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Regain2

ID: 1504813607 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 927 (919)
Sequences: 1193 (993.3)
Seq/Len: 1.298
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: 1.298).

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
166_P183_V3.6681.00
816_H819_L3.5161.00
918_E921_L3.4831.00
811_S819_L3.4801.00
913_V918_E3.4621.00
811_S815_R3.4401.00
811_S816_H3.2181.00
811_S814_D3.0071.00
915_A918_E2.9641.00
815_R819_L2.8441.00
557_V560_W2.8131.00
731_F736_D2.7521.00
814_D819_L2.7191.00
78_R104_V2.7161.00
106_I115_R2.7121.00
913_V921_L2.7081.00
781_F784_P2.6831.00
76_Q377_Q2.6471.00
408_S416_E2.5521.00
811_S817_D2.5501.00
64_I91_A2.5361.00
64_I95_G2.5221.00
915_A921_L2.5101.00
73_C101_G2.4160.99
76_Q165_L2.3810.99
728_F734_D2.3030.99
728_F731_F2.2880.99
668_A692_V2.2760.99
810_S815_R2.2730.99
121_Q171_Y2.2210.99
444_H867_F2.2170.99
811_S822_L2.2160.99
557_V561_V2.2040.99
33_V58_V2.1650.99
206_D285_R2.1370.98
810_S817_D2.1290.98
914_I918_E2.1220.98
218_L260_D2.1110.98
352_V415_I2.1040.98
728_F736_D2.1010.98
371_T400_L2.1010.98
731_F734_D2.1010.98
368_L407_G2.0940.98
819_L822_L2.0920.98
809_E819_L2.0850.98
726_V736_D2.0750.98
726_V731_F2.0570.98
260_D290_S2.0370.98
35_Q39_T2.0340.98
260_D323_W2.0300.98
832_L835_Q2.0240.98
809_E816_H2.0230.98
815_R822_L2.0210.98
816_H822_L2.0160.97
815_R818_W2.0090.97
365_T418_L2.0050.97
73_C99_A1.9860.97
811_S821_Q1.9600.97
90_V223_I1.9590.97
831_L835_Q1.9550.97
918_E922_D1.9510.97
726_V733_V1.9450.97
207_K232_A1.9450.97
728_F733_V1.9450.97
831_L834_P1.9430.97
668_A695_A1.9330.97
811_S818_W1.9120.96
681_V769_L1.8780.96
35_Q38_A1.8750.96
815_R821_Q1.8650.95
353_L369_Y1.8630.95
726_V734_D1.8580.95
212_A218_L1.8540.95
731_F735_Q1.8540.95
726_V729_G1.8470.95
830_I835_Q1.8380.95
310_Q328_V1.8330.95
816_H821_Q1.8320.95
814_D822_L1.8290.95
752_A756_L1.8150.95
553_Y557_V1.8010.94
349_G371_T1.7990.94
814_D817_D1.7660.93
188_A321_A1.7640.93
732_D735_Q1.7560.93
264_A292_D1.7550.93
260_D314_L1.7390.93
467_V864_L1.7350.93
78_R169_I1.7350.93
725_H728_F1.7350.93
218_L323_W1.7290.92
916_A921_L1.7210.92
325_I350_F1.7120.92
726_V732_D1.7070.92
192_T221_Y1.6990.92
553_Y561_V1.6870.91
443_K871_H1.6870.91
191_N347_N1.6750.91
218_L261_S1.6670.91
728_F735_Q1.6620.90
225_G260_D1.6620.90
434_L452_V1.6540.90
560_W564_L1.6500.90
839_K845_F1.6470.90
916_A919_E1.6450.90
52_L91_A1.6430.90
726_V735_Q1.6420.90
75_E165_L1.6360.89
913_V922_D1.6320.89
809_E814_D1.6310.89
438_E452_V1.6260.89
185_S377_Q1.6230.89
352_V407_G1.6210.89
914_I921_L1.6130.89
188_A375_L1.6120.88
808_L811_S1.6070.88
810_S818_W1.6070.88
60_R88_D1.6060.88
221_Y260_D1.6030.88
320_A370_I1.6020.88
773_I779_L1.5980.88
169_I380_V1.5960.88
110_Q118_M1.5950.88
225_G323_W1.5940.88
210_G233_L1.5930.88
249_E253_A1.5900.88
561_V564_L1.5870.87
553_Y560_W1.5830.87
839_K844_G1.5790.87
728_F732_D1.5730.87
810_S819_L1.5720.87
218_L224_F1.5680.87
314_L323_W1.5610.86
829_P835_Q1.5590.86
830_I834_P1.5580.86
62_A98_F1.5560.86
354_D358_R1.5540.86
817_D822_L1.5510.86
73_C77_D1.5460.86
164_D187_R1.5450.85
810_S814_D1.5410.85
226_P233_L1.5400.85
556_L560_W1.5350.85
808_L815_R1.5340.85
206_D257_T1.5340.85
838_D845_F1.5320.85
455_D458_S1.5300.85
729_G736_D1.5180.84
809_E815_R1.5160.84
83_L128_L1.5120.84
211_L323_W1.5110.84
688_T692_V1.5030.83
260_D265_M1.5030.83
560_W563_R1.5000.83
361_P364_V1.4960.83
812_Y819_L1.4950.83
262_V290_S1.4930.83
212_A261_S1.4890.83
192_T260_D1.4840.82
814_D821_Q1.4820.82
742_L772_L1.4770.82
440_A868_L1.4760.82
166_P377_Q1.4730.82
732_D736_D1.4570.81
766_M781_F1.4540.80
357_M369_Y1.4510.80
192_T323_W1.4510.80
262_V323_W1.4470.80
290_S323_W1.4460.80
829_P832_L1.4440.80
95_G99_A1.4330.79
221_Y323_W1.4290.79
58_V156_L1.4230.78
468_E887_L1.4160.78
260_D289_L1.3910.76
261_S323_W1.3880.76
817_D821_Q1.3840.76
89_Q214_L1.3830.76
689_T693_L1.3730.75
81_I93_V1.3630.74
561_V568_G1.3620.74
915_A922_D1.3620.74
838_D844_G1.3610.74
553_Y556_L1.3590.74
39_T42_R1.3560.74
754_G757_E1.3560.74
451_G895_V1.3540.73
289_L294_I1.3490.73
840_L845_F1.3480.73
733_V736_D1.3470.73
218_L262_V1.3460.73
839_K843_L1.3450.73
731_F737_Y1.3430.73
192_T265_M1.3410.72
266_M323_W1.3380.72
729_G734_D1.3340.72
437_I440_A1.3320.72
840_L844_G1.3310.72
77_D101_G1.3270.71
676_L697_E1.3240.71
92_A96_T1.3240.71
264_A293_W1.3220.71
259_W323_W1.3200.71
560_W568_G1.3170.70
58_V98_F1.3170.70
19_T347_N1.3160.70
55_A59_R1.3150.70
212_A260_D1.3150.70
809_E822_L1.3130.70
195_D199_R1.3130.70
756_L784_P1.3120.70
844_G847_L1.3100.70
208_V218_L1.3080.70
17_N347_N1.3050.69
212_A265_M1.3050.69
829_P833_L1.3040.69
263_P298_L1.3010.69
66_G157_I1.3010.69
556_L561_V1.2980.69
260_D266_M1.2980.69
262_V314_L1.2910.68
218_L289_L1.2880.68
202_V231_G1.2880.68
33_V98_F1.2740.67
260_D263_P1.2720.67
43_P51_Q1.2640.66
827_G835_Q1.2630.66
913_V916_A1.2610.66
324_S374_G1.2530.65
197_N221_Y1.2520.65
484_F487_I1.2490.64
452_V465_A1.2480.64
425_V434_L1.2450.64
218_L314_L1.2440.64
702_E746_S1.2400.64
829_P834_P1.2370.63
677_R702_E1.2360.63
206_D258_V1.2340.63
210_G302_M1.2310.63
846_H849_A1.2300.63
286_L312_V1.2240.62
33_V61_A1.2230.62
192_T218_L1.2220.62
639_K715_G1.2210.62
557_V564_L1.2200.62
206_D231_G1.2190.62
192_T322_I1.2180.62
704_V743_S1.2180.62
211_L290_S1.2170.62
683_A705_F1.2160.61
210_G323_W1.2140.61
810_S822_L1.2140.61
564_L568_G1.2130.61
810_S816_H1.2130.61
211_L261_S1.2120.61
80_A124_I1.2110.61
218_L317_A1.2100.61
213_Q260_D1.2090.61
290_S314_L1.2040.60
554_H557_V1.2040.60
211_L262_V1.2030.60
220_V322_I1.2020.60
734_D737_Y1.2010.60
265_M323_W1.2000.60
704_V747_F1.1990.60
220_V224_F1.1980.60
663_L780_V1.1970.60
845_F849_A1.1970.60
220_V260_D1.1930.59
750_V773_I1.1920.59
211_L260_D1.1900.59
62_A66_G1.1890.59
196_I221_Y1.1880.59
77_D125_R1.1870.59
218_L221_Y1.1840.58
827_G830_I1.1840.58
206_D244_P1.1810.58
845_F850_K1.1800.58
845_F848_F1.1790.58
221_Y265_M1.1780.58
680_E703_Y1.1780.58
193_I218_L1.1750.57
789_L843_L1.1750.57
290_S321_A1.1740.57
238_P241_Q1.1720.57
553_Y558_R1.1710.57
550_L553_Y1.1700.57
724_P728_F1.1690.57
290_S317_A1.1660.57
799_M802_P1.1640.56
263_P323_W1.1630.56
29_H161_T1.1620.56
218_L290_S1.1610.56
26_Y34_A1.1610.56
58_V62_A1.1600.56
844_G850_K1.1590.56
288_M314_L1.1580.56
838_D843_L1.1570.56
844_G848_F1.1570.56
260_D324_S1.1560.56
838_D841_T1.1560.56
843_L846_H1.1540.55
261_S266_M1.1530.55
726_V730_V1.1530.55
365_T406_L1.1520.55
289_L323_W1.1510.55
294_I299_P1.1510.55
261_S314_L1.1500.55
917_S921_L1.1490.55
744_P771_E1.1460.55
43_P53_T1.1440.54
410_R414_E1.1440.54
809_E821_Q1.1410.54
218_L324_S1.1410.54
60_R91_A1.1410.54
260_D299_P1.1380.54
801_E805_E1.1380.54
725_H734_D1.1370.54
210_G260_D1.1360.54
220_V323_W1.1360.54
808_L817_D1.1360.54
725_H731_F1.1350.54
317_A323_W1.1340.53
724_P727_S1.1340.53
393_H400_L1.1300.53
327_H340_P1.1290.53
224_F260_D1.1270.53
260_D322_I1.1270.53
263_P266_M1.1270.53
27_A30_Q1.1270.53
104_V118_M1.1240.52
684_G755_V1.1240.52
208_V323_W1.1230.52
182_V376_A1.1210.52
260_D302_M1.1210.52
464_L882_Q1.1210.52
211_L265_M1.1180.52
830_I836_E1.1170.52
104_V122_A1.1170.52
198_R346_A1.1150.52
243_D302_M1.1140.51
839_K842_A1.1120.51
110_Q215_N1.1090.51
210_G261_S1.1080.51
92_A128_L1.1050.51
350_F368_L1.1040.50
192_T290_S1.1020.50
212_A314_L1.1000.50
192_T324_S1.0980.50
221_Y262_V1.0980.50
452_V463_L1.0970.50
812_Y818_W1.0970.50
83_L130_A1.0960.50
195_D314_L1.0960.50
728_F737_Y1.0950.50
196_I212_A1.0920.49
808_L819_L1.0910.49
225_G261_S1.0900.49
270_V302_M1.0890.49
196_I260_D1.0830.48
352_V368_L1.0820.48
466_I901_A1.0810.48
225_G258_V1.0810.48
832_L836_E1.0790.48
210_G218_L1.0780.48
67_K71_L1.0770.48
266_M289_L1.0730.47
46_I254_H1.0720.47
170_I322_I1.0720.47
915_A919_E1.0720.47
192_T212_A1.0720.47
812_Y816_H1.0710.47
211_L302_M1.0710.47
221_Y322_I1.0690.47
76_Q101_G1.0670.47
11_A15_K1.0670.47
58_V61_A1.0670.47
913_V917_S1.0640.46
234_V256_V1.0630.46
212_A262_V1.0610.46
31_P190_A1.0600.46
434_L876_M1.0590.46
455_D459_D1.0580.46
369_Y400_L1.0570.46
118_M215_N1.0560.46
218_L225_G1.0540.46
427_I454_L1.0540.46
558_R561_V1.0530.45
222_D320_A1.0530.45
47_D87_V1.0520.45
840_L846_H1.0510.45
196_I323_W1.0470.45
841_T845_F1.0460.45
189_A225_G1.0450.45
844_G849_A1.0430.44
456_E459_D1.0390.44
224_F323_W1.0380.44
117_A171_Y1.0360.44
299_P323_W1.0360.44
724_P731_F1.0350.44
353_L400_L1.0340.44
261_S265_M1.0340.44
483_E487_I1.0340.44
219_S260_D1.0340.44
209_L236_P1.0330.43
212_A323_W1.0330.43
294_I313_S1.0320.43
221_Y314_L1.0320.43
196_I218_L1.0300.43
224_F266_M1.0290.43
314_L320_A1.0280.43
193_I260_D1.0280.43
129_T133_S1.0270.43
839_K846_H1.0250.43
221_Y324_S1.0230.42
193_I212_A1.0230.42
213_Q323_W1.0220.42
193_I314_L1.0220.42
638_G660_M1.0200.42
212_A226_P1.0200.42
192_T196_I1.0160.42
28_L189_A1.0160.42
839_K847_L1.0150.42
191_N322_I1.0120.41
884_V887_L1.0110.41
729_G733_V1.0110.41
837_D843_L1.0110.41
320_A323_W1.0090.41
803_G807_R1.0070.41
225_G317_A1.0060.41
315_G341_Y1.0050.41
812_Y815_R1.0050.41
192_T225_G1.0050.41
211_L221_Y1.0040.41
202_V258_V1.0040.41
210_G221_Y1.0030.41
816_H820_A1.0030.41
197_N225_G1.0020.40
917_S922_D1.0010.40
261_S299_P1.0010.40
195_D200_F1.0000.40
66_G153_Q1.0000.40
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  
2vsqA10.57711000.555Contact Map
4dg8A10.52971000.583Contact Map
4iz6A20.5621000.608Contact Map
1amuA20.54151000.615Contact Map
4d4iA101000.617Contact Map
4r0mB20.56421000.626Contact Map
3tsyA10.45311000.627Contact Map
3g7sA20.50591000.627Contact Map
3wvnA20.40561000.629Contact Map
4gr5A40.44341000.629Contact 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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