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OPENSEQ.org

GLRA4_MOUSE

ID: 1408920862 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 456 (424)
Sequences: 521 (358.4)
Seq/Len: 1.229
Nf(neff/√len): 17.4

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: 1.229).

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
142_H148_N2.6661.00
131_L201_F2.0580.98
57_Y63_P1.9920.97
58_D63_P1.9320.96
437_N441_W1.8930.95
62_R66_K1.8450.95
58_D62_R1.7740.93
320_W325_L1.7410.92
80_S89_M1.6690.90
279_N310_K1.6470.89
102_N156_N1.5940.87
293_T299_T1.5870.86
91_Y160_L1.5790.86
151_L178_F1.5680.86
262_Y440_Y1.5360.84
256_Y292_T1.5180.83
292_T296_T1.5020.82
221_F282_A1.5010.82
421_I434_L1.4640.80
292_T299_T1.4590.79
293_T297_M1.4570.79
278_I291_I1.4540.79
267_L282_A1.4350.78
232_C243_C1.4310.78
339_N343_R1.4310.78
98_R132_F1.4090.76
273_W289_L1.3940.75
424_I428_V1.3880.74
118_L153_I1.3750.73
300_Q325_L1.3750.73
57_Y62_R1.3670.73
78_I248_F1.3600.72
276_F284_P1.3430.71
430_P441_W1.3370.70
278_I335_Y1.3360.70
425_S429_F1.3350.70
169_L187_M1.3320.70
126_I263_I1.3320.70
422_D430_P1.3300.70
272_S276_F1.3280.70
96_F180_M1.3260.70
271_L294_V1.3200.69
257_Y261_M1.3110.68
298_T331_A1.2940.67
122_M153_I1.2830.66
97_L256_Y1.2820.66
290_G294_V1.2770.65
380_C384_R1.2700.65
434_L438_I1.2690.65
296_T299_T1.2660.64
152_R160_L1.2650.64
250_L274_V1.2550.63
313_Y318_D1.2520.63
198_D287_V1.2420.62
136_E162_S1.2410.62
262_Y276_F1.2400.62
98_R162_S1.2390.62
48_D51_M1.2350.62
256_Y272_S1.2270.61
179_P185_C1.2200.60
367_E370_F1.2190.60
152_R292_T1.2180.60
85_T336_A1.2160.60
245_E268_I1.2140.60
90_D321_M1.2130.59
153_I445_K1.2060.59
78_I85_T1.1980.58
67_G72_V1.1980.58
82_G89_M1.1930.58
259_I330_A1.1890.57
108_Y125_S1.1850.57
231_Y234_K1.1830.57
161_Y305_R1.1790.56
315_K335_Y1.1770.56
296_T426_R1.1710.55
136_E141_F1.1680.55
219_P317_I1.1660.55
83_S90_D1.1660.55
63_P66_K1.1640.55
274_V297_M1.1640.55
300_Q320_W1.1630.55
421_I427_A1.1620.55
51_M54_T1.1610.54
45_D48_D1.1570.54
136_E172_P1.1570.54
441_W444_Y1.1560.54
250_L291_I1.1520.54
133_F436_F1.1520.54
324_C331_A1.1510.53
99_Q180_M1.1510.53
44_S48_D1.1490.53
175_L308_L1.1480.53
190_E335_Y1.1460.53
183_Q315_K1.1450.53
252_R264_P1.1410.52
389_M392_S1.1390.52
384_R387_G1.1350.52
134_A190_E1.1340.52
380_C386_G1.1330.52
171_C185_C1.1290.51
95_V124_D1.1280.51
142_H175_L1.1250.51
427_A438_I1.1230.51
84_V89_M1.1220.51
252_R276_F1.1220.51
244_I268_I1.1200.50
321_M335_Y1.1190.50
368_S372_F1.1160.50
78_I89_M1.1160.50
167_L178_F1.1140.50
422_D429_F1.1140.50
199_L258_L1.1140.50
200_M247_K1.1120.50
195_T238_T1.1120.50
243_C320_W1.1120.50
164_R175_L1.1110.50
284_P300_Q1.1110.50
311_V323_V1.1060.49
245_E255_G1.1030.49
130_D160_L1.1010.49
118_L161_Y1.0970.48
257_Y276_F1.0970.48
278_I437_N1.0960.48
278_I432_T1.0960.48
368_S377_L1.0940.48
324_C332_L1.0940.48
122_M177_N1.0930.48
365_I379_H1.0910.48
84_V263_I1.0900.47
318_D329_F1.0890.47
315_K318_D1.0880.47
136_E257_Y1.0860.47
99_Q145_T1.0850.47
256_Y331_A1.0850.47
148_N262_Y1.0820.47
67_G70_V1.0810.47
45_D51_M1.0810.47
371_Y374_G1.0800.47
352_R447_L1.0800.47
297_M340_F1.0800.47
257_Y300_Q1.0800.47
105_R269_V1.0800.47
47_L51_M1.0790.46
269_V307_S1.0790.46
409_T412_K1.0790.46
190_E314_V1.0780.46
127_W157_G1.0760.46
422_D433_F1.0760.46
83_S86_E1.0740.46
219_P315_K1.0740.46
349_M352_R1.0740.46
139_A300_Q1.0720.46
132_F160_L1.0710.46
250_L339_N1.0710.46
90_D96_F1.0690.45
86_E90_D1.0680.45
46_F51_M1.0680.45
382_Q390_E1.0610.45
291_I294_V1.0570.44
208_P211_Q1.0570.44
371_Y377_L1.0570.44
364_I393_S1.0570.44
145_T294_V1.0560.44
428_V431_F1.0550.44
285_A429_F1.0550.44
276_F285_A1.0540.44
320_W419_K1.0540.44
422_D441_W1.0530.44
81_F84_V1.0510.44
313_Y436_F1.0450.43
386_G390_E1.0450.43
426_R430_P1.0450.43
145_T220_Q1.0440.43
221_F289_L1.0430.43
208_P212_V1.0420.43
178_F331_A1.0420.43
197_N288_G1.0420.43
90_D201_F1.0400.43
158_N199_L1.0380.42
49_K55_S1.0370.42
137_K173_M1.0360.42
357_R374_G1.0310.42
155_K192_F1.0300.42
284_P299_T1.0290.42
240_K265_S1.0290.42
375_Y378_G1.0290.42
198_D268_I1.0270.41
250_L261_M1.0260.41
99_Q305_R1.0260.41
76_I116_L1.0250.41
181_D185_C1.0250.41
70_V83_S1.0240.41
30_D34_G1.0240.41
192_F260_Q1.0240.41
183_Q219_P1.0220.41
232_C236_Y1.0190.41
356_R360_M1.0180.41
420_R427_A1.0180.41
44_S47_L1.0180.41
99_Q131_L1.0170.40
376_G381_L1.0160.40
26_L36_K1.0160.40
145_T166_T1.0160.40
139_A243_C1.0110.40
276_F282_A1.0110.40
138_G256_Y1.0110.40
274_V299_T1.0080.40
162_S178_F1.0080.40
394_I399_P1.0070.40
118_L124_D1.0070.40
406_E409_T1.0070.40
268_I322_A1.0060.39
32_K37_G1.0060.39
207_A211_Q1.0050.39
148_N308_L1.0050.39
132_F152_R1.0050.39
294_V310_K1.0040.39
408_E411_R1.0030.39
103_D157_G1.0020.39
262_Y285_A1.0010.39
318_D334_E1.0010.39
291_I312_S1.0010.39
196_M200_M1.0000.39
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  
4cofA50.74781000.405Contact Map
3rhwA50.73251000.407Contact Map
4hfiA50.67761000.477Contact Map
2bg9E10.78291000.493Contact Map
2bg9C10.78731000.498Contact Map
2bg9B10.79821000.501Contact Map
2bg9A20.79391000.503Contact Map
4aq5A20.79391000.517Contact Map
4aq5E10.7611000.518Contact Map
4aq5C10.75221000.519Contact 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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