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prova1

ID: 1505233249 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 429 (390)
Sequences: 2478 (1581.6)
Seq/Len: 6.354
Nf(neff/√len): 80.1

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: 6.354).

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
118_R122_N4.4741.00
74_E127_K3.7711.00
279_Q410_T3.5251.00
74_E123_Y3.4601.00
131_L164_V3.4211.00
315_D385_T3.3951.00
296_M311_L3.3741.00
70_M123_Y3.1031.00
408_N411_G2.9361.00
316_V414_L2.9301.00
66_E115_H2.8991.00
166_L225_H2.7061.00
407_I411_G2.6831.00
348_A416_Q2.6251.00
265_P292_A2.5551.00
153_D157_Q2.5351.00
244_D356_R2.5261.00
52_C94_C2.5081.00
101_D105_R2.4851.00
121_A131_L2.4801.00
319_I388_L2.4631.00
42_M317_I2.4601.00
282_T412_T2.4221.00
289_I352_A2.4171.00
41_T225_H2.3691.00
157_Q161_D2.3641.00
84_A314_K2.3231.00
105_R154_I2.3201.00
151_Y154_I2.2181.00
90_C295_F2.1981.00
91_I131_L2.1741.00
282_T354_I2.1631.00
81_W296_M2.1581.00
315_D391_K2.1181.00
34_N224_N2.1051.00
305_P309_A2.0891.00
385_T391_K2.0711.00
258_G261_G2.0621.00
278_N411_G2.0551.00
153_D193_R2.0461.00
125_H165_D2.0231.00
199_V225_H1.9911.00
277_W306_Q1.9751.00
291_A342_R1.9631.00
275_L280_Q1.9621.00
87_E130_K1.9451.00
285_A316_V1.9451.00
188_S192_N1.9221.00
158_T161_D1.9121.00
124_V131_L1.8951.00
97_A110_P1.8911.00
115_H119_Q1.8901.00
74_E78_S1.8461.00
67_K71_E1.8391.00
385_T393_K1.8191.00
285_A389_P1.7821.00
281_V411_G1.7531.00
388_L416_Q1.7381.00
234_D280_Q1.7371.00
124_V127_K1.7251.00
121_A124_V1.7231.00
267_M297_S1.7221.00
278_N408_N1.7011.00
280_Q307_A1.6781.00
315_D393_K1.6601.00
185_K189_L1.6441.00
76_M89_L1.6421.00
243_L286_L1.6111.00
285_A414_L1.6061.00
169_F187_M1.6041.00
73_A124_V1.6021.00
121_A164_V1.5931.00
286_L354_I1.5780.99
123_Y127_K1.5750.99
387_L390_V1.5660.99
66_E70_M1.5660.99
84_A312_Q1.5440.99
109_D112_R1.5360.99
123_Y126_S1.5330.99
288_A316_V1.5030.99
68_L72_M1.4990.99
77_V129_L1.4750.99
352_A414_L1.4720.99
154_I158_T1.4610.99
32_L35_G1.4540.99
73_A129_L1.4510.99
45_L90_C1.4490.99
269_V272_N1.4470.99
50_F301_R1.4460.99
81_W312_Q1.4400.99
33_D38_R1.4280.99
158_T162_W1.4270.99
105_R161_D1.4240.99
115_H120_L1.4200.99
319_I414_L1.4160.99
366_T402_R1.4070.99
298_N303_I1.3950.98
156_A191_L1.3930.98
366_T404_R1.3910.98
226_W261_G1.3870.98
71_E301_R1.3740.98
167_L187_M1.3690.98
50_F72_M1.3580.98
135_A159_F1.3460.98
326_K343_P1.3370.98
73_A127_K1.3360.98
278_N281_V1.3360.98
239_I275_L1.3350.98
117_I164_V1.3320.98
72_M301_R1.3320.98
407_I412_T1.3320.98
48_E267_M1.3020.97
316_V388_L1.2910.97
72_M300_L1.2860.97
364_S404_R1.2850.97
82_K129_L1.2790.97
65_S68_L1.2760.97
96_M135_A1.2740.97
117_I131_L1.2640.96
385_T390_V1.2620.96
82_K87_E1.2620.96
70_M119_Q1.2620.96
75_L300_L1.2610.96
160_A198_I1.2520.96
130_K165_D1.2380.96
156_A187_M1.2380.96
77_V127_K1.2290.96
160_A196_R1.2280.96
37_A262_W1.2170.95
46_H69_F1.2080.95
243_L354_I1.2050.95
365_Y407_I1.2000.95
167_L198_I1.1900.95
202_C205_P1.1850.94
304_S307_A1.1830.94
201_S225_H1.1770.94
220_R261_G1.1750.94
338_E356_R1.1620.94
227_R231_D1.1590.94
234_D274_G1.1580.94
353_M405_S1.1390.93
41_T199_V1.1300.92
191_L198_I1.1250.92
81_W308_K1.1230.92
47_W93_D1.1200.92
368_A371_S1.1160.92
117_I121_A1.1060.91
235_S238_S1.1050.91
209_W219_I1.1040.91
35_G38_R1.1020.91
70_M115_H1.0960.91
90_C166_L1.0870.90
37_A199_V1.0850.90
353_M367_I1.0850.90
383_F393_K1.0830.90
188_S222_Y1.0810.90
336_N357_Q1.0810.90
76_M129_L1.0780.90
303_I307_A1.0750.90
303_I308_K1.0750.90
152_Y169_F1.0710.89
122_N126_S1.0670.89
136_D184_Y1.0660.89
157_Q194_T1.0620.89
384_I417_L1.0580.89
259_P262_W1.0550.89
77_V82_K1.0530.88
75_L301_R1.0490.88
117_I162_W1.0480.88
36_L39_T1.0450.88
282_T411_G1.0360.87
315_D390_V1.0350.87
364_S406_H1.0300.87
166_L295_F1.0260.87
352_A412_T1.0260.87
369_V402_R1.0230.86
135_A169_F1.0220.86
23_S26_I1.0080.85
156_A167_L1.0080.85
142_C172_C1.0010.85
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  
3hg3A20.91841000.194Contact Map
3lrkA10.85781000.223Contact Map
3a5vA10.85781000.235Contact Map
1sznA10.85081000.235Contact Map
4do4A20.91381000.244Contact Map
4nzjA10.90681000.25Contact Map
3a21A20.86711000.272Contact Map
3cc1A20.85081000.277Contact Map
1uasA10.83921000.29Contact Map
4nzfA80.85781000.31Contact 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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