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AgainwithJackhammer

ID: 1504717628 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 999 (969)
Sequences: 1543 (1321.6)
Seq/Len: 1.592
Nf(neff/√len): 42.5

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: 1.592).

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_V4.2181.00
76_R102_V3.1091.00
926_L962_L3.1091.00
62_V89_T2.9351.00
62_V93_G2.8691.00
119_Q169_Y2.8201.00
74_Q375_E2.7781.00
104_F113_R2.7161.00
366_L405_G2.6671.00
406_R414_E2.6401.00
779_F782_P2.6341.00
615_A618_L2.6301.00
74_Q163_L2.4341.00
71_C99_A2.4081.00
614_N618_L2.3331.00
929_V958_V2.3061.00
820_L827_N2.3000.99
204_D283_R2.2750.99
944_S947_K2.2710.99
442_H865_F2.2570.99
618_L626_Q2.2480.99
780_T783_T2.2310.99
666_A690_V2.2090.99
350_V413_I2.2030.99
33_Q37_N2.1790.99
363_T416_L2.1770.99
953_L962_L2.1590.99
618_L623_S2.1580.99
31_V56_V2.1520.99
216_L258_N2.1450.99
351_L367_Y2.1200.99
64_N155_I2.0960.99
93_G97_A2.0700.99
56_V154_P2.0590.99
258_N288_S2.0470.99
205_R230_A2.0460.99
951_D956_A2.0410.99
820_L831_L2.0360.98
951_D962_L2.0350.98
369_T398_L2.0340.98
258_N321_W2.0320.98
71_C97_A1.9770.98
162_D185_R1.9620.98
953_L956_A1.9480.98
33_Q36_A1.9460.98
347_G369_T1.9400.98
308_Q326_I1.9330.98
962_L966_L1.9220.98
210_A216_L1.8860.97
465_V862_L1.8830.97
932_E961_K1.8640.97
980_L983_Q1.8530.97
953_L988_P1.8490.97
951_D954_I1.8470.97
216_L321_W1.8360.97
90_A126_L1.8310.97
611_V614_N1.8250.96
73_A163_L1.8060.96
820_L825_D1.8040.96
618_L622_L1.7980.96
189_N345_N1.7960.96
953_L966_L1.7950.96
951_D966_L1.7910.96
183_S375_E1.7890.96
615_A619_L1.7760.96
186_A373_L1.7690.96
922_L998_R1.7660.95
352_D356_R1.7640.95
929_V962_L1.7580.95
167_I378_A1.7490.95
88_V221_I1.7340.95
813_H820_L1.7230.95
190_T219_Y1.7210.95
247_E251_E1.7200.95
262_A290_D1.7190.95
750_A754_L1.7150.94
679_V767_L1.7120.94
359_P362_V1.7090.94
783_T787_L1.7080.94
820_L830_S1.7030.94
258_N312_L1.6990.94
312_L321_W1.6920.94
76_R167_I1.6830.94
216_L259_S1.6810.94
318_A368_I1.6800.94
350_V405_G1.6800.94
60_F96_L1.6760.94
81_M126_L1.6720.93
186_A319_S1.6680.93
323_N348_F1.6590.93
50_M89_T1.6510.93
920_D998_R1.6480.93
441_K869_H1.6460.93
615_A623_S1.6300.92
614_N619_L1.6230.92
288_S321_W1.6220.92
666_A693_A1.6100.92
204_D256_V1.6060.91
209_L321_W1.6060.91
287_L292_I1.5990.91
219_Y258_N1.5980.91
71_C75_D1.5780.91
951_D981_L1.5770.90
365_E400_R1.5750.90
449_G893_I1.5740.90
930_W990_V1.5740.90
781_E787_L1.5700.90
966_L981_L1.5690.90
249_M281_A1.5680.90
204_D255_T1.5660.90
208_G231_L1.5650.90
56_V96_L1.5590.90
164_P375_E1.5550.90
778_V781_E1.5480.89
216_L260_V1.5430.89
700_E725_R1.5420.89
951_D988_P1.5390.89
926_L958_V1.5380.89
916_E942_T1.5330.89
108_Q116_M1.5310.89
210_A259_S1.5310.89
260_V288_S1.5300.89
260_V321_W1.5300.89
619_L623_S1.5250.88
953_L981_L1.5170.88
453_D456_S1.5160.88
355_M367_Y1.5130.88
830_S834_E1.5120.88
223_G258_N1.5080.88
87_Q212_L1.5040.88
623_S626_Q1.5010.87
102_V120_A1.5000.87
951_D955_M1.4950.87
223_G321_W1.4940.87
75_D99_A1.4930.87
436_E450_V1.4680.86
922_L966_L1.4650.86
963_R969_D1.4640.86
956_A962_L1.4580.85
260_V312_L1.4570.85
686_T690_V1.4550.85
53_E57_K1.4550.85
37_N40_R1.4510.85
615_A626_Q1.4500.85
224_P231_L1.4480.85
190_T320_I1.4470.85
771_I777_L1.4430.84
190_T258_N1.4400.84
209_L260_V1.4330.84
752_G755_E1.4330.84
464_V899_A1.4280.84
919_L941_R1.4270.84
614_N622_L1.4230.83
204_D229_G1.4140.83
258_N287_L1.4080.82
614_N617_K1.4060.82
778_V783_T1.4050.82
219_Y321_W1.4040.82
258_N263_L1.4030.82
615_A622_L1.4020.82
820_L832_P1.4010.82
820_L833_E1.3990.82
941_R990_V1.3990.82
190_T321_W1.3980.82
820_L829_L1.3970.82
780_T787_L1.3940.82
778_V787_L1.3910.81
846_F849_R1.3900.81
921_M924_E1.3890.81
824_G834_E1.3870.81
168_I320_I1.3840.81
681_A703_F1.3830.81
209_L259_S1.3740.80
380_D383_L1.3730.80
58_R86_H1.3690.80
210_A258_N1.3680.80
31_V96_L1.3670.80
959_A984_M1.3600.79
15_N345_N1.3600.79
81_M128_T1.3560.79
450_V463_G1.3560.79
363_T404_L1.3550.79
955_M981_L1.3540.79
619_L626_Q1.3540.79
882_V885_L1.3540.79
115_A169_Y1.3530.79
200_V229_G1.3490.78
216_L222_F1.3480.78
831_L834_E1.3460.78
956_A981_L1.3460.78
824_G831_L1.3440.78
90_A94_A1.3430.78
209_L258_N1.3430.78
41_P51_T1.3430.78
259_S321_W1.3430.78
780_T791_A1.3390.78
258_N320_I1.3370.78
216_L322_S1.3350.77
31_V59_A1.3330.77
258_N264_M1.3300.77
351_L398_L1.3290.77
208_G300_M1.3270.77
987_Y992_A1.3270.77
261_P296_L1.3270.77
208_G216_L1.3240.77
832_P835_N1.3210.76
425_I452_L1.3200.76
27_H159_A1.3180.76
641_V645_Y1.3180.76
210_A263_L1.3140.76
218_V222_F1.3120.76
482_F485_L1.3120.76
916_E941_R1.3110.76
618_L621_L1.3100.76
920_D924_E1.3050.75
781_E791_A1.3030.75
208_G321_W1.3020.75
325_H338_P1.3020.75
348_F366_L1.2970.75
17_T345_N1.2950.74
423_V432_L1.2940.74
391_H398_L1.2910.74
64_N151_Q1.2870.74
956_A966_L1.2850.74
989_T992_A1.2850.74
206_V216_L1.2840.74
258_N261_P1.2810.73
813_H831_L1.2750.73
208_G258_N1.2730.73
128_T131_I1.2720.73
466_E885_L1.2700.72
41_P49_H1.2690.72
79_I91_V1.2680.72
195_N219_Y1.2650.72
734_D766_R1.2550.71
209_L300_M1.2530.71
292_I297_P1.2520.71
194_I219_Y1.2510.71
946_Y950_A1.2480.70
825_D831_L1.2460.70
956_A968_E1.2450.70
783_T791_A1.2440.70
257_W321_W1.2440.70
432_L450_V1.2430.70
677_L745_F1.2420.70
259_S264_M1.2400.70
216_L287_L1.2390.70
940_G943_Q1.2390.70
367_Y398_L1.2380.70
216_L315_A1.2350.69
923_E941_R1.2350.69
752_G756_N1.2340.69
60_F64_N1.2340.69
116_M213_S1.2330.69
759_D763_S1.2330.69
641_V644_L1.2290.69
740_L770_L1.2270.69
191_I216_L1.2190.68
832_P839_S1.2170.68
962_L988_P1.2170.68
810_Y813_H1.2150.68
729_F739_G1.2150.68
764_M779_F1.2150.68
927_A990_V1.2150.68
778_V791_A1.2150.68
119_Q380_D1.2140.67
44_F252_H1.2110.67
216_L219_Y1.2060.67
58_R89_T1.2050.67
190_T210_A1.2050.67
258_N300_M1.2040.66
218_V320_I1.2020.66
239_Q260_V1.2010.66
391_H396_E1.1950.66
440_L447_A1.1940.66
190_T216_L1.1940.66
674_L695_E1.1930.65
194_I258_N1.1920.65
464_V901_W1.1920.65
292_I311_S1.1890.65
611_V618_L1.1870.65
454_S457_E1.1870.65
958_V984_M1.1860.65
208_G259_S1.1850.65
288_S319_S1.1840.65
258_N297_P1.1840.65
209_L263_L1.1830.65
162_D183_S1.1830.65
236_A239_Q1.1810.64
832_P837_K1.1810.64
190_T263_L1.1800.64
830_S837_K1.1800.64
704_T734_D1.1790.64
781_E784_V1.1760.64
349_R398_L1.1750.64
678_E701_Y1.1750.64
264_M321_W1.1750.64
180_V374_A1.1740.64
210_A312_L1.1740.64
611_V615_A1.1730.64
45_D85_A1.1730.64
168_I316_T1.1720.63
438_A866_L1.1720.63
930_W950_A1.1720.63
987_Y996_F1.1720.63
675_R700_E1.1710.63
211_Q258_N1.1690.63
829_L834_E1.1690.63
262_A291_W1.1680.63
682_G753_V1.1680.63
955_M986_N1.1640.63
232_V254_I1.1630.63
322_S368_I1.1610.62
408_T412_E1.1610.62
25_C28_E1.1590.62
207_L254_I1.1590.62
284_L310_V1.1580.62
9_A13_S1.1570.62
263_L321_W1.1570.62
65_K69_L1.1570.62
216_L312_L1.1560.62
75_D123_R1.1530.62
702_V745_F1.1520.61
209_L288_S1.1520.61
439_L463_G1.1500.61
747_V751_A1.1490.61
641_V650_M1.1480.61
315_A321_W1.1440.61
962_L968_E1.1420.60
210_A321_W1.1400.60
268_V307_V1.1370.60
811_L820_L1.1370.60
787_L791_A1.1370.60
966_L988_P1.1360.60
729_F734_D1.1330.60
261_P321_W1.1330.60
795_F799_E1.1310.59
24_Y32_K1.1300.59
687_T691_L1.1300.59
190_T319_S1.1280.59
942_T991_A1.1280.59
287_L321_W1.1270.59
181_V378_A1.1260.59
160_N163_L1.1250.59
8_I12_N1.1220.58
194_I210_A1.1220.58
193_D343_L1.1190.58
259_S263_L1.1190.58
183_S186_A1.1190.58
59_A96_L1.1180.58
208_G219_Y1.1180.58
927_A941_R1.1180.58
819_L830_S1.1170.58
108_Q213_S1.1150.58
258_N322_S1.1130.58
813_H819_L1.1130.58
962_L981_L1.1130.58
312_L318_A1.1130.58
919_L991_A1.1120.57
945_F950_A1.1090.57
216_L288_S1.1080.57
78_A122_V1.1070.57
264_M287_L1.1070.57
955_M987_Y1.1060.57
439_L448_A1.1050.57
288_S315_A1.1040.57
831_L837_K1.1040.57
619_L622_L1.1020.56
784_V787_L1.1020.56
675_R678_E1.1010.56
819_L823_E1.1000.56
190_T322_S1.1000.56
120_A169_Y1.1000.56
944_S988_P1.1000.56
190_T223_G1.0990.56
833_E837_K1.0950.56
640_H644_L1.0930.55
750_A753_V1.0930.55
963_R968_E1.0930.55
771_I775_G1.0930.55
41_P44_F1.0910.55
71_C77_V1.0900.55
223_G315_A1.0900.55
211_Q321_W1.0880.55
51_T54_E1.0880.55
820_L823_E1.0860.55
259_S312_L1.0860.55
962_L987_Y1.0850.55
220_D318_A1.0840.55
200_V256_V1.0840.55
955_M962_L1.0820.54
259_S287_L1.0800.54
702_V741_A1.0790.54
951_D968_E1.0790.54
956_A960_G1.0770.54
449_G452_L1.0760.54
56_V59_A1.0760.54
866_L875_L1.0730.53
194_I209_L1.0720.53
189_N320_I1.0720.53
554_I558_W1.0710.53
781_E785_E1.0710.53
210_A224_P1.0700.53
207_L234_P1.0700.53
297_P337_I1.0680.53
690_V701_Y1.0680.53
193_D197_R1.0670.53
193_D344_A1.0670.53
348_F368_I1.0670.53
209_L262_A1.0670.53
981_L988_P1.0660.53
982_R986_N1.0660.53
124_F140_Q1.0640.52
680_G705_D1.0640.52
67_K159_A1.0630.52
217_S262_A1.0620.52
240_T263_L1.0620.52
313_G339_Y1.0610.52
191_I210_A1.0600.52
258_N292_I1.0590.52
223_G288_S1.0590.52
732_D762_A1.0590.52
780_T784_V1.0580.52
700_E744_S1.0550.51
216_L223_G1.0540.51
820_L834_E1.0540.51
520_M523_A1.0520.51
830_S833_E1.0520.51
56_V60_F1.0520.51
383_L387_R1.0510.51
217_S258_N1.0490.51
219_Y260_V1.0490.51
813_H830_S1.0480.51
196_R344_A1.0480.51
257_W260_V1.0480.51
218_V321_W1.0470.51
191_I312_L1.0460.51
286_L312_L1.0460.51
915_E938_R1.0460.51
241_D244_H1.0460.51
637_K650_M1.0450.50
829_L832_P1.0440.50
832_P836_N1.0440.50
962_L997_I1.0440.50
224_P258_N1.0430.50
195_N223_G1.0400.50
318_A321_W1.0400.50
272_D299_I1.0400.50
957_Q961_K1.0390.50
834_E839_S1.0380.50
218_V258_N1.0380.50
223_G259_S1.0380.50
392_H396_E1.0370.50
691_L724_V1.0350.49
239_Q258_N1.0350.49
922_L997_I1.0340.49
783_T788_W1.0340.49
610_Y614_N1.0340.49
193_D260_V1.0330.49
322_S372_G1.0330.49
746_D749_L1.0330.49
393_A396_E1.0320.49
747_V750_A1.0310.49
926_L993_L1.0290.49
827_N831_L1.0290.49
955_M959_A1.0290.49
748_V767_L1.0290.49
814_E831_L1.0280.49
219_Y312_L1.0270.49
261_P264_M1.0270.49
288_S312_L1.0260.48
10_E14_V1.0260.48
208_G260_V1.0250.48
198_F286_L1.0250.48
817_M820_L1.0240.48
380_D386_E1.0230.48
193_D198_F1.0210.48
30_I34_A1.0180.48
193_D292_I1.0170.47
636_G658_M1.0170.47
81_M87_Q1.0160.47
209_L219_Y1.0160.47
300_M309_I1.0140.47
182_I319_S1.0140.47
440_L448_A1.0140.47
369_T373_L1.0140.47
681_A687_T1.0130.47
845_L849_R1.0130.47
259_S297_P1.0120.47
254_I259_S1.0110.47
222_F258_N1.0110.47
706_V728_V1.0100.47
813_H824_G1.0090.47
194_I259_S1.0080.47
467_A858_R1.0070.46
216_L263_L1.0060.46
241_D300_M1.0060.46
219_Y263_L1.0060.46
702_V727_G1.0060.46
232_V248_L1.0050.46
824_G830_S1.0040.46
268_V300_M1.0030.46
814_E820_L1.0030.46
955_M988_P1.0020.46
615_A621_L1.0010.46
21_L371_H1.0010.46
100_V164_P1.0010.46
193_D312_L1.0000.46
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  
2vsqA10.59461000.461Contact Map
4dg8A10.49151000.488Contact Map
4r0mB20.58761000.521Contact Map
4iz6A20.58261000.526Contact Map
4d4iA101000.577Contact Map
1amuA20.50251000.595Contact Map
3wvnA20.37541000.597Contact Map
3vnrA10.48951000.599Contact Map
3ni2A10.50151000.599Contact Map
3tsyA10.72471000.599Contact 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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