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OPENSEQ.org

VGAT

ID: 1485219343 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 525 (415)
Sequences: 641 (422.9)
Seq/Len: 1.545
Nf(neff/√len): 20.8

HHblits Results: (2016_02)
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: 1.545).

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
279_I283_A3.2191.00
146_Y360_L2.1540.99
442_F445_L1.9890.98
147_L151_L1.9200.97
246_I495_A1.9110.97
322_F447_A1.8980.97
377_S381_V1.8840.97
331_Q478_L1.8620.97
353_L357_V1.7880.96
162_T496_I1.7710.95
455_L518_A1.6400.92
283_A287_S1.6090.91
335_E338_C1.5620.89
194_C479_R1.5540.89
161_Y330_M1.5380.88
441_V456_L1.5360.88
459_L515_L1.5320.88
275_F279_I1.5320.88
146_Y354_F1.5250.88
452_H455_L1.5030.87
151_L154_F1.4770.86
438_A442_F1.4730.85
250_V391_L1.4650.85
209_A464_T1.4540.84
357_V456_L1.4530.84
311_G461_G1.4330.83
232_S384_L1.4240.83
458_G511_S1.4200.82
241_K448_I1.4160.82
144_G310_I1.4100.82
513_E516_I1.3900.81
259_N429_K1.3870.80
190_A202_G1.3800.80
215_V442_F1.3610.79
500_G507_G1.3570.78
136_G316_S1.3460.77
238_V246_I1.3330.77
358_A388_A1.3250.76
208_V212_I1.3230.76
274_H471_L1.3100.75
486_L490_V1.3030.74
156_A165_I1.3030.74
501_G505_V1.3020.74
335_E400_A1.3010.74
157_V425_D1.2930.73
318_T323_L1.2930.73
374_L382_V1.2880.73
213_E468_L1.2830.73
393_S396_L1.2750.72
282_I460_T1.2620.71
156_A355_A1.2620.71
359_Y363_A1.2610.71
313_I453_F1.2600.71
252_L441_V1.2580.70
311_G436_R1.2570.70
210_Q325_S1.2500.70
161_Y493_D1.2430.69
460_T491_F1.2410.69
164_K459_L1.2400.69
214_L317_Y1.2400.69
216_M503_C1.2280.68
117_T165_I1.2240.67
140_A153_I1.2220.67
331_Q491_F1.2210.67
239_S242_S1.2140.67
268_L272_L1.2110.66
463_L503_C1.2020.65
495_A499_I1.2020.65
138_P475_L1.1990.65
252_L405_L1.1990.65
213_E465_G1.1950.65
356_L441_V1.1920.64
252_L440_V1.1890.64
467_G504_S1.1860.64
330_M336_F1.1820.63
212_I218_C1.1800.63
371_T382_V1.1800.63
368_E454_A1.1760.63
474_S497_F1.1750.63
294_W365_E1.1710.62
263_V395_P1.1670.62
295_E365_E1.1640.62
400_A406_E1.1640.62
405_L435_L1.1630.62
163_G323_L1.1620.62
405_L520_R1.1600.61
131_G221_Y1.1590.61
229_M323_L1.1560.61
356_L360_L1.1550.61
155_A466_A1.1520.61
331_Q461_G1.1490.60
219_I459_L1.1480.60
345_I349_V1.1480.60
214_L453_F1.1430.60
276_V280_L1.1410.59
461_G473_P1.1400.59
453_F457_M1.1380.59
290_R357_V1.1360.59
388_A391_L1.1340.59
155_A279_I1.1260.58
144_G149_L1.1240.58
284_Y374_L1.1230.58
293_A438_A1.1220.58
163_G340_M1.1200.57
340_M398_F1.1190.57
197_R205_V1.1190.57
168_A212_I1.1190.57
325_S470_F1.1180.57
204_R208_V1.1170.57
254_C463_L1.1160.57
370_I478_L1.1160.57
152_I486_L1.1140.57
132_M355_A1.1100.56
387_V409_L1.1080.56
441_V445_L1.1020.55
339_M397_P1.1010.55
324_P393_S1.0990.55
417_F421_C1.0990.55
310_I442_F1.0980.55
186_Y473_P1.0970.55
185_S312_I1.0950.55
138_P370_I1.0940.55
148_G153_I1.0910.54
188_A515_L1.0910.54
258_K340_M1.0910.54
150_F472_L1.0900.54
453_F477_H1.0890.54
353_L435_L1.0880.54
430_S434_T1.0870.54
209_A217_T1.0850.54
139_Y143_H1.0850.54
165_I477_H1.0850.54
239_S413_G1.0830.53
187_V207_N1.0830.53
244_S315_F1.0830.53
269_L463_L1.0830.53
320_Q504_S1.0820.53
316_S469_C1.0790.53
505_V513_E1.0780.53
310_I463_L1.0770.53
339_M461_G1.0760.53
394_Y443_T1.0750.53
194_C474_S1.0740.53
217_T465_G1.0710.52
120_E223_V1.0680.52
140_A249_A1.0680.52
488_H495_A1.0670.52
368_E453_F1.0650.52
307_P371_T1.0650.52
246_I396_L1.0640.52
161_Y220_L1.0630.51
212_I349_V1.0620.51
242_S245_I1.0590.51
405_L501_G1.0570.51
316_S457_M1.0570.51
517_E521_T1.0560.51
310_I503_C1.0540.50
153_I352_G1.0540.50
253_P505_V1.0540.50
151_L157_V1.0520.50
441_V502_I1.0510.50
148_G246_I1.0510.50
222_V248_T1.0510.50
442_F496_I1.0500.50
190_A234_P1.0490.50
161_Y517_E1.0480.50
138_P193_C1.0480.50
438_A498_V1.0480.50
170_L324_P1.0480.50
228_L465_G1.0470.50
308_I458_G1.0470.50
280_L385_F1.0470.50
157_V197_R1.0470.50
136_G223_V1.0440.49
441_V446_M1.0430.49
307_P326_L1.0420.49
127_N320_Q1.0420.49
331_Q447_A1.0390.49
438_A441_V1.0380.49
246_I308_I1.0370.49
131_G473_P1.0350.48
441_V499_I1.0330.48
280_L512_L1.0330.48
218_C398_F1.0320.48
147_L153_I1.0300.48
309_S313_I1.0280.48
312_I468_L1.0280.48
129_I465_G1.0270.48
207_N404_V1.0250.47
141_I152_I1.0240.47
152_I384_L1.0230.47
376_G437_C1.0210.47
459_L508_F1.0190.47
267_S280_L1.0180.47
168_A339_M1.0170.47
162_T312_I1.0170.47
248_T444_L1.0170.47
210_Q504_S1.0170.47
465_G500_G1.0130.46
139_Y445_L1.0100.46
281_V371_T1.0100.46
249_A441_V1.0090.46
262_A266_F1.0080.46
316_S351_K1.0080.46
162_T439_L1.0040.45
147_L495_A1.0040.45
250_V384_L1.0030.45
405_L411_Q1.0030.45
121_A326_L1.0020.45
129_I318_T1.0010.45
401_A406_E1.0010.45
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  
3l1lA10.729599.80.843Contact Map
4djkA20.716299.80.857Contact Map
3giaA10.744899.80.858Contact Map
3dh4A40.729598.70.918Contact Map
2xq2A10.765798.10.932Contact Map
2jlnA10.7697.60.939Contact Map
4wgvA20.66195.60.952Contact Map
4xp4A1045.40.973Contact Map
3ukmA40.365743.10.974Contact Map
4o6yA20.390539.30.974Contact 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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