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Again -force run

ID: 1504714023 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 999 (992)
Sequences: 778 (673.4)
Seq/Len: 0.784
Nf(neff/√len): 21.4

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: 0.784).

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
164_P181_V3.5841.00
350_V413_I2.9931.00
104_F113_R2.9701.00
62_V93_G2.4770.99
351_L367_Y2.4560.98
406_R414_E2.4530.98
366_L405_G2.3760.98
74_Q375_E2.3720.98
204_D283_R2.3550.98
216_L258_N2.3470.98
926_L962_L2.3440.98
31_V56_V2.3310.98
183_S375_E2.3210.98
205_R230_A2.2870.97
260_V288_S2.2520.97
216_L259_S2.2230.97
186_A319_S2.1940.96
350_V405_G2.1920.96
119_Q169_Y2.1870.96
953_L956_A2.1810.96
288_S319_S2.1790.96
216_L321_W2.1640.96
929_V958_V2.1640.96
953_L962_L2.1220.95
50_M89_T2.1030.95
258_N321_W2.0820.95
189_N345_N2.0590.94
62_V89_T2.0490.94
262_A290_D2.0470.94
951_D956_A2.0450.94
347_G369_T2.0000.93
71_C99_A1.9860.93
76_R102_V1.9650.92
210_A216_L1.9650.92
258_N261_P1.9450.92
74_Q163_L1.9390.91
932_E961_K1.9300.91
323_N348_F1.9050.90
258_N288_S1.8780.90
264_M321_W1.8710.89
209_L321_W1.8620.89
223_G321_W1.8620.89
33_Q37_N1.8560.89
355_M367_Y1.8550.89
33_Q36_A1.8510.89
258_N312_L1.8440.88
312_L321_W1.8370.88
53_E57_K1.8320.88
167_I378_A1.8140.87
190_T216_L1.8090.87
369_T398_L1.8090.87
223_G258_N1.7990.87
204_D255_T1.7880.86
259_S321_W1.7750.86
93_G97_A1.7710.86
380_D383_L1.7650.85
436_E450_V1.7640.85
210_A259_S1.7580.85
210_A312_L1.7580.85
922_L998_R1.7540.85
210_A224_P1.7280.84
260_V312_L1.7260.84
60_F96_L1.7140.83
195_N219_Y1.7110.83
190_T321_W1.7040.83
442_H865_F1.6970.82
210_A263_L1.6910.82
216_L260_V1.6760.81
209_L259_S1.6600.80
288_S321_W1.6590.80
190_T258_N1.6430.79
308_Q326_I1.6410.79
263_L321_W1.6380.79
56_V59_A1.6370.79
216_L315_A1.6340.79
194_I210_A1.6300.78
367_Y398_L1.6260.78
210_A258_N1.6240.78
76_R167_I1.6150.78
216_L322_S1.6070.77
951_D955_M1.6050.77
128_T131_I1.5980.77
216_L222_F1.5960.76
190_T263_L1.5850.76
210_A321_W1.5820.76
216_L288_S1.5790.75
190_T288_S1.5780.75
190_T320_I1.5760.75
259_S263_L1.5750.75
223_G259_S1.5660.75
315_A346_Q1.5650.74
78_A122_V1.5640.74
288_S312_L1.5630.74
258_N287_L1.5620.74
81_M126_L1.5610.74
941_R990_V1.5500.73
216_L263_L1.5470.73
191_I210_A1.5460.73
219_Y258_N1.5450.73
921_M924_E1.5390.73
78_A169_Y1.5340.72
219_Y321_W1.5270.72
219_Y263_L1.5250.72
211_Q258_N1.5240.72
958_V984_M1.5190.71
207_L234_P1.5170.71
315_A321_W1.5120.71
391_H396_E1.5020.70
288_S318_A1.5010.70
56_V96_L1.4960.70
946_Y950_A1.4910.69
26_L187_A1.4900.69
218_V321_W1.4890.69
216_L219_Y1.4890.69
951_D962_L1.4870.69
216_L287_L1.4790.68
929_V962_L1.4790.68
258_N263_L1.4790.68
259_S315_A1.4780.68
190_T219_Y1.4720.68
955_M962_L1.4720.68
216_L312_L1.4720.68
194_I288_S1.4700.68
210_A290_D1.4670.67
264_M287_L1.4590.67
86_H128_T1.4570.67
919_L991_A1.4550.67
209_L260_V1.4520.66
101_Y217_S1.4500.66
31_V96_L1.4460.66
259_S312_L1.4430.66
930_W950_A1.4410.65
369_T373_L1.4360.65
236_A239_Q1.4300.65
164_P375_E1.4270.64
204_D256_V1.4270.64
450_V463_G1.4250.64
261_P296_L1.4220.64
930_W990_V1.4190.64
210_A292_I1.4160.63
286_L312_L1.4160.63
190_T194_I1.4150.63
208_G231_L1.4100.63
955_M986_N1.4090.63
210_A287_L1.4080.63
926_L958_V1.4070.63
313_G339_Y1.4050.63
260_V321_W1.4040.62
88_V221_I1.4030.62
182_I231_L1.4020.62
752_G755_E1.4010.62
210_A315_A1.3950.62
352_D356_R1.3950.62
441_K869_H1.3950.62
208_G321_W1.3930.62
211_Q321_W1.3920.61
355_M373_L1.3900.61
261_P321_W1.3890.61
186_A373_L1.3840.61
247_E251_E1.3830.61
953_L988_P1.3820.61
383_L387_R1.3760.60
194_I223_G1.3760.60
194_I312_L1.3750.60
191_I216_L1.3730.60
257_W321_W1.3730.60
56_V60_F1.3710.60
218_V258_N1.3700.60
312_L320_I1.3690.60
287_L312_L1.3690.60
194_I216_L1.3640.59
223_G315_A1.3630.59
312_L315_A1.3600.59
953_L966_L1.3600.59
318_A321_W1.3590.59
284_L310_V1.3580.59
108_Q116_M1.3580.59
953_L997_I1.3540.58
260_V264_M1.3510.58
190_T319_S1.3490.58
365_E400_R1.3450.58
189_N368_I1.3440.57
208_G322_S1.3380.57
701_Y705_D1.3370.57
75_D99_A1.3350.57
71_C77_V1.3330.57
79_I91_V1.3330.57
351_L398_L1.3290.56
190_T209_L1.3270.56
33_Q373_L1.3260.56
210_A223_G1.3240.56
204_D229_G1.3220.56
223_G312_L1.3210.55
193_D344_A1.3210.55
944_S947_K1.3190.55
73_A163_L1.3160.55
874_M892_K1.3150.55
287_L321_W1.3080.54
222_F321_W1.3070.54
218_V222_F1.3060.54
190_T322_S1.3060.54
115_A169_Y1.3030.54
193_D321_W1.3030.54
423_V432_L1.3020.54
193_D197_R1.3020.54
432_L450_V1.3020.54
866_L875_L1.3020.54
962_L997_I1.3010.54
259_S264_M1.3000.54
288_S315_A1.2970.53
363_T416_L1.2970.53
258_N320_I1.2960.53
311_S323_N1.2950.53
31_V59_A1.2940.53
190_T259_S1.2920.53
315_A337_I1.2920.53
950_A955_M1.2920.53
296_L321_W1.2910.53
194_I321_W1.2900.53
210_A239_Q1.2900.53
951_D981_L1.2900.53
210_A260_V1.2870.53
193_D260_V1.2840.52
100_V164_P1.2830.52
209_L286_L1.2790.52
209_L322_S1.2780.52
164_P183_S1.2760.52
259_S322_S1.2760.52
224_P231_L1.2750.51
193_D292_I1.2710.51
677_L680_G1.2710.51
208_G259_S1.2710.51
45_D85_A1.2700.51
209_L320_I1.2640.51
955_M981_L1.2640.51
209_L263_L1.2630.50
258_N264_M1.2620.50
210_A346_Q1.2620.50
222_F260_V1.2620.50
209_L258_N1.2610.50
942_T991_A1.2580.50
30_I52_Y1.2550.50
223_G320_I1.2540.50
27_H59_A1.2520.49
194_I258_N1.2500.49
208_G216_L1.2500.49
876_P892_K1.2470.49
71_C75_D1.2460.49
315_A339_Y1.2460.49
82_D128_T1.2450.49
916_E941_R1.2410.49
119_Q380_D1.2400.48
58_R86_H1.2390.48
222_F264_M1.2390.48
194_I259_S1.2360.48
927_A990_V1.2360.48
953_L957_Q1.2340.48
210_A219_Y1.2340.48
224_P258_N1.2320.48
75_D123_R1.2310.48
449_G452_L1.2280.47
311_S339_Y1.2250.47
348_F366_L1.2250.47
190_T220_D1.2240.47
31_V60_F1.2220.47
439_L448_A1.2210.47
115_A176_Q1.2200.47
17_T345_N1.2190.47
190_T210_A1.2170.46
209_L219_Y1.2170.46
923_E994_A1.2170.46
264_M312_L1.2160.46
257_W260_V1.2110.46
24_Y32_K1.2090.46
193_D209_L1.2090.46
261_P320_I1.2050.45
208_G229_G1.2040.45
41_P51_T1.2040.45
920_D998_R1.2030.45
953_L981_L1.2030.45
209_L216_L1.2020.45
207_L213_S1.2000.45
223_G229_G1.1960.45
297_P315_A1.1960.45
218_V288_S1.1910.44
59_A93_G1.1880.44
959_A984_M1.1860.44
116_M213_S1.1850.44
261_P264_M1.1850.44
187_A223_G1.1840.44
193_D312_L1.1840.44
190_T318_A1.1820.43
218_V320_I1.1820.43
200_V229_G1.1820.43
287_L315_A1.1780.43
182_I319_S1.1780.43
745_F775_G1.1760.43
440_L448_A1.1740.43
259_S287_L1.1730.43
956_A981_L1.1700.42
194_I219_Y1.1670.42
205_R254_I1.1650.42
258_N315_A1.1620.42
951_D954_I1.1620.42
232_V248_L1.1600.42
290_D415_F1.1590.41
391_H398_L1.1550.41
287_L292_I1.1530.41
920_D924_E1.1530.41
190_T223_G1.1520.41
312_L318_A1.1520.41
320_I346_Q1.1520.41
367_Y392_H1.1510.41
945_F950_A1.1490.41
258_N297_P1.1480.41
231_L264_M1.1470.40
194_I209_L1.1460.40
926_L929_V1.1440.40
223_G310_V1.1440.40
258_N322_S1.1420.40
920_D941_R1.1420.40
294_L334_W1.1400.40
990_V993_L1.1380.40
209_L312_L1.1380.40
223_G264_M1.1380.40
50_M164_P1.1380.40
682_G753_V1.1370.40
191_I194_I1.1360.40
389_L398_L1.1340.39
29_Q188_A1.1290.39
291_W321_W1.1290.39
44_F51_T1.1280.39
168_I320_I1.1270.39
263_L320_I1.1270.39
30_I92_L1.1270.39
257_W315_A1.1270.39
191_I312_L1.1260.39
258_N292_I1.1250.39
288_S313_G1.1250.39
219_Y259_S1.1240.39
946_Y985_L1.1230.38
325_H338_P1.1190.38
263_L337_I1.1180.38
209_L288_S1.1180.38
238_R244_H1.1160.38
216_L257_W1.1160.38
216_L264_M1.1160.38
29_Q192_A1.1150.38
311_S315_A1.1150.38
678_E701_Y1.1150.38
15_N345_N1.1140.38
223_G287_L1.1130.38
222_F258_N1.1130.38
406_R416_L1.1120.38
211_Q287_L1.1110.38
37_N40_R1.1110.38
927_A939_I1.1110.38
198_F310_V1.1100.37
25_C28_E1.1090.37
962_L981_L1.1040.37
206_V321_W1.1040.37
189_N321_W1.1030.37
168_I218_V1.1030.37
292_I297_P1.1020.37
90_A120_A1.1010.37
286_L321_W1.1000.37
373_L396_E1.1000.37
240_T263_L1.0990.37
190_T312_L1.0990.37
739_G744_S1.0990.37
450_V461_L1.0990.37
435_I862_L1.0980.36
200_V256_V1.0960.36
220_D339_Y1.0940.36
440_L447_A1.0940.36
678_E705_D1.0920.36
341_L412_E1.0920.36
87_Q212_L1.0910.36
240_T312_L1.0890.36
259_S267_L1.0870.36
30_I34_A1.0860.35
406_R895_R1.0860.35
949_G952_S1.0840.35
74_Q183_S1.0800.35
263_L300_M1.0800.35
323_N339_Y1.0800.35
219_Y292_I1.0790.35
206_V216_L1.0780.35
41_P49_H1.0770.35
81_M128_T1.0760.35
218_V261_P1.0760.35
209_L234_P1.0760.35
259_S310_V1.0740.35
127_T131_I1.0730.34
218_V260_V1.0730.34
257_W322_S1.0720.34
264_M318_A1.0720.34
288_S346_Q1.0710.34
193_D224_P1.0690.34
892_K898_L1.0690.34
232_V254_I1.0680.34
94_A877_S1.0670.34
216_L318_A1.0660.34
307_V312_L1.0650.34
200_V204_D1.0630.34
292_I312_L1.0620.34
349_R357_D1.0610.34
223_G290_D1.0610.34
321_W337_I1.0600.33
466_E885_L1.0600.33
355_M398_L1.0590.33
122_V398_L1.0560.33
216_L339_Y1.0560.33
290_D313_G1.0550.33
318_A368_I1.0550.33
219_Y320_I1.0530.33
955_M958_V1.0510.33
919_L941_R1.0510.33
293_P321_W1.0500.33
876_P894_D1.0490.33
234_P245_W1.0490.33
464_V898_L1.0490.33
206_V224_P1.0480.33
216_L346_Q1.0480.33
956_A960_G1.0480.33
223_G260_V1.0480.33
297_P337_I1.0470.32
191_I222_F1.0470.32
321_W346_Q1.0460.32
687_T691_L1.0460.32
208_G300_M1.0450.32
258_N284_L1.0440.32
392_H398_L1.0440.32
746_D749_L1.0440.32
193_D219_Y1.0430.32
951_D988_P1.0430.32
193_D210_A1.0430.32
60_F64_N1.0410.32
204_D258_N1.0410.32
956_A962_L1.0390.32
389_L451_V1.0390.32
217_S258_N1.0390.32
224_P292_I1.0380.32
208_G213_S1.0380.32
348_F368_I1.0360.32
684_G705_D1.0340.31
220_D318_A1.0340.31
989_T992_A1.0340.31
258_N296_L1.0330.31
216_L223_G1.0320.31
223_G346_Q1.0310.31
194_I320_I1.0300.31
211_Q224_P1.0300.31
200_V219_Y1.0290.31
679_V682_G1.0290.31
349_R398_L1.0280.31
206_V318_A1.0260.31
793_Q796_M1.0260.31
962_L979_A1.0260.31
359_P362_V1.0240.31
207_L256_V1.0230.31
351_L357_D1.0230.31
186_A374_A1.0230.31
216_L337_I1.0230.31
90_A126_L1.0220.31
264_M293_P1.0220.31
239_Q287_L1.0190.30
291_W415_F1.0190.30
312_L324_Y1.0190.30
249_M267_L1.0190.30
83_K234_P1.0170.30
168_I213_S1.0170.30
259_S337_I1.0160.30
101_Y218_V1.0160.30
425_I452_L1.0160.30
222_F288_S1.0150.30
257_W339_Y1.0150.30
187_A226_S1.0130.30
297_P321_W1.0120.30
216_L291_W1.0120.30
205_R312_L1.0120.30
219_Y310_V1.0110.30
102_V120_A1.0100.30
216_L285_A1.0090.30
191_I259_S1.0070.29
189_N320_I1.0070.29
220_D313_G1.0070.29
224_P259_S1.0050.29
50_M85_A1.0040.29
257_W262_A1.0040.29
956_A988_P1.0030.29
222_F312_L1.0020.29
367_Y419_E1.0010.29
196_R344_A1.0010.29
234_P238_R1.0010.29
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  
2vsqA10.59461000.416Contact Map
4dg8A10.49151000.446Contact Map
4iz6A20.58261000.49Contact Map
4r0mB20.58761000.503Contact Map
4d4iA101000.553Contact Map
1amuA20.50251000.559Contact Map
3tsyA10.48351000.583Contact Map
4gr5A40.40841000.599Contact Map
3wvnA20.37841000.601Contact Map
3g7sA20.46951000.601Contact 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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