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OPENSEQ.org

test3 spot

ID: 1421664706 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 702 (699)
Sequences: 1644 (1067.5)
Seq/Len: 2.352
Nf(neff/√len): 40.4

HHblits Results: (2013_03)
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: 2.352).

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
86_E91_K4.4811.00
427_D441_Q3.8701.00
411_Y419_H3.7761.00
75_I82_Y3.2181.00
426_V431_Y3.1901.00
25_Q88_L3.0691.00
269_D272_T2.9991.00
61_L134_L2.9721.00
685_M697_V2.9481.00
407_V460_F2.9171.00
461_V470_I2.8241.00
223_R226_E2.8051.00
145_R181_E2.7331.00
631_V688_I2.6321.00
232_R325_E2.5441.00
636_H642_N2.4851.00
483_V525_A2.4791.00
220_I280_M2.4741.00
23_L66_L2.4371.00
266_I325_E2.4031.00
268_N325_E2.3841.00
230_P268_N2.3771.00
152_P155_R2.3481.00
490_L527_I2.3191.00
64_E92_S2.2951.00
22_R67_M2.2791.00
417_I447_T2.2331.00
437_L443_V2.2141.00
252_Q257_I2.0120.99
75_I85_M2.0050.99
212_M312_G1.9800.99
201_V254_F1.9720.99
392_T398_V1.9580.99
463_S466_A1.9480.99
517_L526_E1.8960.99
234_S328_D1.8750.99
198_I240_L1.8710.99
657_L671_I1.8670.99
633_M639_A1.8550.99
11_I23_L1.8540.99
82_Y98_E1.8310.98
56_L65_T1.8220.98
160_R164_E1.8220.98
147_L158_I1.7940.98
629_I685_M1.7930.98
191_Y194_R1.7750.98
406_P424_A1.7550.98
435_Q438_T1.7530.98
61_L65_T1.7350.98
40_S150_L1.7270.98
77_D143_N1.7230.97
147_L189_A1.7060.97
436_P462_V1.7050.97
29_V80_A1.6990.97
221_E225_Q1.6890.97
143_N146_T1.6750.97
73_D77_D1.6640.97
587_S593_V1.6500.97
215_K314_H1.6250.96
628_E672_R1.6160.96
519_T522_D1.6120.96
636_H639_A1.6070.96
202_V240_L1.5930.96
84_D87_Q1.5760.95
574_C599_C1.5740.95
415_T419_H1.5680.95
271_D275_R1.5580.95
22_R64_E1.5510.95
76_E143_N1.5460.94
53_A66_L1.5330.94
425_R444_E1.5330.94
647_I654_I1.5300.94
73_D76_E1.5280.94
426_V435_Q1.5040.93
152_P156_R1.5040.93
73_D143_N1.5030.93
155_R189_A1.4960.93
673_L684_I1.4910.93
30_A46_I1.4590.92
238_K246_K1.4570.92
144_M182_L1.4500.92
55_I145_R1.4490.92
595_H599_C1.4470.91
652_S680_H1.4440.91
102_K143_N1.4390.91
49_P143_N1.4340.91
267_V276_V1.4250.91
77_D146_T1.4220.91
487_R524_L1.4220.91
223_R283_L1.4210.90
213_I235_G1.4190.90
39_R45_Y1.4180.90
39_R77_D1.4160.90
39_R146_T1.4120.90
448_A451_A1.4120.90
574_C595_H1.4100.90
142_H146_T1.4050.90
210_K214_Q1.4030.90
77_D102_K1.4010.90
95_E128_Q1.4000.90
34_H73_D1.3990.90
479_R522_D1.3970.89
34_H143_N1.3860.89
406_P426_V1.3820.89
139_D143_N1.3820.89
56_L69_A1.3810.89
573_C599_C1.3760.89
558_L582_I1.3730.88
39_R143_N1.3670.88
290_R309_S1.3650.88
576_P599_C1.3650.88
76_E146_T1.3640.88
338_H341_Y1.3620.88
281_H308_T1.3590.88
39_R42_G1.3560.88
404_A688_I1.3530.87
246_K319_E1.3390.87
199_K240_L1.3390.87
99_G121_K1.3380.87
639_A691_M1.3350.86
304_Q330_M1.3310.86
212_M313_P1.3280.86
583_I602_I1.3230.86
163_L241_Y1.3190.86
96_L135_I1.3160.85
76_E101_S1.3160.85
268_N272_T1.3140.85
639_A642_N1.3130.85
222_G226_E1.3110.85
34_H37_Q1.3110.85
144_M147_L1.3060.85
48_H72_H1.3040.85
48_H142_H1.3000.84
77_D101_S1.2990.84
150_L154_K1.2960.84
483_V521_D1.2960.84
72_H76_E1.2940.84
67_M93_V1.2940.84
204_A316_V1.2920.84
34_H48_H1.2890.84
39_R102_K1.2880.84
584_A613_M1.2870.84
80_A84_D1.2860.84
34_H45_Y1.2850.83
272_T275_R1.2850.83
147_L159_A1.2810.83
328_D332_E1.2810.83
24_R28_L1.2790.83
455_A474_L1.2790.83
34_H72_H1.2740.83
216_I318_V1.2740.83
53_A69_A1.2720.83
10_L58_E1.2720.83
99_G132_V1.2670.82
151_R154_K1.2660.82
34_H39_R1.2550.81
34_H77_D1.2530.81
205_A208_N1.2520.81
22_R25_Q1.2510.81
197_V201_V1.2510.81
32_D35_E1.2500.81
82_Y86_E1.2420.81
39_R76_E1.2420.81
34_H76_E1.2420.81
56_L66_L1.2420.81
63_Y67_M1.2390.80
77_D142_H1.2390.80
415_T469_K1.2390.80
573_C595_H1.2360.80
594_I615_V1.2300.80
52_V139_D1.2280.79
640_L657_L1.2270.79
478_K481_D1.2260.79
325_E329_Q1.2260.79
26_A30_A1.2260.79
39_R49_P1.2210.79
72_H143_N1.2200.79
82_Y95_E1.2190.79
39_R142_H1.2180.79
643_L647_I1.2160.79
48_H73_D1.2160.79
150_L158_I1.2150.78
64_E67_M1.2150.78
73_D78_T1.2150.78
238_K338_H1.2140.78
39_R72_H1.2130.78
66_L69_A1.2110.78
43_E48_H1.2110.78
218_S222_G1.2100.78
638_G653_N1.2100.78
585_H611_K1.2100.78
75_I98_E1.2090.78
206_R237_E1.2080.78
159_A186_G1.2030.77
33_A84_D1.2020.77
102_K139_D1.2000.77
29_V88_L1.2000.77
49_P73_D1.2000.77
49_P102_K1.1970.77
180_T239_H1.1970.77
28_L31_R1.1940.77
412_A465_K1.1930.77
276_V279_Q1.1920.77
73_D146_T1.1920.77
221_E232_R1.1910.77
73_D142_H1.1900.76
48_H143_N1.1900.76
49_P77_D1.1880.76
101_S143_N1.1880.76
246_K338_H1.1870.76
39_R73_D1.1820.76
21_K25_Q1.1810.76
274_Y281_H1.1800.76
76_E139_D1.1790.75
144_M162_T1.1770.75
64_E93_V1.1770.75
576_P595_H1.1760.75
224_L276_V1.1730.75
421_C433_L1.1690.75
78_T143_N1.1660.74
425_R430_P1.1650.74
73_D101_S1.1630.74
55_I181_E1.1610.74
72_H142_H1.1600.74
68_A96_L1.1570.74
34_H49_P1.1550.73
73_D102_K1.1550.73
77_D139_D1.1500.73
42_G48_H1.1500.73
647_I671_I1.1500.73
280_M310_M1.1450.72
194_R197_V1.1420.72
22_R93_V1.1420.72
34_H101_S1.1420.72
48_H77_D1.1410.72
76_E142_H1.1390.72
180_T206_R1.1360.72
72_H146_T1.1360.72
49_P76_E1.1350.71
49_P142_H1.1340.71
220_I320_V1.1330.71
13_T404_A1.1320.71
246_K259_D1.1310.71
34_H146_T1.1310.71
39_R139_D1.1300.71
45_Y73_D1.1300.71
387_E399_E1.1280.71
72_H139_D1.1230.70
211_E215_K1.1230.70
72_H77_D1.1220.70
561_K616_E1.1210.70
647_I652_S1.1210.70
573_C576_P1.1170.70
219_E284_Y1.1130.69
581_P597_E1.1130.69
388_I403_G1.1120.69
45_Y143_N1.1100.69
359_M388_I1.1100.69
246_K262_A1.1100.69
126_M130_I1.1090.69
11_I16_P1.1090.69
76_E102_K1.1080.69
217_L221_E1.1080.69
116_A383_L1.1080.69
246_K264_R1.1060.69
45_Y72_H1.1060.69
73_D162_T1.1010.68
635_N667_Y1.1000.68
34_H142_H1.0990.68
319_E338_H1.0970.68
277_L322_I1.0960.68
49_P72_H1.0940.67
636_H667_Y1.0910.67
82_Y94_A1.0900.67
320_V461_V1.0850.67
274_Y277_L1.0830.66
238_K336_A1.0800.66
512_L520_L1.0780.66
72_H101_S1.0770.66
587_S601_N1.0750.65
175_I179_K1.0750.65
45_Y48_H1.0740.65
390_V437_L1.0710.65
39_R48_H1.0700.65
435_Q441_Q1.0690.65
45_Y102_K1.0690.65
278_G281_H1.0680.65
154_K158_I1.0670.65
139_D146_T1.0600.64
264_R319_E1.0590.64
407_V461_V1.0550.63
518_A522_D1.0540.63
48_H52_V1.0540.63
48_H146_T1.0530.63
83_Q87_Q1.0530.63
637_Q653_N1.0530.63
139_D142_H1.0530.63
524_L643_L1.0520.63
336_A341_Y1.0520.63
101_S139_D1.0510.63
86_E94_A1.0500.63
262_A338_H1.0490.63
78_T146_T1.0490.63
14_Y60_K1.0460.62
71_L93_V1.0440.62
45_Y142_H1.0440.62
277_L281_H1.0430.62
41_S77_D1.0410.62
34_H102_K1.0410.62
238_K319_E1.0360.61
76_E154_K1.0360.61
48_H76_E1.0360.61
274_Y278_G1.0350.61
75_I101_S1.0340.61
238_K321_Q1.0340.61
659_T669_A1.0330.61
45_Y77_D1.0330.61
187_F194_R1.0320.61
264_R342_K1.0310.61
55_I140_R1.0310.61
180_T237_E1.0300.61
39_R44_P1.0290.60
34_H78_T1.0290.60
629_I671_I1.0280.60
321_Q338_H1.0270.60
102_K146_T1.0270.60
477_L480_D1.0250.60
101_S146_T1.0250.60
102_K142_H1.0230.60
246_K336_A1.0220.60
636_H691_M1.0220.60
225_Q521_D1.0220.60
264_R321_Q1.0180.59
231_C276_V1.0180.59
403_G436_P1.0180.59
526_E532_A1.0170.59
629_I697_V1.0170.59
424_A445_I1.0160.59
388_I435_Q1.0150.59
8_N20_I1.0150.59
490_L524_L1.0140.59
238_K262_A1.0130.59
380_K384_F1.0130.59
517_L523_L1.0120.59
216_I263_F1.0110.58
77_D154_K1.0110.58
313_P640_L1.0110.58
338_H342_K1.0100.58
188_E199_K1.0080.58
647_I673_L1.0080.58
45_Y146_T1.0080.58
241_Y245_C1.0070.58
49_P52_V1.0070.58
143_N154_K1.0060.58
42_G143_N1.0060.58
424_A431_Y1.0050.58
224_L231_C1.0050.58
6_S10_L1.0040.58
339_W573_C1.0040.58
78_T102_K1.0030.58
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: (06Sep14)
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  
1vj7A20.47581000.514Contact Map
3l9dA20.26641000.794Contact Map
2be3A20.27351000.83Contact Map
3nqwA20.24791000.841Contact Map
3nr1A20.24361000.844Contact Map
2ekiA10.111199.90.915Contact Map
4ce4c10.34999.70.936Contact Map
3hvzA60.091299.50.942Contact Map
1wxqA10.417499.40.945Contact Map
1wwtA10.123999.20.95Contact 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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