V212_K1.2240.69
259_F268_E1.2230.69
77_V254_R1.2190.69
79_N86_W1.2170.69
217_D229_H1.2150.69
107_I203_V1.2110.68
203_V311_L1.2110.68
119_N314_V1.2040.68
64_F97_F1.1910.66
78_C95_T1.1890.66
233_R250_G1.1880.66
205_G249_W1.1860.66
89_E103_F1.1650.64
18_P37_G1.1620.64
146_I300_I1.1610.63
90_E252_E1.1510.62
278_F292_H1.1510.62
17_I23_I1.1470.62
77_V252_E1.1460.62
207_V287_S1.1370.61
14_N148_S1.1350.61
35_I192_N1.1340.61
105_I118_V1.1240.60
27_L33_I1.1230.60
109_V132_P1.1220.60
97_F242_N1.1220.60
212_K305_I1.1210.59
250_G293_R1.1200.59
114_F271_I1.1170.59
213_S233_R1.1150.59
88_R305_I1.1120.59
113_K125_L1.1110.58
242_N250_G1.1080.58
233_R240_V1.1070.58
31_T234_L1.1050.58
239_F287_S1.1040.58
195_M273_C1.1030.58
67_N79_N1.1010.57
201_V316_S1.1000.57
65_H252_E1.0900.56
12_I19_Y1.0880.56
149_I301_D1.0870.56
242_N252_E1.0830.55
229_H252_E1.0820.55
18_P23_I1.0780.55
48_V107_I1.0750.55
217_D264_G1.0740.55
80_T240_V1.0720.54
229_H293_R1.0690.54
53_G60_A1.0690.54
70_F99_R1.0660.54
172_R179_G1.0630.53
303_L308_D1.0620.53
91_I254_R1.0610.53
46_F214_F1.0600.53
273_C292_H1.0590.53
207_V309_I1.0510.52
226_I233_R1.0500.52
158_Q162_A1.0470.52
118_V123_T1.0450.51
226_I231_N1.0450.51
87_G126_Y1.0420.51
203_V314_V1.0330.50
32_L106_V1.0280.50
11_I16_V1.0280.50
231_N242_N1.0250.49
180_T183_L1.0250.49
215_N232_P1.0210.49
64_F131_G1.0190.49
95_T118_V1.0180.49
23_I34_V1.0170.49
70_F284_G1.0140.48
50_L252_E1.0140.48
194_P285_V1.0100.48
305_I308_D1.0040.47
23_I151_F1.0020.47
66_F278_F1.0020.47
220_A299_S1.0010.47
71_K75_C1.0010.47
35_I107_I1.0000.47
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  
3vklA20.91171000.129Contact Map
3wv6A201000.155Contact Map
4hl0A20.87381000.178Contact Map
2wsuA40.91171000.189Contact Map
3ap9A10.47631000.541Contact Map
2d6mA20.47631000.549Contact Map
2zhnA10.45431000.561Contact Map
3i8tA10.44161000.569Contact Map
4xbqA201000.571Contact Map
2yroA10.471000.575Contact 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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