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OPENSEQ.org

QEGE_VIPMR

ID: 1497551972 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 672 (641)
Sequences: 1164 (1024.8)
Seq/Len: 1.816
Nf(neff/√len): 40.5

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: 1.816).

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
332_A335_E3.5101.00
402_S429_A2.9361.00
385_T428_F2.9281.00
336_V387_A2.9031.00
369_M417_A2.8671.00
293_L339_I2.7941.00
362_Q373_S2.7531.00
344_E395_R2.7461.00
268_T356_H2.7381.00
116_H142_S2.7241.00
185_L416_G2.7241.00
333_E390_E2.6781.00
265_Y353_G2.6141.00
389_H432_Q2.5361.00
397_N400_F2.4691.00
448_W476_G2.4321.00
385_T425_V2.4141.00
381_K418_Y2.3991.00
355_I480_M2.3621.00
353_G399_L2.3571.00
359_G453_M2.3561.00
221_E238_R2.3101.00
278_V403_S2.3041.00
386_I424_F2.2080.99
336_V391_A2.2040.99
426_E442_C2.1900.99
233_Y238_R2.1790.99
340_I391_A2.1650.99
363_E415_V2.1550.99
351_L392_A2.1270.99
336_V339_I2.1170.99
601_W621_G2.0720.99
289_H322_K2.0710.99
231_A238_R2.0380.99
444_S490_L2.0230.99
418_Y422_N2.0170.99
221_E231_A2.0120.99
429_A440_P2.0020.99
400_F432_Q1.9780.99
273_G451_I1.9750.99
381_K422_N1.9550.98
363_E417_A1.9470.98
330_I384_G1.9420.98
273_G452_G1.9180.98
281_Q481_L1.9030.98
94_P148_K1.9010.98
163_S166_A1.8700.98
274_I278_V1.8680.98
116_H139_G1.8650.98
649_H658_W1.8630.98
354_I392_A1.8580.98
267_I279_S1.8570.98
471_I476_G1.8030.97
386_I389_H1.7970.97
363_E414_T1.7850.97
613_G653_G1.7820.97
279_S292_L1.7770.97
389_H438_V1.7740.97
202_D234_R1.7690.97
50_F118_W1.7660.96
180_A427_Q1.7620.96
343_H351_L1.7610.96
358_A418_Y1.7500.96
403_S445_F1.7490.96
295_R381_K1.7460.96
361_I417_A1.7320.96
295_R418_Y1.7280.96
418_Y453_M1.7250.96
147_T189_V1.7010.95
400_F440_P1.6870.95
330_I336_V1.6680.95
93_R96_D1.6660.95
389_H431_Y1.6560.94
52_D55_G1.6470.94
617_F621_G1.6420.94
280_E311_L1.6370.94
50_F73_V1.6320.94
377_M415_V1.6320.94
387_A391_A1.6300.94
597_L633_V1.6160.93
589_P660_D1.6100.93
374_L417_A1.6080.93
645_V649_H1.5890.93
228_C242_F1.5880.93
377_M417_A1.5880.93
266_V351_L1.5720.92
398_V403_S1.5700.92
143_A161_F1.5670.92
382_V385_T1.5490.91
201_L218_M1.5460.91
261_S287_Q1.5420.91
445_F448_W1.5350.91
362_Q376_D1.5350.91
426_E444_S1.5220.90
393_S436_S1.5180.90
158_A199_Q1.5160.90
356_H381_K1.5020.90
144_L148_K1.5000.90
289_H324_L1.4930.89
272_G359_G1.4780.89
279_S290_L1.4740.89
407_R415_V1.4730.88
268_T422_N1.4670.88
272_G295_R1.4660.88
228_C240_I1.4600.88
402_S440_P1.4590.88
272_G381_K1.4570.88
361_I415_V1.4520.88
392_A395_R1.4410.87
293_L336_V1.4390.87
283_L319_H1.4380.87
202_D232_A1.4370.87
272_G418_Y1.4350.87
389_H436_S1.4340.87
96_D99_Q1.4320.87
316_A321_G1.4310.86
398_V405_S1.4280.86
259_F282_L1.4150.86
185_L366_L1.4130.86
333_E391_A1.4110.85
644_A649_H1.4040.85
90_H96_D1.4030.85
432_Q438_V1.4030.85
616_F621_G1.4020.85
116_H119_N1.3880.84
389_H440_P1.3760.83
295_R329_D1.3750.83
285_S481_L1.3700.83
326_E339_I1.3660.83
294_G325_Y1.3590.82
340_I344_E1.3520.82
96_D100_L1.3510.82
295_R358_A1.3510.82
265_Y399_L1.3390.81
358_A381_K1.3370.81
340_I392_A1.3340.81
432_Q440_P1.3190.80
365_L368_D1.3040.79
480_M484_L1.3010.78
272_G358_A1.2990.78
359_G421_A1.2990.78
64_A67_E1.2990.78
616_F647_F1.2970.78
274_I403_S1.2890.77
364_E373_S1.2890.77
269_G418_Y1.2840.77
269_G295_R1.2820.77
274_I448_W1.2790.77
364_E368_D1.2790.77
161_F164_T1.2760.76
191_H229_H1.2720.76
162_V165_H1.2660.76
405_S408_T1.2560.75
389_H400_F1.2560.75
621_G625_K1.2550.75
594_E656_A1.2540.75
351_L395_R1.2510.74
397_N403_S1.2470.74
34_A240_I1.2430.74
392_A432_Q1.2400.74
278_V355_I1.2390.73
593_T660_D1.2380.73
310_S313_E1.2370.73
362_Q369_M1.2370.73
99_Q103_T1.2370.73
219_M222_L1.2330.73
431_Y436_S1.2300.73
389_H428_F1.2300.73
377_M380_A1.2270.72
450_E453_M1.2240.72
611_S614_D1.2240.72
363_E410_K1.2230.72
52_D57_A1.2220.72
373_S417_A1.2210.72
335_E338_A1.2200.72
73_V100_L1.2140.71
644_A647_F1.2130.71
337_E391_A1.2100.71
260_E398_V1.2080.71
272_G448_W1.2040.70
283_L290_L1.2010.70
177_V181_T1.2010.70
295_R359_G1.1990.70
371_S375_N1.1960.70
260_E352_D1.1930.69
497_R500_K1.1930.69
615_H621_G1.1850.69
621_G626_A1.1840.69
626_A630_L1.1780.68
262_S288_A1.1780.68
163_S202_D1.1780.68
370_T373_S1.1760.68
115_I162_V1.1760.68
373_S392_A1.1740.68
364_E377_M1.1710.67
397_N405_S1.1710.67
472_S476_G1.1670.67
263_G352_D1.1660.67
260_E265_Y1.1640.67
49_I61_K1.1620.66
622_H625_K1.1600.66
161_F165_H1.1560.66
448_W453_M1.1550.66
333_E337_E1.1530.66
278_V480_M1.1530.66
100_L104_L1.1510.65
403_S408_T1.1490.65
151_S193_W1.1490.65
160_T163_S1.1470.65
403_S406_A1.1460.65
273_G453_M1.1430.65
292_L323_V1.1420.64
328_A336_V1.1390.64
634_R640_D1.1390.64
586_N611_S1.1380.64
614_D621_G1.1370.64
91_P118_W1.1340.64
163_S167_M1.1330.64
634_R639_F1.1320.63
338_A342_R1.1300.63
422_N453_M1.1290.63
328_A339_I1.1290.63
97_Y101_F1.1230.63
284_T319_H1.1230.63
79_F96_D1.1220.62
64_A68_Q1.1220.62
586_N589_P1.1210.62
596_L636_K1.1170.62
352_D398_V1.1160.62
450_E454_S1.1140.62
47_V113_H1.1110.61
180_A192_E1.1090.61
329_D381_K1.1070.61
140_S374_L1.1060.61
369_M392_A1.0980.60
589_P593_T1.0980.60
269_G381_K1.0940.60
369_M373_S1.0900.59
595_K598_A1.0870.59
27_Y31_W1.0860.59
495_L500_K1.0850.59
265_Y398_V1.0840.59
408_T411_G1.0830.58
364_E417_A1.0820.58
283_L288_A1.0810.58
89_I96_D1.0790.58
408_T444_S1.0790.58
335_E339_I1.0780.58
365_L417_A1.0770.58
159_I163_S1.0770.58
336_V379_E1.0740.57
593_T605_L1.0730.57
389_H417_A1.0720.57
180_A202_D1.0720.57
397_N401_L1.0720.57
462_M466_R1.0700.57
313_E317_K1.0700.57
33_P237_V1.0690.57
642_P645_V1.0690.57
364_E415_V1.0690.57
369_M389_H1.0670.57
183_A200_C1.0650.56
22_L25_W1.0620.56
331_T379_E1.0590.56
89_I97_Y1.0570.56
273_G450_E1.0570.56
283_L321_G1.0550.55
369_M380_A1.0530.55
136_Q139_G1.0530.55
186_M197_K1.0520.55
614_D618_L1.0520.55
291_V326_E1.0510.55
398_V401_L1.0510.55
603_E632_A1.0500.55
50_F116_H1.0500.55
626_A648_E1.0500.55
117_L162_V1.0490.55
186_M200_C1.0480.55
410_K413_M1.0460.54
633_V644_A1.0440.54
361_I377_M1.0420.54
188_A191_H1.0420.54
97_Y100_L1.0400.54
136_Q181_T1.0380.54
647_F650_T1.0350.53
389_H392_A1.0340.53
645_V658_W1.0320.53
51_A57_A1.0320.53
191_H412_G1.0280.52
301_L304_D1.0270.52
600_I632_A1.0260.52
360_I415_V1.0250.52
266_V340_I1.0240.52
622_H644_A1.0230.52
356_H422_N1.0190.52
363_E377_M1.0180.51
79_F103_T1.0160.51
268_T358_A1.0110.51
361_I392_A1.0080.50
79_F87_F1.0080.50
594_E601_W1.0070.50
364_E392_A1.0050.50
410_K417_A1.0040.50
293_L328_A1.0020.50
363_E373_S1.0000.49
270_G381_K1.0000.49
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  
3qp9A40.69491000.502Contact Map
3mjeA20.68751000.526Contact Map
4impA40.71881000.528Contact Map
2fr1A10.66821000.534Contact Map
2z5lA10.66221000.538Contact Map
4l4xA10.70541000.551Contact Map
4hxyA20.62951000.551Contact Map
4j1qA10.60421000.605Contact Map
2vz8A20.66071000.628Contact Map
3slkA20.62951000.646Contact 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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