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OPENSEQ.org

GLRA1_MOUSE

ID: 1408920788 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 457 (431)
Sequences: 520 (345.6)
Seq/Len: 1.206
Nf(neff/√len): 16.6

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: 1.206).

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
137_H143_N2.5041.00
53_D58_P2.1120.98
439_N443_W2.1020.98
126_L196_F1.9870.97
57_R61_K1.9140.96
52_Y58_P1.9010.95
53_D57_R1.7940.93
97_N151_N1.7540.92
93_R127_F1.7500.92
75_S84_M1.7130.91
73_I242_F1.6610.89
256_Y442_Y1.6510.89
314_W319_L1.6120.87
287_T293_T1.5900.86
267_W283_L1.5870.86
215_F276_A1.5550.84
273_N304_K1.5270.83
426_I430_G1.5220.83
117_M148_I1.5170.82
286_T293_T1.5000.81
86_Y155_L1.4820.80
226_C237_C1.4670.79
146_L173_F1.4580.79
85_D315_M1.3960.75
265_L288_V1.3800.73
147_R286_T1.3780.73
286_T290_T1.3780.73
244_L268_I1.3770.73
43_D46_M1.3740.73
261_L276_A1.3660.72
318_C325_A1.3520.71
78_S85_D1.3500.71
290_T293_T1.3500.71
427_S431_F1.3450.71
424_D432_P1.3410.70
307_Y312_D1.3410.70
272_I285_I1.3390.70
246_R258_P1.3340.70
290_T428_R1.3320.69
190_T232_T1.3310.69
39_S42_L1.3260.69
166_C176_D1.3100.68
132_K137_H1.3060.67
94_Q175_M1.3030.67
41_F46_M1.2950.66
113_L148_I1.2930.66
166_C180_C1.2910.66
251_Y255_M1.2860.66
432_P443_W1.2850.65
287_T291_M1.2830.65
42_L46_M1.2810.65
46_M49_T1.2800.65
305_V317_V1.2780.65
266_S270_F1.2770.65
80_A330_A1.2770.65
178_Q309_K1.2730.64
174_P180_C1.2700.64
272_I329_Y1.2700.64
129_A185_E1.2640.64
387_G391_K1.2520.63
250_Y266_S1.2470.62
213_P311_I1.2450.62
182_M242_F1.2430.62
213_P309_K1.2400.61
151_N437_I1.2350.61
315_M329_Y1.2340.61
270_F278_P1.2320.61
176_D180_C1.2320.61
148_I447_K1.2300.60
333_N337_R1.2290.60
423_I436_L1.2250.60
58_P61_K1.2220.60
42_L49_T1.2210.60
294_Q314_W1.2200.60
94_Q140_T1.2190.59
170_L302_L1.2190.59
147_R155_L1.2170.59
40_D43_D1.2100.59
166_C174_P1.2040.58
40_D46_M1.2040.58
78_S81_E1.1990.58
250_Y286_T1.1990.58
131_E136_F1.1980.57
266_S280_R1.1970.57
253_I324_S1.1970.57
130_N249_G1.1910.57
401_P404_A1.1910.57
131_E167_P1.1900.57
285_I288_V1.1880.56
423_I439_N1.1840.56
113_L435_F1.1690.55
131_E157_S1.1680.55
127_F147_R1.1640.54
164_L182_M1.1610.54
244_L255_M1.1610.54
260_L299_R1.1580.54
93_R157_S1.1560.53
288_V291_M1.1510.53
294_Q319_L1.1510.53
214_Q265_L1.1470.53
40_D44_K1.1460.52
39_S43_D1.1450.52
224_R227_T1.1430.52
166_C186_S1.1430.52
284_G288_V1.1420.52
310_A321_F1.1400.52
127_F155_L1.1390.52
251_Y294_Q1.1340.51
91_F265_L1.1320.51
185_E329_Y1.1300.51
268_I291_M1.1280.51
239_E262_I1.1270.51
318_C435_F1.1160.50
262_I281_V1.1150.49
292_T325_A1.1150.49
308_V320_L1.1150.49
279_A431_F1.1140.49
242_F249_G1.1130.49
59_N79_I1.1120.49
154_V444_I1.1100.49
424_D431_F1.1090.49
85_D91_F1.1060.49
422_K429_I1.1060.49
269_S289_L1.1050.48
436_L440_M1.1040.48
252_L257_I1.1040.48
256_Y270_F1.1040.48
112_D148_I1.1030.48
22_A26_A1.1010.48
137_H330_A1.1000.48
91_F175_M1.1000.48
361_Q364_E1.0990.48
132_K143_N1.0990.48
430_G433_M1.0980.48
268_I287_T1.0960.48
238_I262_I1.0950.47
60_F285_I1.0950.47
52_Y57_R1.0940.47
340_K347_R1.0930.47
288_V304_K1.0930.47
256_Y280_R1.0910.47
203_A314_W1.0900.47
77_G84_M1.0900.47
263_V277_A1.0890.47
279_A284_G1.0860.47
190_T281_V1.0840.46
145_L310_A1.0830.46
134_A304_K1.0790.46
244_L269_S1.0790.46
128_F305_V1.0790.46
29_A32_A1.0740.45
250_Y325_A1.0730.45
293_T329_Y1.0720.45
93_R167_P1.0720.45
26_A29_A1.0700.45
79_I84_M1.0700.45
89_N265_L1.0650.45
432_P439_N1.0640.44
125_D147_R1.0610.44
152_G159_R1.0600.44
246_R270_F1.0590.44
295_S333_N1.0580.44
104_N151_N1.0560.44
278_P293_T1.0550.44
121_I257_I1.0550.44
239_E249_G1.0550.44
94_Q126_L1.0530.43
288_V294_Q1.0530.43
89_N288_V1.0530.43
214_Q288_V1.0530.43
95_Q148_I1.0510.43
318_C326_L1.0510.43
192_N282_G1.0510.43
348_K352_H1.0510.43
428_R432_P1.0510.43
424_D443_W1.0500.43
153_N445_I1.0490.43
140_T288_V1.0490.43
301_S317_V1.0470.43
390_V393_A1.0460.43
137_H159_R1.0450.43
195_I241_R1.0440.43
225_Y228_K1.0430.42
387_G403_P1.0420.42
215_F283_L1.0420.42
292_T330_A1.0420.42
144_K253_I1.0410.42
119_D257_I1.0410.42
132_K330_A1.0400.42
429_I440_M1.0400.42
167_P421_K1.0380.42
193_D281_V1.0380.42
22_A25_E1.0360.42
246_R266_S1.0360.42
246_R280_R1.0350.42
227_T230_Y1.0340.42
280_R284_G1.0330.41
81_E85_D1.0310.41
248_M251_Y1.0280.41
289_L293_T1.0250.41
325_A435_F1.0240.41
309_K329_Y1.0240.41
263_V301_S1.0240.41
42_L48_R1.0220.40
202_G205_Q1.0200.40
100_R263_V1.0180.40
411_E414_K1.0170.40
388_I391_K1.0160.40
76_F83_T1.0160.40
240_A305_V1.0150.40
93_R168_M1.0150.40
70_N173_F1.0140.40
125_D140_T1.0140.40
325_A333_N1.0140.40
170_L204_V1.0140.40
140_T161_T1.0140.40
81_E178_Q1.0130.40
25_E28_A1.0120.40
159_R170_L1.0120.40
102_A120_S1.0110.39
143_N291_M1.0080.39
150_R187_F1.0080.39
347_R378_G1.0070.39
258_P266_S1.0070.39
300_A306_S1.0050.39
76_F446_Y1.0050.39
68_S81_E1.0040.39
347_R350_R1.0020.39
28_A31_S1.0020.39
363_D366_G1.0010.38
125_D156_Y1.0000.38
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  
4cofA50.7441000.412Contact Map
3rhwA50.73091000.413Contact Map
4hfiA50.67611000.48Contact Map
2bg9E10.79211000.505Contact Map
2bg9C10.78561000.51Contact Map
2bg9B10.79651000.513Contact Map
2bg9A20.78991000.513Contact Map
3rqwA100.63241000.526Contact Map
4aq5A20.78121000.528Contact Map
4aq5E10.78561000.535Contact 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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