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extra-L-M-L-T-extra3

ID: 1504799843 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 923 (915)
Sequences: 1185 (993.1)
Seq/Len: 1.295
Nf(neff/√len): 32.8

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: 1.295).

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_V3.6461.00
809_S813_H3.2551.00
555_V558_W2.8761.00
814_E817_M2.7941.00
809_S817_M2.7891.00
806_A809_S2.7841.00
76_R102_V2.7741.00
809_S814_E2.7501.00
74_Q375_E2.6971.00
104_F113_R2.6851.00
779_F782_P2.6761.00
809_S812_D2.6321.00
912_A915_E2.6001.00
910_T915_E2.5371.00
729_F734_D2.5341.00
406_R414_E2.5331.00
62_V93_G2.5111.00
808_T813_H2.4961.00
71_C99_A2.4771.00
809_S815_G2.4531.00
555_V559_I2.3920.99
74_Q163_L2.3910.99
62_V89_T2.3790.99
806_A813_H2.3670.99
813_H817_M2.3510.99
726_F732_D2.3190.99
666_A690_V2.2820.99
726_F729_F2.2810.99
442_H865_F2.2610.99
119_Q169_Y2.2300.99
812_D817_M2.2220.99
31_V56_V2.1390.98
216_L258_N2.1390.98
366_L405_G2.1380.98
551_Y555_V2.1330.98
369_T398_L2.0990.98
666_A693_A2.0980.98
204_D283_R2.0850.98
363_T416_L2.0750.98
808_T815_G2.0720.98
258_N321_W2.0210.97
258_N288_S2.0120.97
829_L832_P2.0100.97
829_L833_E1.9970.97
350_V413_I1.9960.97
33_Q37_N1.9940.97
465_V862_L1.9660.97
205_R230_A1.9420.97
308_Q326_I1.9410.97
56_V154_P1.9370.97
726_F734_D1.9300.96
724_V729_F1.9300.96
915_E918_G1.9240.96
88_V221_I1.9190.96
750_A754_L1.9120.96
351_L367_Y1.9070.96
551_Y554_I1.9070.96
729_F732_D1.9030.96
71_C97_A1.8910.96
679_V767_L1.8840.96
724_V734_D1.8820.96
33_Q36_A1.8820.96
837_K842_G1.8810.96
828_V833_E1.8720.96
813_H820_L1.8560.95
551_Y559_I1.8490.95
809_S816_W1.8460.95
809_S820_L1.8460.95
817_M820_L1.8240.95
830_S833_E1.8160.95
262_A290_D1.8120.94
347_G369_T1.7910.94
210_A216_L1.7890.94
216_L321_W1.7730.94
828_V832_P1.7630.93
837_K843_F1.7610.93
806_A815_G1.7530.93
551_Y556_R1.7470.93
258_N312_L1.7470.93
724_V732_D1.7450.93
216_L259_S1.7370.93
50_M89_T1.7280.92
814_E820_L1.7130.92
729_F733_K1.7110.92
186_A319_S1.7090.92
730_D733_K1.7040.92
189_N345_N1.6960.91
223_G258_N1.6920.91
58_R86_H1.6890.91
812_D815_G1.6860.91
183_S375_E1.6770.91
797_M800_P1.6760.91
190_T219_Y1.6710.91
554_I558_W1.6700.91
219_Y258_N1.6640.90
813_H816_W1.6630.90
813_H819_L1.6610.90
60_F96_L1.6450.90
837_K840_S1.6420.90
186_A373_L1.6390.90
724_V727_G1.6380.89
108_Q116_M1.6350.89
723_N726_F1.6340.89
558_W561_K1.6310.89
453_D456_S1.6290.89
441_K869_H1.6280.89
204_D255_T1.6260.89
726_F731_V1.6240.89
323_N348_F1.6230.89
73_A163_L1.6070.88
808_T812_D1.6030.88
350_V405_G1.6020.88
93_G97_A1.5970.88
726_F733_K1.5960.88
216_L222_F1.5940.88
558_W562_L1.5940.88
208_G231_L1.5920.88
838_L842_G1.5910.88
551_Y558_W1.5790.87
837_K841_L1.5760.87
76_R167_I1.5750.87
223_G321_W1.5740.87
312_L321_W1.5730.87
209_L321_W1.5720.87
247_E251_E1.5720.87
807_E814_E1.5720.87
686_T690_V1.5700.87
318_A368_I1.5660.86
548_L551_Y1.5640.86
827_N833_E1.5610.86
167_I378_A1.5570.86
727_G734_D1.5560.86
210_A259_S1.5480.86
224_P231_L1.5420.85
352_D356_R1.5360.85
809_S819_L1.5350.85
162_D185_R1.5320.85
807_E817_M1.5320.85
771_I777_L1.5290.85
764_M779_F1.5290.85
552_Q555_V1.5270.85
812_D820_L1.5180.84
827_N832_P1.5180.84
740_L770_L1.5150.84
724_V730_D1.5080.84
815_G820_L1.5040.83
164_P375_E1.5000.83
258_N263_L1.4960.83
806_A812_D1.4930.83
436_E450_V1.4890.82
260_V288_S1.4880.82
432_L450_V1.4870.82
64_N155_I1.4850.82
554_I559_I1.4800.82
359_P362_V1.4770.82
71_C75_D1.4690.81
912_A918_G1.4660.81
789_I792_S1.4630.81
808_T816_W1.4630.81
260_V321_W1.4630.81
911_I915_E1.4620.81
190_T258_N1.4590.81
814_E819_L1.4550.80
726_F730_D1.4540.80
827_N830_S1.4450.80
466_E885_L1.4410.80
190_T321_W1.4410.80
259_S321_W1.4290.79
288_S321_W1.4220.78
355_M367_Y1.4200.78
287_L292_I1.4180.78
827_N831_L1.4150.78
727_G732_D1.4140.78
438_A866_L1.4110.78
843_F846_F1.4060.77
808_T817_M1.4050.77
825_D833_E1.4020.77
216_L260_V1.3980.77
219_Y321_W1.3970.77
87_Q212_L1.3960.76
37_N40_R1.3950.76
41_P49_H1.3880.76
258_N287_L1.3840.76
75_D99_A1.3800.75
81_M126_L1.3740.75
190_T263_L1.3740.75
838_L843_F1.3730.75
195_N219_Y1.3720.75
724_V733_K1.3680.74
752_G755_E1.3620.74
806_A817_M1.3570.74
260_V312_L1.3550.73
56_V96_L1.3520.73
795_F799_E1.3490.73
210_A258_N1.3470.73
193_D197_R1.3420.72
210_A263_L1.3380.72
724_V731_V1.3370.72
806_A814_E1.3370.72
687_T691_L1.3360.72
910_T918_G1.3360.72
258_N264_M1.3350.72
206_V216_L1.3330.72
730_D734_D1.3330.72
815_G819_L1.3300.71
830_S834_E1.3280.71
637_K713_G1.3260.71
257_W321_W1.3260.71
322_S372_G1.3240.71
803_L809_S1.3240.71
825_D828_V1.3200.71
216_L287_L1.3160.70
264_M321_W1.3140.70
31_V59_A1.3100.70
216_L312_L1.3090.70
435_I438_A1.3090.70
53_E57_K1.3050.69
258_N261_P1.3030.69
152_D155_I1.2990.69
559_I562_L1.2980.69
555_V563_T1.2980.69
262_A291_W1.2830.67
236_A239_Q1.2820.67
808_T820_L1.2800.67
261_P296_L1.2780.67
423_V432_L1.2750.67
841_L844_H1.2740.67
190_T216_L1.2720.66
843_F848_K1.2720.66
702_V745_F1.2700.66
700_E744_S1.2670.66
200_V229_G1.2660.66
810_Y817_M1.2640.66
209_L259_S1.2640.66
674_L695_E1.2640.66
151_Q155_I1.2620.66
79_I91_V1.2620.66
748_V771_I1.2610.65
190_T320_I1.2580.65
204_D256_V1.2530.65
218_V320_I1.2490.64
90_A94_A1.2450.64
807_E813_H1.2440.64
194_I219_Y1.2420.64
78_A122_V1.2400.64
808_T814_E1.2370.63
64_N151_Q1.2340.63
723_N732_D1.2320.63
209_L260_V1.2310.63
754_L782_P1.2300.63
208_G321_W1.2290.63
913_E918_G1.2280.62
408_T412_E1.2260.62
31_V96_L1.2240.62
453_D457_E1.2240.62
288_S312_L1.2230.62
208_G300_M1.2200.62
209_L258_N1.2180.62
219_Y263_L1.2180.62
284_L310_V1.2170.61
204_D229_G1.2170.61
209_L288_S1.2150.61
816_W820_L1.2120.61
675_R700_E1.2070.60
806_A816_W1.2060.60
259_S264_M1.2050.60
829_L834_E1.2040.60
555_V562_L1.2030.60
837_K845_L1.2030.60
842_G845_L1.2020.60
425_I452_L1.2010.60
449_G893_I1.2000.60
218_V222_F1.1980.60
806_A820_L1.1970.60
723_N729_F1.1970.60
216_L315_A1.1950.59
263_L321_W1.1950.59
241_D300_M1.1940.59
836_N842_G1.1940.59
729_F735_Y1.1910.59
325_H338_P1.1890.59
286_L312_L1.1870.59
661_L778_V1.1850.58
15_N345_N1.1850.58
216_L322_S1.1840.58
725_R734_D1.1830.58
191_I216_L1.1810.58
219_Y320_I1.1780.58
681_A703_F1.1740.57
216_L219_Y1.1730.57
391_H398_L1.1710.57
702_V741_A1.1710.57
90_A126_L1.1700.57
211_Q258_N1.1700.57
75_D123_R1.1700.57
732_D735_Y1.1690.57
102_V120_A1.1680.57
742_P769_E1.1670.57
56_V60_F1.1630.56
206_V321_W1.1550.55
60_F64_N1.1510.55
678_E701_Y1.1500.55
210_A260_V1.1490.55
287_L321_W1.1480.55
218_V258_N1.1470.55
209_L263_L1.1460.55
208_G258_N1.1450.54
810_Y816_W1.1440.54
208_G259_S1.1420.54
24_Y32_K1.1390.54
837_K844_H1.1390.54
65_K69_L1.1370.54
258_N320_I1.1370.54
836_N843_F1.1360.54
25_C28_E1.1330.53
180_V374_A1.1330.53
464_V899_A1.1330.53
807_E812_D1.1320.53
787_L841_L1.1310.53
288_S315_A1.1310.53
292_I297_P1.1300.53
315_A321_W1.1290.53
168_I320_I1.1240.52
636_G658_M1.1240.52
416_L435_I1.1220.52
258_N322_S1.1210.52
288_S319_S1.1210.52
363_T404_L1.1200.52
56_V59_A1.1190.52
559_I566_G1.1190.52
190_T322_S1.1170.52
450_V463_G1.1130.51
218_V321_W1.1110.51
837_K846_F1.1090.51
127_T131_I1.1080.51
558_W566_G1.1080.51
259_S312_L1.1070.51
190_T288_S1.1050.50
222_F258_N1.1050.50
216_L288_S1.1030.50
807_E820_L1.1030.50
724_V728_V1.1020.50
261_P321_W1.1010.50
462_L880_Q1.1000.50
190_T223_G1.0970.50
210_A321_W1.0970.50
292_I311_S1.0960.50
264_M287_L1.0950.50
365_E400_R1.0950.50
108_Q213_S1.0940.49
811_L816_W1.0930.49
17_T345_N1.0920.49
58_R89_T1.0910.49
210_A312_L1.0910.49
558_W563_T1.0910.49
26_L187_A1.0900.49
312_L318_A1.0890.49
258_N297_P1.0890.49
552_Q556_R1.0880.49
726_F735_Y1.0880.49
9_A13_S1.0870.49
194_I258_N1.0860.49
204_D242_P1.0860.49
27_H159_A1.0850.49
196_R344_A1.0820.48
828_V834_E1.0810.48
41_P51_T1.0810.48
193_D312_L1.0800.48
217_S262_A1.0780.48
882_V885_L1.0780.48
190_T210_A1.0760.48
190_T194_I1.0750.48
220_D318_A1.0740.47
351_L398_L1.0730.47
258_N300_M1.0710.47
812_D819_L1.0710.47
723_N730_D1.0700.47
194_I210_A1.0690.47
81_M128_T1.0680.47
23_D185_R1.0670.47
367_Y398_L1.0670.47
682_G753_V1.0670.47
838_L841_L1.0660.47
913_E916_E1.0640.46
219_Y260_V1.0630.46
216_L223_G1.0630.46
44_F252_H1.0620.46
810_Y813_H1.0620.46
191_I312_L1.0600.46
803_L806_A1.0600.46
450_V461_L1.0590.46
796_M799_E1.0580.46
704_T734_D1.0570.46
210_A224_P1.0520.45
209_L219_Y1.0510.45
548_L554_I1.0480.45
348_F366_L1.0460.45
839_S843_F1.0460.45
45_D85_A1.0450.45
731_V734_D1.0430.44
194_I312_L1.0420.44
209_L300_M1.0410.44
844_H847_A1.0410.44
454_S457_E1.0400.44
217_S258_N1.0390.44
259_S263_L1.0390.44
189_N320_I1.0380.44
194_I321_W1.0380.44
219_Y312_L1.0370.44
842_G848_K1.0370.44
208_G216_L1.0360.44
556_R559_I1.0350.44
223_G259_S1.0350.44
207_L234_P1.0340.43
723_N727_G1.0320.43
264_M300_M1.0310.43
787_L791_A1.0310.43
796_M800_P1.0310.43
193_D321_W1.0300.43
700_E725_R1.0280.43
318_A321_W1.0270.43
725_R729_F1.0270.43
914_T918_G1.0270.43
810_Y814_E1.0270.43
261_P264_M1.0260.43
194_I216_L1.0260.43
223_G315_A1.0250.43
223_G256_V1.0240.42
369_T373_L1.0230.42
8_I12_N1.0220.42
676_V690_V1.0220.42
239_Q258_N1.0220.42
59_A96_L1.0210.42
727_G733_K1.0200.42
836_N841_L1.0190.42
74_Q99_A1.0190.42
222_F264_M1.0190.42
741_A744_S1.0170.42
102_V116_M1.0160.42
115_A169_Y1.0130.41
193_D344_A1.0130.41
562_L566_G1.0120.41
789_I795_F1.0110.41
313_G339_Y1.0110.41
116_M213_S1.0110.41
393_A396_E1.0100.41
211_Q321_W1.0080.41
380_D383_L1.0060.41
187_A223_G1.0040.41
200_V310_V1.0040.41
198_F286_L1.0030.40
259_S322_S1.0030.40
467_A858_R1.0030.40
816_W830_S1.0020.40
86_H128_T1.0020.40
350_V366_L1.0020.40
810_Y841_L1.0020.40
297_P321_W1.0010.40
191_I210_A1.0000.40
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  
2vsqA10.57641000.547Contact Map
4dg8A10.5321000.576Contact Map
4iz6A20.56451000.604Contact Map
1amuA20.54391000.61Contact Map
4d4iA101000.61Contact Map
3tsyA10.45181000.619Contact Map
4r0mB20.56451000.619Contact Map
3g7sA20.50811000.621Contact Map
4gr5A40.44421000.625Contact Map
3wvnA20.40951000.626Contact 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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