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OPENSEQ.org

hA10

ID: 1487683907 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 459 (454)
Sequences: 529 (352.1)
Seq/Len: 1.165
Nf(neff/√len): 16.5

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: 1.165).

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
285_K288_K4.4621.00
292_P299_T2.7201.00
257_E284_L2.5331.00
312_R333_S2.4280.99
37_V168_F2.4250.99
248_G259_D2.2080.98
308_S322_I2.1840.98
170_H174_H2.1780.98
292_P301_Q2.1430.98
298_C302_C2.0750.97
289_Q303_A2.0710.97
174_H180_H2.0180.97
15_T33_I2.0110.97
321_G333_S1.9950.97
248_G256_E1.9500.96
311_C317_C1.9480.96
426_C432_C1.9390.96
195_G200_G1.9360.96
247_C259_D1.9230.96
249_N256_E1.8840.95
419_C426_C1.8810.95
260_C266_C1.8700.95
272_F281_K1.8500.94
247_C256_E1.8500.94
170_H180_H1.8400.94
249_N259_D1.8370.94
282_C290_C1.8020.93
174_H181_D1.7750.92
249_N253_E1.7620.92
256_E259_D1.7050.90
168_F172_V1.7010.90
292_P300_A1.6820.89
268_D291_S1.6540.88
259_D270_C1.6520.88
381_C385_C1.6310.87
316_D336_K1.5930.86
416_G419_C1.5810.85
82_I90_L1.5790.85
136_L140_G1.5740.85
103_Y150_I1.5700.84
248_G270_C1.5610.84
354_C359_C1.5590.84
248_G261_G1.5120.81
13_I33_I1.4990.81
419_C432_C1.4900.80
171_E174_H1.4840.80
271_C290_C1.4790.79
55_I176_F1.4590.78
59_V292_P1.4570.78
170_H181_D1.4420.77
171_E180_H1.4210.75
257_E283_K1.4100.75
181_D204_M1.4020.74
43_I200_G1.3970.74
330_C349_C1.3890.73
413_L417_S1.3890.73
247_C261_G1.3820.72
305_K309_E1.3810.72
284_L289_Q1.3620.71
325_G330_C1.3600.71
105_F168_F1.3600.71
163_V167_T1.3580.71
369_C384_C1.3570.71
248_G253_E1.3490.70
117_L121_G1.3370.69
11_L37_V1.3370.69
381_C426_C1.3310.68
170_H173_G1.3310.68
43_I208_A1.3170.67
256_E271_C1.3120.67
193_N197_K1.3090.67
253_E256_E1.3030.66
256_E270_C1.2940.65
297_C317_C1.2940.65
118_A171_E1.2910.65
48_D53_R1.2870.65
247_C271_C1.2820.64
286_P418_P1.2800.64
261_G271_C1.2790.64
381_C419_C1.2750.64
248_G258_C1.2750.64
258_C261_G1.2710.63
169_A203_I1.2670.63
297_C311_C1.2640.63
100_C146_N1.2640.63
114_V208_A1.2620.62
178_S227_I1.2570.62
283_K336_K1.2470.61
318_A333_S1.2440.61
259_D271_C1.2430.61
342_C349_C1.2390.60
40_I57_F1.2380.60
231_L236_N1.2370.60
419_C424_G1.2330.60
223_S232_E1.2280.59
122_A132_E1.2280.59
260_C264_D1.2240.59
317_C325_G1.2160.58
103_Y168_F1.2150.58
338_N352_G1.2120.58
427_D433_R1.2100.58
330_C342_C1.2010.57
253_E259_D1.2010.57
116_G171_E1.1960.56
310_K322_I1.1890.56
249_N270_C1.1870.55
261_G270_C1.1850.55
271_C282_C1.1830.55
88_L116_G1.1750.54
349_C352_G1.1730.54
247_C258_C1.1690.54
20_F29_V1.1680.54
317_C323_C1.1680.54
129_G239_F1.1680.54
180_H223_S1.1670.53
92_S119_W1.1670.53
50_S53_R1.1670.53
211_G223_S1.1650.53
312_R321_G1.1640.53
247_C253_E1.1590.53
15_T64_I1.1570.52
97_D266_C1.1570.52
318_A321_G1.1560.52
180_H204_M1.1540.52
247_C270_C1.1510.52
96_H102_A1.1500.52
288_K338_N1.1430.51
148_G175_N1.1430.51
249_N261_G1.1430.51
29_V103_Y1.1420.51
65_N147_T1.1410.51
413_L443_R1.1400.51
174_H204_M1.1390.51
116_G170_H1.1350.50
11_L16_D1.1340.50
337_P340_T1.1330.50
316_D420_N1.1290.50
188_P202_Y1.1250.49
311_C323_C1.1240.49
248_G271_C1.1240.49
117_L211_G1.1210.49
438_D443_R1.1200.49
331_P352_G1.1200.49
270_C290_C1.1200.49
24_G66_T1.1160.49
130_I239_F1.1130.48
338_N427_D1.1120.48
284_L363_G1.1110.48
317_C331_P1.1070.48
70_E418_P1.1060.48
252_V284_L1.1040.47
437_A446_K1.1040.47
103_Y175_N1.1010.47
338_N351_N1.1010.47
87_F149_I1.0990.47
290_C298_C1.0990.47
181_D223_S1.0980.47
325_G331_P1.0960.47
44_Y118_A1.0950.46
83_G86_K1.0900.46
194_L202_Y1.0890.46
248_G255_G1.0890.46
101_L163_V1.0870.46
270_C297_C1.0870.46
40_I172_V1.0870.46
312_R318_A1.0860.46
292_P302_C1.0850.46
73_P257_E1.0850.46
13_I168_F1.0820.45
36_H168_F1.0800.45
260_C268_D1.0790.45
282_C297_C1.0780.45
448_I451_P1.0770.45
305_K382_H1.0750.45
34_S59_V1.0750.45
21_K280_R1.0740.44
254_Q383_V1.0730.44
312_R320_E1.0700.44
249_N352_G1.0690.44
201_N208_A1.0690.44
203_I252_V1.0680.44
162_K272_F1.0650.44
75_N347_Q1.0630.43
171_E181_D1.0620.43
40_I168_F1.0620.43
338_N425_Y1.0620.43
113_G231_L1.0610.43
348_V418_P1.0610.43
173_G181_D1.0600.43
325_G349_C1.0590.43
385_C419_C1.0590.43
15_T20_F1.0580.43
170_H204_M1.0580.43
223_S239_F1.0570.43
220_S223_S1.0530.42
204_M222_C1.0480.42
106_T146_N1.0460.42
225_R229_Q1.0460.42
248_G252_V1.0420.41
13_I37_V1.0410.41
50_S255_G1.0410.41
140_G203_I1.0410.41
256_E261_G1.0400.41
287_G290_C1.0370.41
72_D316_D1.0370.41
194_L427_D1.0370.41
167_T257_E1.0360.41
270_C282_C1.0350.41
241_E337_P1.0350.41
75_N78_R1.0320.40
338_N363_G1.0300.40
282_C298_C1.0300.40
146_N151_T1.0250.40
249_N271_C1.0210.39
259_D282_C1.0190.39
249_N317_C1.0160.39
189_G195_G1.0140.39
247_C282_C1.0110.39
183_G205_Y1.0110.39
187_T232_E1.0100.38
308_S313_D1.0070.38
122_A230_V1.0040.38
189_G200_G1.0020.38
168_F386_M1.0010.38
247_C252_V1.0000.38
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  
3k7lA10.78871000.383Contact Map
2dw0A20.81051000.385Contact Map
2e3xA10.81481000.391Contact Map
2eroA20.81921000.394Contact Map
3g5cA20.86061000.415Contact Map
3k7nA10.77341000.44Contact Map
2rjpA40.59481000.588Contact Map
2v4bA20.5731000.591Contact Map
2i47A40.50331000.605Contact Map
2rjqA10.58821000.626Contact 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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