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nram1

ID: 1516636551 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 550 (482)
Sequences: 519 (258.6)
Seq/Len: 1.077
Nf(neff/√len): 11.8

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: 1.077).

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
450_T461_N3.2801.00
119_K127_L2.4190.99
160_F168_I1.9500.95
219_P378_T1.8600.94
438_L442_A1.8280.93
256_N260_H1.8220.93
414_L418_F1.8180.92
386_V460_A1.8150.92
174_V409_I1.7340.90
228_L300_L1.7080.89
97_L228_L1.6520.87
310_F433_V1.6300.86
463_L467_V1.6230.85
468_V471_S1.6080.85
57_K279_E1.5630.82
145_I386_V1.5300.80
142_E153_V1.5150.80
229_F300_L1.5040.79
103_G295_S1.4920.78
140_T438_L1.4890.78
45_I49_K1.4820.77
428_N431_L1.4780.77
159_A369_L1.4620.76
149_D405_R1.4580.76
79_E83_Q1.4390.75
157_A174_V1.4360.74
59_W68_M1.4260.74
73_L303_M1.4200.73
226_R230_L1.4190.73
257_I446_I1.4020.72
468_V472_I1.3960.71
72_F253_M1.3860.71
508_L512_T1.3770.70
125_C390_F1.3730.69
142_E149_D1.3660.69
505_A512_T1.3630.69
425_S429_D1.3620.69
500_A516_W1.3540.68
97_L296_F1.3530.68
453_P460_A1.3460.67
172_G460_A1.3440.67
198_F484_V1.3380.67
90_F368_L1.3300.66
72_F439_L1.3190.65
38_Y46_P1.3160.65
117_T390_F1.3140.65
88_A239_P1.3100.64
406_S472_I1.3070.64
351_I420_D1.3070.64
109_L125_C1.3060.64
66_F291_A1.3060.64
142_E254_P1.2930.63
90_F160_F1.2900.62
278_R453_P1.2900.62
197_A202_L1.2890.62
139_L474_V1.2840.62
369_L440_P1.2770.61
74_D77_N1.2730.61
293_S297_I1.2710.61
428_N432_N1.2670.60
252_I443_V1.2650.60
492_P496_Y1.2650.60
253_M384_Q1.2640.60
251_I303_M1.2600.60
100_T103_G1.2560.59
53_F59_W1.2520.59
102_L472_I1.2490.59
502_L509_G1.2490.59
213_E229_F1.2460.58
376_T379_G1.2380.58
320_N326_S1.2370.58
306_F364_W1.2350.57
364_W367_G1.2330.57
73_L151_Q1.2290.57
220_E485_V1.2280.57
474_V508_L1.2280.57
237_G240_E1.2250.57
257_I447_L1.2230.56
171_W298_I1.2220.56
101_V386_V1.2190.56
296_F300_L1.2180.56
58_L194_K1.2150.56
464_L508_L1.2100.55
496_Y505_A1.2050.55
105_L197_A1.1970.54
163_L383_G1.1920.53
219_P296_F1.1890.53
250_A386_V1.1890.53
117_T121_L1.1880.53
151_Q432_N1.1840.53
78_I88_A1.1800.52
78_I103_G1.1800.52
57_K61_F1.1790.52
227_G259_L1.1790.52
199_F364_W1.1770.52
223_A226_R1.1760.52
79_E302_V1.1750.52
175_L179_V1.1720.52
186_F503_L1.1700.51
267_R280_A1.1680.51
78_I287_E1.1580.50
64_P67_L1.1570.50
231_P480_N1.1560.50
436_S483_F1.1550.50
407_C417_V1.1470.49
99_A112_R1.1460.49
367_G435_Q1.1410.49
375_S379_G1.1400.49
373_Q383_G1.1400.49
198_F423_D1.1390.48
376_T387_M1.1360.48
521_A525_T1.1340.48
153_V174_V1.1320.48
88_A159_A1.1270.47
114_G137_L1.1270.47
82_L357_G1.1260.47
509_G522_H1.1260.47
370_A376_T1.1210.47
274_R458_E1.1190.47
103_G367_G1.1180.46
508_L520_L1.1170.46
172_G179_V1.1160.46
491_L517_T1.1150.46
38_Y45_I1.1150.46
87_V468_V1.1140.46
64_P68_M1.1140.46
68_M245_V1.1120.46
116_V144_A1.1070.45
193_R375_S1.1070.45
205_I225_L1.1050.45
366_I409_I1.1010.45
73_L78_I1.1000.45
307_G438_L1.0980.45
125_C440_P1.0980.45
422_R512_T1.0970.44
213_E224_L1.0960.44
241_L469_T1.0960.44
109_L476_V1.0960.44
222_G311_Y1.0950.44
55_L64_P1.0920.44
134_R138_W1.0920.44
192_L198_F1.0900.44
432_N479_I1.0880.44
75_P405_R1.0870.44
151_Q367_G1.0870.44
257_I439_L1.0870.44
164_S412_T1.0840.43
103_G435_Q1.0830.43
99_A454_T1.0830.43
65_G71_A1.0820.43
78_I251_I1.0820.43
124_V257_I1.0820.43
75_P142_E1.0800.43
151_Q180_D1.0790.43
178_I186_F1.0790.43
255_H439_L1.0780.43
191_G256_N1.0780.43
86_A170_L1.0770.43
420_D453_P1.0760.43
213_E360_A1.0740.42
100_T295_S1.0740.42
493_H506_A1.0740.42
170_L230_L1.0720.42
149_D404_T1.0700.42
167_R481_L1.0690.42
380_T384_Q1.0690.42
250_A253_M1.0680.42
391_L408_A1.0680.42
103_G306_F1.0660.42
90_F308_Q1.0660.42
289_T302_V1.0630.41
194_K197_A1.0610.41
390_F440_P1.0610.41
469_T512_T1.0610.41
450_T456_M1.0570.41
522_H525_T1.0570.41
203_I374_S1.0570.41
392_R488_L1.0560.41
149_D254_P1.0540.40
203_I260_H1.0530.40
57_K296_F1.0520.40
67_L457_Q1.0510.40
491_L496_Y1.0490.40
136_V467_V1.0490.40
206_M302_V1.0470.40
88_A364_W1.0410.39
364_W435_Q1.0410.39
65_G69_S1.0400.39
521_A524_A1.0400.39
106_C258_Y1.0400.39
139_L505_A1.0400.39
74_D249_G1.0390.39
154_I477_C1.0380.39
64_P267_R1.0360.39
191_G376_T1.0360.39
267_R283_Y1.0360.39
152_E408_A1.0340.39
410_L463_L1.0330.39
256_N261_S1.0330.39
198_F360_A1.0320.39
75_P254_P1.0320.39
245_V349_G1.0310.38
355_L371_A1.0300.38
410_L494_P1.0290.38
83_Q87_V1.0280.38
117_T125_C1.0280.38
141_I150_M1.0280.38
124_V448_T1.0250.38
149_D383_G1.0250.38
364_W432_N1.0230.38
88_A103_G1.0230.38
58_L70_I1.0220.38
143_L297_I1.0210.38
255_H260_H1.0210.38
345_I519_C1.0210.38
103_G364_W1.0190.37
320_N324_N1.0180.37
214_Y221_Q1.0150.37
148_S435_Q1.0150.37
374_S442_A1.0140.37
120_D262_A1.0140.37
138_W379_G1.0120.37
413_V509_G1.0120.37
73_L144_A1.0110.37
151_Q364_W1.0090.36
396_S399_A1.0070.36
222_G466_K1.0060.36
72_F75_P1.0060.36
126_H503_L1.0050.36
101_V515_V1.0050.36
139_L207_A1.0040.36
396_S500_A1.0040.36
506_A514_L1.0040.36
72_F84_A1.0040.36
71_A171_W1.0020.36
44_P48_T1.0020.36
67_L302_V1.0010.36
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  
4wgvA20.70181000.511Contact Map
3dh4A40.897.90.956Contact Map
2jlnA10.783697.60.959Contact Map
3giaA10.741893.70.971Contact Map
4djkA20.732792.40.972Contact Map
2xq2A10.891.80.972Contact Map
3l1lA10.709190.20.973Contact Map
4xp4A1053.60.981Contact Map
4us3A10.6832.30.983Contact Map
4lz6A10.730926.60.984Contact 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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