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OPENSEQ.org

glp1 -force run

ID: 1443537512 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 463 (398)
Sequences: 298 (195.7)
Seq/Len: 0.749
Nf(neff/√len): 9.8

HHblits Results: (2015_06)
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: 0.749).

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
75_G81_V2.6350.99
326_R329_C2.3610.98
324_F349_L2.0090.93
244_L324_F1.9260.90
252_Y329_C1.8310.87
395_G406_N1.7210.82
189_L236_C1.6970.81
352_S412_E1.6550.79
403_C406_N1.6530.79
395_G403_C1.6510.79
245_L323_I1.6240.77
151_G159_L1.5950.75
126_C296_C1.5520.72
155_S159_L1.5310.71
148_Y179_I1.5290.71
244_L352_S1.5250.70
231_L285_G1.5240.70
235_Y247_E1.5150.70
107_E366_I1.5010.69
120_W124_S1.4890.68
163_S181_L1.4830.67
244_L349_L1.4730.66
171_H324_F1.4620.66
324_F412_E1.4610.66
151_G161_I1.4430.64
324_F352_S1.4420.64
151_G155_S1.4370.64
192_L196_I1.4290.63
349_L352_S1.3970.60
252_Y326_R1.3910.60
165_I169_F1.3800.59
266_F276_V1.3630.58
64_R74_D1.3620.58
243_W274_W1.3580.57
317_I352_S1.3560.57
247_E251_L1.3550.57
188_I351_K1.3550.57
177_N284_W1.3470.56
186_S240_N1.3450.56
174_C177_N1.3390.56
122_D126_C1.3360.55
287_V308_I1.3340.55
307_L311_L1.3260.55
258_S328_I1.3200.54
233_M360_L1.3160.54
123_L126_C1.3130.53
255_L338_N1.3100.53
243_W247_E1.3040.53
227_R353_T1.2980.52
264_W365_V1.2950.52
402_Y408_E1.2940.52
148_Y152_Y1.2910.52
142_L399_A1.2900.51
247_E274_W1.2880.51
359_L404_F1.2880.51
155_S162_A1.2860.51
412_E417_W1.2780.50
158_A396_L1.2750.50
395_G408_E1.2730.50
289_Y321_F1.2700.50
79_S203_W1.2690.50
182_N262_E1.2670.49
187_F190_R1.2640.49
161_I185_A1.2620.49
321_F367_F1.2620.49
245_L249_V1.2580.49
197_K324_F1.2560.49
70_A122_D1.2540.48
182_N360_L1.2480.48
235_Y273_G1.2470.48
335_L359_L1.2460.48
359_L399_A1.2450.48
86_P296_C1.2440.47
66_F254_L1.2420.47
352_S387_E1.2400.47
63_N360_L1.2390.47
400_I405_V1.2350.47
383_K388_L1.2250.46
157_S286_I1.2150.45
86_P353_T1.2140.45
244_L255_L1.2090.44
105_T109_L1.2050.44
107_E201_L1.2000.44
186_S363_H1.1980.44
62_C67_D1.1930.43
188_I399_A1.1870.43
187_F353_T1.1860.43
177_N402_Y1.1850.42
178_Y198_D1.1840.42
352_S384_L1.1820.42
151_G174_C1.1810.42
349_L412_E1.1800.42
250_Y273_G1.1780.42
160_V287_V1.1770.42
165_I399_A1.1770.42
180_H183_L1.1740.42
244_L412_E1.1730.41
275_G402_Y1.1670.41
350_A412_E1.1670.41
247_E250_Y1.1640.41
116_S126_C1.1580.40
193_S420_W1.1540.40
37_Q41_E1.1540.40
174_C190_R1.1540.40
174_C187_F1.1540.40
42_Y45_Q1.1530.40
242_Y398_V1.1470.39
248_G317_I1.1450.39
352_S422_L1.1430.39
211_Q214_W1.1390.39
151_G392_S1.1380.39
176_R408_E1.1310.38
335_L358_P1.1260.38
156_F335_L1.1230.37
298_T387_E1.1220.37
269_Y340_M1.1220.37
181_L407_N1.1210.37
235_Y243_W1.1200.37
209_A214_W1.1190.37
193_S339_L1.1190.37
398_V406_N1.1180.37
284_W306_W1.1170.37
248_G251_L1.1160.37
238_A313_I1.1140.37
321_F329_C1.1110.36
156_F404_F1.1110.36
285_G325_V1.1100.36
121_R126_C1.1090.36
174_C178_Y1.1070.36
159_L331_V1.1050.36
327_V359_L1.1020.36
360_L404_F1.1010.36
364_E392_S1.1000.36
63_N196_I1.0990.35
151_G169_F1.0980.35
273_G408_E1.0980.35
177_N190_R1.0950.35
165_I172_L1.0950.35
76_E322_L1.0930.35
190_R284_W1.0930.35
247_E273_G1.0900.35
239_A309_I1.0890.35
107_E282_V1.0880.35
246_V272_I1.0860.34
84_S124_S1.0850.34
66_F69_Y1.0840.34
195_F410_Q1.0840.34
142_L322_L1.0830.34
46_C50_L1.0830.34
372_D397_M1.0800.34
70_A83_V1.0780.34
119_P126_C1.0770.34
152_Y240_N1.0760.34
248_G320_N1.0750.34
363_H412_E1.0750.34
151_G158_A1.0740.34
142_L232_L1.0710.33
363_H370_V1.0680.33
359_L408_E1.0680.33
104_C247_E1.0650.33
392_S404_F1.0630.33
235_Y274_W1.0620.33
399_A422_L1.0550.32
67_D71_C1.0540.32
190_R353_T1.0520.32
156_F392_S1.0520.32
177_N246_V1.0520.32
169_F172_L1.0500.32
100_V347_C1.0490.32
356_L394_Q1.0480.32
195_F352_S1.0470.31
174_C392_S1.0450.31
102_R179_I1.0430.31
241_Y398_V1.0430.31
308_I404_F1.0390.31
234_Q300_N1.0370.31
149_T166_L1.0360.31
427_I430_D1.0340.31
317_I393_F1.0330.30
328_I399_A1.0310.30
276_V322_L1.0310.30
72_W404_F1.0310.30
184_F191_A1.0300.30
327_V335_L1.0300.30
348_R355_T1.0290.30
323_I338_N1.0280.30
323_I360_L1.0270.30
252_Y321_F1.0260.30
307_L328_I1.0240.30
182_N259_V1.0240.30
174_C240_N1.0230.30
245_L254_L1.0220.30
266_F401_L1.0200.30
395_G398_V1.0180.29
170_R255_L1.0180.29
321_F326_R1.0130.29
163_S262_E1.0100.29
84_S289_Y1.0090.29
312_P358_P1.0090.29
244_L317_I1.0060.29
44_R58_T1.0050.28
240_N274_W1.0030.28
358_P406_N1.0030.28
43_R49_S1.0020.28
403_C408_E1.0020.28
300_N309_I1.0010.28
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  
4k5yA30.54641000.614Contact Map
4l6rA10.82721000.676Contact Map
3c5tA10.22461000.828Contact Map
4jkvA20.80991000.831Contact Map
4rwfA1099.90.838Contact Map
4ersA10.207399.90.84Contact Map
2qkhA10.20399.90.844Contact Map
4hj0A20.196599.90.845Contact Map
4qinA10.667499.90.85Contact Map
1u34A10.254999.90.856Contact 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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