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OPENSEQ.org

GLRA2_MOUSE

ID: 1408920810 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 452 (408)
Sequences: 445 (279)
Seq/Len: 1.091
Nf(neff/√len): 13.8

HHblits Results: (2013_03)
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: 1.091).

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
262_Y437_Y2.2170.98
132_L202_F2.1370.98
143_H149_N2.0470.97
58_Y64_P1.7870.92
63_R67_K1.7510.91
434_N438_W1.7460.91
250_L261_M1.7250.90
59_D64_P1.7130.89
59_D63_R1.6940.89
278_I291_I1.6510.87
172_C182_D1.6240.86
320_W325_L1.6170.85
293_T297_M1.6160.85
273_W289_L1.6060.85
274_V297_M1.5770.83
221_F282_A1.5680.83
172_C186_C1.5640.83
279_N310_K1.5440.82
81_S90_M1.5350.81
99_R133_F1.5270.81
221_F289_L1.5170.80
152_L179_F1.5100.80
133_F153_R1.4670.77
250_L274_V1.4640.77
182_D186_C1.4530.76
156_K193_F1.4390.75
103_N157_N1.4350.75
210_V213_A1.4300.74
250_L291_I1.4030.72
153_R161_L1.3850.71
272_S276_F1.3850.71
92_Y161_L1.3810.71
87_E91_D1.3690.70
68_G291_I1.3450.68
58_Y63_R1.3430.67
324_C331_A1.3350.67
219_P317_I1.3300.66
137_E173_P1.3190.65
68_G73_V1.3150.65
199_D287_V1.3140.65
84_S87_E1.3130.65
146_T167_T1.3090.65
296_T299_T1.3090.65
293_T299_T1.3080.64
256_Y272_S1.2980.64
276_F284_P1.2900.63
257_Y261_M1.2850.62
127_I263_I1.2810.62
313_Y318_D1.2700.61
99_R163_S1.2660.61
170_L188_M1.2610.60
45_S49_D1.2580.60
196_T287_V1.2580.60
292_T299_T1.2510.59
68_G287_V1.2510.59
82_F88_T1.2500.59
300_Q320_W1.2490.59
274_V293_T1.2480.59
54_R57_G1.2470.59
276_F285_A1.2460.59
52_M55_T1.2420.58
219_P315_K1.2420.58
317_I333_L1.2350.58
100_Q181_M1.2290.57
201_I247_K1.2280.57
291_I294_V1.2280.57
137_E142_F1.2270.57
176_L308_L1.2270.57
137_E163_S1.2230.57
252_R286_R1.2210.57
208_G212_V1.2200.56
133_F161_L1.2180.56
170_L243_C1.2120.56
271_L294_V1.2120.56
85_V90_M1.2080.55
314_V326_L1.2060.55
269_V307_S1.1950.54
267_L282_A1.1940.54
136_N255_G1.1920.54
83_G90_M1.1910.54
123_M154_I1.1880.53
169_T436_F1.1880.53
200_L342_S1.1880.53
422_S426_F1.1850.53
356_K370_F1.1830.53
118_D340_F1.1820.53
275_S297_M1.1790.53
100_Q119_L1.1780.52
311_V323_V1.1760.52
294_V310_K1.1730.52
292_T296_T1.1690.52
387_T390_K1.1640.51
281_D335_Y1.1630.51
297_M329_F1.1610.51
43_S46_D1.1580.51
403_D406_A1.1560.50
315_K318_D1.1560.50
300_Q325_L1.1520.50
133_F423_R1.1510.50
252_R264_P1.1500.50
262_Y276_F1.1500.50
262_Y285_A1.1460.49
324_C332_L1.1460.49
339_N343_R1.1460.49
418_I431_L1.1440.49
188_M323_V1.1390.49
391_A396_P1.1390.49
424_A435_I1.1370.49
184_Q315_K1.1340.48
230_G233_T1.1330.48
316_A327_F1.1330.48
254_M257_Y1.1310.48
331_A430_F1.1310.48
181_M193_F1.1300.48
119_L316_A1.1290.48
150_K259_I1.1280.48
95_N141_N1.1260.48
170_L179_F1.1260.48
133_F154_I1.1230.47
108_A126_S1.1220.47
262_Y274_V1.1210.47
153_R292_T1.1200.47
58_Y61_R1.1200.47
243_C320_W1.1180.47
131_D153_R1.1160.47
131_D162_Y1.1130.46
66_F291_I1.1120.46
97_F181_M1.1110.46
69_P258_L1.1110.46
76_N179_F1.1100.46
149_N274_V1.1090.46
127_I152_L1.1070.46
329_F334_E1.1070.46
321_M335_Y1.1060.46
173_P416_K1.1040.45
133_F296_T1.1030.45
297_M336_A1.1000.45
98_L190_L1.0940.45
245_E268_I1.0900.44
146_T294_V1.0870.44
131_D161_L1.0870.44
172_C192_S1.0860.44
165_R176_L1.0850.44
232_C236_Y1.0830.44
363_D366_R1.0820.43
171_S184_Q1.0770.43
45_S48_L1.0770.43
137_E257_Y1.0770.43
55_T58_Y1.0760.43
154_I442_K1.0750.43
99_R113_P1.0740.43
278_I335_Y1.0720.42
77_I117_L1.0710.42
95_N320_W1.0700.42
200_L263_I1.0700.42
208_G211_Q1.0660.42
119_L335_Y1.0630.42
40_Q43_S1.0620.42
318_D329_F1.0610.41
140_A310_K1.0590.41
252_R276_F1.0540.41
250_L271_L1.0530.41
388_A393_P1.0500.40
97_F271_L1.0480.40
124_L135_A1.0450.40
250_L278_I1.0440.40
421_I425_A1.0430.40
294_V299_T1.0430.40
256_Y292_T1.0410.40
80_N83_G1.0390.39
64_P67_K1.0390.39
258_L263_I1.0380.39
384_K399_Q1.0380.39
232_C243_C1.0370.39
425_A432_I1.0350.39
174_M184_Q1.0330.39
294_V297_M1.0320.39
174_M182_D1.0300.39
198_N288_A1.0280.38
115_D156_K1.0280.38
331_A334_E1.0280.38
82_F85_V1.0260.38
318_D334_E1.0250.38
58_Y62_I1.0240.38
125_D160_V1.0240.38
109_Y125_D1.0240.38
356_K383_M1.0210.38
57_G63_R1.0210.38
87_E282_A1.0200.38
181_M339_N1.0200.38
290_G294_V1.0200.38
324_C430_F1.0190.38
143_H165_R1.0180.38
298_T331_A1.0170.37
92_Y305_R1.0160.37
254_M271_L1.0160.37
134_F311_V1.0150.37
285_A299_T1.0150.37
157_N432_I1.0130.37
131_D146_T1.0110.37
315_K335_Y1.0110.37
100_Q146_T1.0110.37
295_L299_T1.0100.37
232_C235_H1.0100.37
48_L52_M1.0090.37
257_Y300_Q1.0080.37
317_I332_L1.0070.37
146_T220_Q1.0060.37
125_D263_I1.0040.36
143_H336_A1.0030.36
282_A289_L1.0030.36
252_R262_Y1.0030.36
311_V339_N1.0020.36
264_P276_F1.0000.36
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: (17Jul14)
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  
3rhwA50.73671000.482Contact Map
4cofA50.75221000.483Contact Map
4hfiA50.68361000.548Contact Map
2bg9E10.80091000.58Contact Map
2bg9A20.80091000.584Contact Map
2bg9B10.80751000.584Contact Map
2bg9C10.79421000.585Contact Map
3rqwA100.63941000.587Contact Map
4aq5A20.78321000.61Contact Map
4aq5B10.76771000.612Contact 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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