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OPENSEQ.org

125-352_p2_x1012

ID: 1492167998 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 464 (463)
Sequences: 866 (767.9)
Seq/Len: 1.870
Nf(neff/√len): 35.7

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: 1.870).

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
5_E37_R3.0951.00
5_E9_E2.6341.00
44_L71_V2.4961.00
444_Q451_K2.4541.00
231_G256_N2.3111.00
421_G424_F2.1340.99
339_K344_E1.9630.99
418_S421_G1.9450.98
192_L214_L1.9170.98
138_N147_A1.8960.98
166_L196_G1.8720.98
77_P88_P1.8470.98
269_K335_P1.7660.97
191_N215_E1.7490.96
292_Q295_A1.7470.96
94_Q119_N1.7220.96
409_L412_Q1.7180.96
46_L69_E1.6950.96
146_V175_I1.6890.95
273_K334_A1.6820.95
430_Q435_T1.6770.95
258_L393_T1.6640.95
112_G115_P1.6590.95
270_L336_L1.6540.95
366_L369_E1.6310.94
191_N197_S1.6270.94
283_H287_Q1.6270.94
146_V446_T1.6140.94
407_K410_A1.6140.94
109_M112_G1.6130.94
165_S197_S1.5940.93
417_A421_G1.5800.93
205_E208_G1.5590.92
415_E418_S1.5570.92
3_K6_T1.5380.91
446_T451_K1.5330.91
255_L258_L1.5070.90
418_S424_F1.4790.89
44_L47_L1.4740.89
136_P150_G1.4740.89
278_D327_G1.4710.89
415_E421_G1.4700.89
38_G42_S1.4640.89
130_S155_L1.4590.88
275_G330_V1.4530.88
409_L416_G1.4480.88
292_Q296_L1.4400.87
29_E32_Y1.4370.87
380_K437_S1.4370.87
430_Q433_T1.4280.87
267_S339_K1.4230.87
187_L315_E1.4220.87
149_S171_Q1.4130.86
438_L445_I1.4130.86
129_S156_N1.3980.85
168_G171_Q1.3970.85
421_G427_T1.3910.85
99_N104_K1.3840.85
3_K7_H1.3730.84
35_Y73_H1.3710.84
453_P456_D1.3690.84
34_N45_Q1.3640.83
266_G338_W1.3630.83
421_G425_R1.3440.82
232_M235_S1.3410.82
285_F333_I1.3380.82
2_K37_R1.3370.82
412_Q415_E1.3340.81
345_S387_M1.3330.81
77_P329_P1.3320.81
153_F168_G1.3160.80
37_R73_H1.3140.80
278_D281_A1.3130.80
416_G421_G1.3120.80
95_T118_I1.3060.80
67_F99_N1.3010.79
295_A300_P1.2990.79
90_M124_Y1.2990.79
107_F110_A1.2940.79
216_K230_E1.2860.78
149_S172_S1.2850.78
225_E228_L1.2830.78
7_H10_D1.2800.78
117_E133_S1.2770.77
385_V429_L1.2760.77
71_V91_A1.2580.76
84_L338_W1.2560.76
309_Y313_V1.2470.75
231_G234_I1.2400.74
333_I336_L1.2350.74
75_P124_Y1.2340.74
155_L166_L1.2330.74
250_Q273_K1.2320.74
167_S195_D1.2310.74
277_I286_S1.2200.73
402_Q405_Q1.2170.72
141_Q144_E1.2150.72
50_P53_G1.2080.72
101_E104_K1.2070.72
219_I429_L1.2040.71
313_V317_F1.2020.71
297_L300_P1.2020.71
246_T276_Q1.2000.71
414_V421_G1.1990.71
107_F111_K1.1980.71
393_T397_K1.1970.71
20_K23_A1.1970.71
6_T430_Q1.1950.70
347_L379_A1.1940.70
30_V33_Q1.1910.70
18_Q22_T1.1910.70
104_K108_D1.1910.70
114_T135_K1.1900.70
369_E372_R1.1880.70
384_P387_M1.1880.70
18_Q21_L1.1840.69
424_F427_T1.1830.69
365_T369_E1.1820.69
289_Y293_T1.1810.69
4_I71_V1.1800.69
37_R120_S1.1800.69
93_I97_L1.1780.69
404_D414_V1.1750.69
188_T218_T1.1750.69
120_S130_S1.1740.68
447_L459_G1.1730.68
86_L153_F1.1690.68
227_A232_M1.1680.68
230_E233_E1.1670.68
411_K415_E1.1620.67
193_K213_S1.1600.67
191_N219_I1.1600.67
35_Y42_S1.1590.67
363_P366_L1.1580.67
28_L33_Q1.1530.66
445_I457_F1.1480.66
23_A27_N1.1460.66
458_V462_A1.1460.66
110_A137_L1.1450.66
407_K412_Q1.1450.66
317_F320_A1.1420.65
306_P310_Q1.1370.65
370_V373_S1.1350.65
301_E311_E1.1350.65
166_L187_L1.1290.64
342_Q390_E1.1270.64
95_T120_S1.1260.64
231_G236_G1.1250.64
101_E105_P1.1240.64
46_L50_P1.1240.64
416_G424_F1.1230.63
107_F356_P1.1220.63
184_K187_L1.1170.63
405_Q408_K1.1160.63
444_Q453_P1.1140.63
36_H47_L1.1140.63
364_Q368_Q1.1120.62
120_S128_S1.1120.62
414_V419_A1.1070.62
377_L438_L1.1050.62
287_Q291_A1.1040.62
43_Q70_S1.1030.61
52_A55_E1.1030.61
90_M349_L1.1010.61
72_D79_A1.0980.61
14_Q31_S1.0980.61
76_F463_M1.0980.61
106_L326_K1.0940.60
140_E145_K1.0890.60
21_L24_P1.0880.60
407_K411_K1.0870.60
29_E34_N1.0850.60
223_G230_E1.0830.59
148_F172_S1.0780.59
406_A412_Q1.0770.59
236_G240_L1.0750.58
37_R453_P1.0740.58
31_S34_N1.0720.58
135_K277_I1.0710.58
222_E226_L1.0700.58
223_G226_L1.0690.58
288_Q291_A1.0680.58
164_I173_G1.0670.58
445_I452_M1.0660.58
369_E373_S1.0650.57
272_L333_I1.0630.57
324_M327_G1.0620.57
126_G171_Q1.0600.57
268_G338_W1.0590.57
220_S234_I1.0580.57
307_E316_A1.0570.57
277_I282_W1.0570.57
106_L109_M1.0540.56
117_E132_I1.0530.56
330_V443_G1.0530.56
118_I130_S1.0530.56
232_M236_G1.0530.56
164_I229_L1.0480.56
405_Q416_G1.0450.55
201_A205_E1.0450.55
59_I62_G1.0440.55
332_T377_L1.0420.55
32_Y35_Y1.0420.55
190_N194_T1.0410.55
378_D384_P1.0400.55
148_F329_P1.0400.55
416_G420_M1.0400.55
133_S152_E1.0400.55
75_P329_P1.0380.54
110_A190_N1.0380.54
71_V336_L1.0370.54
365_T368_Q1.0360.54
35_Y38_G1.0360.54
311_E314_T1.0350.54
301_E304_N1.0330.54
143_D258_L1.0330.54
33_Q36_H1.0290.53
80_Q89_S1.0290.53
203_F279_G1.0290.53
458_V461_F1.0250.53
38_G95_T1.0240.53
37_R71_V1.0240.53
55_E59_I1.0220.53
111_K138_N1.0210.53
403_E407_K1.0200.53
294_Q297_L1.0200.53
40_F75_P1.0180.52
138_N229_L1.0180.52
164_I331_I1.0160.52
64_S182_N1.0150.52
45_Q68_N1.0150.52
83_K256_N1.0120.52
362_A372_R1.0100.51
84_L116_F1.0070.51
32_Y44_L1.0070.51
340_N440_Y1.0060.51
108_D112_G1.0060.51
198_S201_A1.0030.51
192_L254_S1.0020.51
269_K337_S1.0020.51
313_V318_F1.0010.50
409_L413_Q1.0010.50
40_F46_L1.0000.50
164_I175_I1.0000.50
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  
1gnyA10.325418.40.968Contact Map
4rb5I10.0948160.969Contact Map
3j7aM10.094812.70.97Contact Map
4tp8I10.094812.50.97Contact Map
2jwkA20.073312.30.97Contact Map
3j60Q10.066811.80.97Contact Map
3bbnI10.092790.972Contact Map
3j20K10.09780.973Contact Map
2pfuA10.10997.80.973Contact Map
4bpeI10.10346.50.974Contact 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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