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hoip-jackhmmer

ID: 1506434809 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 374 (350)
Sequences: 684 (485.1)
Seq/Len: 1.954
Nf(neff/√len): 25.9

Jackhmmer Results: (2016_04)
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: 1.954).

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
287_A290_K2.4831.00
99_L131_K2.3701.00
325_V329_E1.9140.98
309_V313_N1.8850.98
191_H198_Q1.8290.98
230_R237_R1.8200.98
286_E290_K1.8010.97
327_E331_A1.7990.97
200_C203_C1.7460.97
292_T295_G1.6970.96
192_C195_C1.6750.96
310_S313_N1.6580.95
290_K294_A1.6530.95
104_C109_I1.6530.95
287_A294_A1.6410.95
172_D179_S1.6220.94
289_G293_P1.5960.94
286_E289_G1.5920.94
289_G294_A1.5450.92
313_N324_E1.5420.92
289_G292_T1.5400.92
326_E329_E1.5320.92
290_K293_P1.5300.92
195_C203_C1.5260.92
326_E330_T1.5180.91
288_C296_Y1.5130.91
161_G164_M1.5070.91
324_E329_E1.5060.91
104_C110_Y1.4980.91
306_E309_V1.4940.91
100_W107_G1.4900.90
127_C130_C1.4690.90
286_E293_P1.4600.89
189_H207_F1.4490.89
195_C200_C1.4440.88
291_E294_A1.4350.88
244_L248_L1.4340.88
303_H307_Y1.4200.87
291_E295_G1.4170.87
106_F109_I1.3980.86
199_F213_C1.3960.86
314_A318_D1.3960.86
294_A300_C1.3930.86
316_S324_E1.3910.86
318_D325_V1.3890.86
303_H306_E1.3870.86
325_V328_L1.3820.85
309_V312_I1.3780.85
178_F194_Q1.3680.85
328_L331_A1.3630.84
106_F110_Y1.3610.84
152_M157_Y1.3600.84
24_C27_C1.3580.84
320_A324_E1.3530.84
329_E332_T1.3400.83
324_E327_E1.3280.82
104_C107_G1.3240.82
316_S320_A1.3220.82
288_C292_T1.3190.81
287_A292_T1.3090.81
322_L330_T1.3060.81
311_L318_D1.2910.80
4_C27_C1.2870.79
318_D326_E1.2870.79
324_E328_L1.2750.78
318_D324_E1.2670.78
322_L325_V1.2640.77
287_A293_P1.2610.77
353_A357_Q1.2600.77
306_E313_N1.2410.76
330_T335_Y1.2380.75
127_C200_C1.2260.74
323_Y326_E1.2230.74
23_I48_A1.2200.74
328_L333_E1.2190.74
312_I318_D1.2180.74
304_Y309_V1.2090.73
329_E335_Y1.2060.73
341_Q344_A1.2060.73
313_N320_A1.2060.73
317_L321_T1.2030.72
192_C200_C1.1980.72
104_C112_R1.1980.72
148_N151_R1.1980.72
319_P322_L1.1930.72
296_Y300_C1.1930.72
189_H198_Q1.1910.71
316_S323_Y1.1910.71
346_E349_P1.1840.71
38_E74_S1.1750.70
288_C294_A1.1750.70
303_H308_L1.1750.70
155_P161_G1.1740.70
321_T328_L1.1730.70
289_G297_A1.1720.70
286_E294_A1.1720.70
316_S319_P1.1710.70
346_E354_R1.1700.69
313_N316_S1.1680.69
192_C203_C1.1670.69
183_A186_G1.1610.69
288_C295_G1.1600.68
104_C108_F1.1590.68
289_G296_Y1.1590.68
109_I112_R1.1560.68
285_D288_C1.1470.67
4_C24_C1.1390.66
307_Y310_S1.1380.66
276_Q283_L1.1320.66
318_D322_L1.1300.66
327_E335_Y1.1280.65
15_A22_T1.1230.65
183_A201_S1.1220.65
327_E330_T1.1210.65
332_T335_Y1.1190.64
349_P352_Q1.1150.64
153_N161_G1.1120.64
330_T333_E1.1110.64
76_E79_A1.1010.63
322_L326_E1.0990.62
299_L307_Y1.0950.62
335_Y338_V1.0920.62
290_K299_L1.0910.62
157_Y164_M1.0900.61
173_C176_C1.0900.61
119_C127_C1.0900.61
340_P347_D1.0900.61
165_Y170_G1.0890.61
349_P357_Q1.0880.61
343_L347_D1.0870.61
331_A335_Y1.0870.61
327_E332_T1.0850.61
41_I47_P1.0850.61
294_A299_L1.0810.60
306_E310_S1.0810.60
2_A5_G1.0800.60
287_A291_E1.0790.60
352_Q357_Q1.0790.60
187_C190_F1.0780.60
315_H318_D1.0770.60
291_E296_Y1.0760.60
103_Q107_G1.0750.60
311_L315_H1.0740.60
272_R279_V1.0730.60
321_T324_E1.0700.59
23_I43_D1.0690.59
329_E336_L1.0660.59
308_L313_N1.0660.59
341_Q345_G1.0660.59
341_Q347_D1.0630.59
317_L324_E1.0630.59
325_V331_A1.0600.58
314_A317_L1.0560.58
260_P278_E1.0550.58
326_E331_A1.0500.57
181_A201_S1.0470.57
245_Q248_L1.0470.57
332_T338_V1.0450.57
317_L326_E1.0440.56
319_P323_Y1.0440.56
283_L287_A1.0420.56
207_F213_C1.0400.56
322_L328_L1.0360.56
127_C138_H1.0340.55
312_I319_P1.0340.55
350_A353_A1.0330.55
101_C176_C1.0330.55
106_F111_E1.0320.55
322_L329_E1.0270.55
340_P343_L1.0270.55
316_S325_V1.0190.54
316_S321_T1.0190.54
25_P29_R1.0170.53
284_R291_E1.0170.53
312_I316_S1.0160.53
201_S204_Y1.0150.53
318_D321_T1.0150.53
174_P197_H1.0140.53
339_R342_P1.0130.53
127_C143_C1.0120.53
325_V330_T1.0120.53
279_V282_G1.0110.53
331_A336_L1.0100.53
314_A320_A1.0100.53
328_L332_T1.0090.53
288_C291_E1.0080.52
289_G295_G1.0080.52
300_C309_V1.0080.52
259_P263_A1.0060.52
273_V280_P1.0060.52
215_E233_L1.0020.52
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  
4kblA20.83961000.429Contact Map
5c1zA201000.529Contact Map
4i1fA10.50531000.53Contact Map
4k95A120.47331000.531Contact Map
5cawA201000.547Contact Map
4ljoA10.57491000.559Contact Map
2m48A10.33161000.688Contact Map
2ct7A10.229999.70.799Contact Map
1wimA10.227399.40.835Contact Map
4cfgA20.344999.30.85Contact 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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