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OPENSEQ.org

GLRA3_MOUSE

ID: 1408920846 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 464 (434)
Sequences: 446 (305.6)
Seq/Len: 1.028
Nf(neff/√len): 14.7

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: 1.028).

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_N2.2770.98
131_L201_F2.1170.97
57_Y63_P2.0670.97
80_S89_M2.0470.96
58_D63_P2.0010.96
58_D62_R1.9710.95
261_Y447_Y1.9030.94
220_F281_A1.8700.93
278_N309_K1.8640.93
62_R66_K1.8290.92
98_R132_F1.8010.91
444_N448_W1.7820.91
291_T298_T1.7020.88
151_L178_F1.6260.85
272_W288_L1.5990.83
319_W324_L1.5850.83
78_I247_F1.4620.75
256_Y260_M1.4560.74
76_I116_L1.4390.73
122_M153_I1.4320.73
231_C242_C1.4220.72
312_Y317_D1.4200.72
218_P316_I1.4160.71
102_N156_N1.4140.71
48_D51_M1.3920.70
126_I262_I1.3850.69
118_L153_I1.3660.68
266_L281_A1.3660.68
91_Y160_L1.3640.67
270_L293_V1.3580.67
295_T433_R1.3570.67
291_T295_T1.3560.67
44_S47_L1.3530.66
85_A335_A1.3470.66
255_Y291_T1.3470.66
152_R291_T1.3450.66
244_E267_I1.3370.65
441_L445_I1.3360.65
249_L260_M1.3280.64
428_I441_L1.3270.64
249_L273_V1.3260.64
51_M54_T1.3210.64
295_T298_T1.3190.64
320_M334_Y1.3180.63
261_Y275_F1.3130.63
175_L307_L1.3080.63
251_R263_P1.3020.62
292_T298_T1.2930.61
338_N342_R1.2910.61
99_Q180_M1.2890.61
132_F160_L1.2860.61
90_D96_F1.2820.60
314_K334_Y1.2820.60
142_H335_A1.2740.60
251_R275_F1.2690.59
271_S275_F1.2680.59
45_D48_D1.2670.59
47_L51_M1.2650.59
84_I89_M1.2640.59
195_T237_T1.2580.58
261_Y284_A1.2580.58
297_T330_A1.2540.58
183_Q314_K1.2530.58
434_A445_I1.2470.57
133_F310_V1.2460.57
82_G89_M1.2450.57
136_E172_P1.2430.57
275_F283_P1.2410.57
136_E141_F1.2400.56
431_I435_C1.2360.56
273_V296_M1.2350.56
292_T296_M1.2310.56
57_Y62_R1.2250.55
145_T166_T1.2100.54
137_K142_H1.2080.54
273_V292_T1.2000.53
219_Q270_L1.1980.53
218_P314_K1.1980.53
181_D185_C1.1970.53
156_N442_I1.1940.52
323_C330_A1.1930.52
46_F51_M1.1900.52
284_A436_F1.1870.52
178_F314_K1.1870.52
313_V325_L1.1710.50
98_R162_S1.1710.50
83_S86_E1.1700.50
277_I290_I1.1680.50
81_F451_Y1.1680.50
198_D286_V1.1660.50
96_F180_M1.1630.49
261_Y285_R1.1570.49
275_F284_A1.1570.49
168_T446_F1.1500.48
136_E162_S1.1460.48
63_P66_K1.1440.48
130_D145_T1.1400.47
86_E90_D1.1390.47
27_A30_E1.1390.47
142_H164_R1.1340.47
187_M247_F1.1340.47
277_I334_Y1.1320.46
310_V322_V1.1320.46
427_K434_A1.1300.46
175_L451_Y1.1290.46
293_V309_K1.1290.46
172_P426_K1.1280.46
148_N307_L1.1260.46
275_F285_R1.1260.46
255_Y271_S1.1230.46
166_T304_R1.1230.46
27_A31_T1.1230.46
190_E334_Y1.1220.46
364_E368_R1.1200.45
249_L274_S1.1200.45
208_P319_W1.1190.45
94_N270_L1.1170.45
435_C438_L1.1160.45
99_Q145_T1.1160.45
243_I267_I1.1140.45
158_N290_I1.1140.45
145_T219_Q1.1130.45
98_R172_P1.1130.45
428_I444_N1.1120.45
159_V449_V1.1120.45
171_C181_D1.1100.44
271_S285_R1.1090.44
271_S274_S1.1050.44
215_L267_I1.1020.44
90_D320_M1.1020.44
83_S190_E1.1010.44
92_R169_L1.1000.43
197_N287_A1.0970.43
150_L315_A1.0950.43
178_F330_A1.0950.43
153_I452_K1.0930.43
290_I293_V1.0910.43
145_T293_V1.0910.43
378_E381_F1.0900.43
94_N293_V1.0880.42
137_K148_N1.0880.42
188_Q334_Y1.0880.42
145_T148_N1.0880.42
75_N178_F1.0870.42
274_S296_M1.0860.42
410_M414_P1.0850.42
249_L270_L1.0840.42
169_L242_C1.0830.42
205_D208_P1.0830.42
116_L175_L1.0820.42
299_Q319_W1.0820.42
99_Q118_L1.0800.42
47_L54_T1.0790.42
134_A190_E1.0760.41
149_K258_I1.0760.41
83_S90_D1.0740.41
219_Q334_Y1.0740.41
217_L307_L1.0740.41
397_G401_K1.0730.41
416_E419_K1.0680.41
299_Q324_L1.0670.40
290_I311_S1.0640.40
409_V414_P1.0610.40
263_P275_F1.0600.40
195_T286_V1.0590.40
179_P185_C1.0550.39
67_G72_V1.0550.39
242_C319_W1.0540.39
256_Y299_Q1.0530.39
72_V85_A1.0510.39
268_V306_S1.0510.39
91_Y291_T1.0490.39
230_Y233_K1.0480.39
253_M256_Y1.0460.39
72_V89_M1.0450.39
267_I286_V1.0440.38
258_I329_S1.0440.38
139_A309_K1.0420.38
397_G403_P1.0390.38
151_L310_V1.0370.38
432_S436_F1.0360.38
247_F261_Y1.0350.38
123_L134_A1.0320.37
318_I432_S1.0310.37
171_C185_C1.0310.37
268_V283_P1.0280.37
220_F288_L1.0270.37
132_F237_T1.0260.37
372_T409_V1.0260.37
200_I246_R1.0250.37
285_R289_G1.0240.37
437_P448_W1.0240.37
130_D160_L1.0240.37
107_A125_S1.0240.37
199_L341_S1.0230.37
180_M192_F1.0220.36
44_S48_D1.0210.36
401_K410_M1.0180.36
99_Q166_T1.0180.36
78_I89_M1.0180.36
351_R454_L1.0170.36
47_L53_R1.0160.36
398_V401_K1.0150.36
72_V155_K1.0150.36
267_I321_A1.0150.36
228_L391_C1.0130.36
139_A299_Q1.0120.36
266_L329_S1.0100.35
384_T409_V1.0100.35
400_P403_P1.0090.35
25_L28_T1.0080.35
95_I124_D1.0080.35
68_P257_L1.0060.35
152_R160_L1.0060.35
284_A289_G1.0030.35
130_D148_N1.0020.35
414_P417_M1.0010.35
29_K32_N1.0010.35
427_K439_A1.0000.35
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  
3rhwA50.71981000.427Contact Map
4cofA50.73281000.427Contact Map
4hfiA50.66591000.494Contact Map
2bg9E10.78021000.512Contact Map
2bg9C10.77371000.517Contact Map
2bg9A20.7781000.52Contact Map
2bg9B10.78661000.521Contact Map
4aq5A20.76941000.534Contact Map
3rqwA100.62281000.537Contact Map
4aq5C10.74571000.538Contact 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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