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OPENSEQ.org

BI 110-785

ID: 1445303360 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 676 (669)
Sequences: 1351 (786)
Seq/Len: 2.019
Nf(neff/√len): 30.4

Jackhmmer Results: (2015_08)
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: 2.019).

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
542_I606_A3.5781.00
446_N478_S3.1151.00
97_A134_I2.7921.00
572_G595_P2.6901.00
32_N394_T2.6421.00
437_N500_H2.5941.00
517_E557_A2.3841.00
405_T435_A2.3471.00
566_L619_P2.2841.00
517_E550_R2.2571.00
449_F512_A2.2201.00
626_L630_S2.2091.00
554_N557_A2.1751.00
517_E554_N2.1591.00
96_S125_I2.1550.99
82_G91_S2.1500.99
342_I361_A2.1450.99
148_Y152_G2.1440.99
74_Y117_A2.1410.99
542_I546_V2.1390.99
604_L624_A2.1360.99
484_S544_G2.1060.99
542_I561_A2.1010.99
80_D91_S2.0970.99
570_L589_N2.0670.99
480_V516_L2.0340.99
449_F508_A2.0050.99
13_N670_S1.9670.99
329_G652_I1.9560.99
521_R534_F1.9450.99
386_H437_N1.9430.99
91_S124_W1.9270.99
333_S337_D1.9120.99
122_R126_L1.8800.98
604_L623_A1.8600.98
563_H567_S1.8540.98
385_I441_S1.8310.98
24_S357_T1.8270.98
300_E304_S1.8250.98
74_Y108_E1.7560.97
608_I672_R1.7440.97
599_N643_M1.7030.96
112_G117_A1.6890.96
277_D283_I1.6860.96
243_G246_Y1.6690.96
409_L489_A1.6590.96
36_D326_R1.6550.95
123_S127_E1.6540.95
574_G595_P1.6470.95
190_G266_M1.6410.95
267_K271_E1.6350.95
366_K431_R1.5960.94
487_M509_L1.5940.94
604_L627_L1.5770.94
480_V521_R1.5770.94
282_Y286_G1.5750.94
270_M274_H1.5710.93
542_I558_I1.5700.93
276_E284_C1.5500.93
16_L663_I1.5490.93
104_R118_M1.5450.93
550_R554_N1.5420.93
532_V579_Y1.5420.93
439_L486_T1.5410.93
566_L617_P1.5370.92
175_W473_I1.5350.92
204_L208_L1.5290.92
387_K434_D1.5290.92
124_W128_R1.5210.92
50_A295_L1.5180.92
559_R612_Q1.5110.92
234_H239_D1.5030.91
188_L299_V1.5030.91
285_L451_S1.4940.91
402_S439_L1.4920.91
561_A606_A1.4900.91
101_V147_V1.4840.91
140_L185_M1.4770.90
347_S668_E1.4710.90
373_D378_P1.4680.90
294_M310_H1.4680.90
514_N518_N1.4580.90
575_W623_A1.4580.90
657_Y665_A1.4550.89
584_N588_T1.4470.89
556_V560_K1.4420.89
532_V644_G1.4360.89
108_E112_G1.4340.89
246_Y249_Y1.4270.88
146_G194_V1.4230.88
271_E275_Y1.4170.88
538_G561_A1.4150.88
382_F441_S1.4140.88
535_T568_K1.4110.87
139_K148_Y1.4060.87
295_L299_V1.3890.86
429_K433_C1.3840.86
562_C612_Q1.3780.86
277_D310_H1.3760.86
276_E279_N1.3750.86
370_I391_P1.3750.86
30_D394_T1.3730.85
347_S664_W1.3720.85
632_L638_P1.3690.85
487_M544_G1.3670.85
483_T512_A1.3660.85
369_Q388_G1.3660.85
318_L327_M1.3620.85
119_T123_S1.3560.85
181_V289_N1.3530.84
570_L593_N1.3520.84
494_K506_D1.3500.84
93_M125_I1.3480.84
282_Y288_V1.3470.84
130_G133_A1.3350.83
284_C289_N1.3330.83
603_V623_A1.3310.83
444_N478_S1.3310.83
35_S333_S1.3300.83
563_H566_L1.3270.83
546_V558_I1.3210.82
536_Y657_Y1.3210.82
274_H297_C1.3130.82
286_G327_M1.3110.82
27_Q31_G1.3070.81
47_L327_M1.3050.81
535_T565_L1.3040.81
68_E320_L1.3030.81
550_R557_A1.3000.81
316_D332_G1.3000.81
170_H173_R1.3000.81
598_V643_M1.2980.81
290_K294_M1.2940.81
294_M299_V1.2920.80
570_L595_P1.2890.80
617_P620_L1.2820.80
277_D282_Y1.2650.78
559_R562_C1.2640.78
171_P183_L1.2580.78
68_E71_R1.2560.78
269_A296_C1.2550.78
449_F486_T1.2540.78
274_H278_E1.2540.78
278_E281_R1.2520.77
414_M492_L1.2500.77
339_A365_V1.2460.77
562_C610_A1.2440.77
559_R622_R1.2430.77
80_D124_W1.2380.76
347_S608_I1.2370.76
515_F519_M1.2360.76
551_T554_N1.2350.76
342_I411_A1.2330.76
631_Q635_G1.2330.76
273_I296_C1.2290.76
570_L576_G1.2280.75
580_L583_Q1.2270.75
64_H67_Q1.2260.75
278_E282_Y1.2190.75
276_E282_Y1.2170.75
245_I249_Y1.2170.75
575_W603_V1.2150.74
291_V294_M1.2120.74
221_S224_T1.2100.74
654_Y657_Y1.2080.74
278_E286_G1.2060.74
28_T34_A1.2060.74
342_I365_V1.1980.73
23_Y341_S1.1970.73
644_G654_Y1.1970.73
24_S355_G1.1950.73
359_R363_H1.1950.73
312_Q315_P1.1940.73
282_Y290_K1.1870.72
480_V519_M1.1860.72
234_H238_Q1.1860.72
621_H625_R1.1840.72
608_I623_A1.1840.72
350_L355_G1.1830.72
605_M608_I1.1820.71
281_R286_G1.1810.71
272_H288_V1.1810.71
277_D286_G1.1790.71
445_E455_T1.1780.71
630_S640_Q1.1780.71
12_V16_L1.1760.71
26_I35_S1.1760.71
272_H276_E1.1760.71
480_V515_F1.1750.71
165_Y170_H1.1750.71
612_Q619_P1.1730.71
494_K509_L1.1720.71
97_A125_I1.1700.70
15_T18_R1.1680.70
281_R396_D1.1660.70
108_E117_A1.1650.70
272_H277_D1.1630.70
12_V670_S1.1620.70
272_H286_G1.1620.70
276_E286_G1.1600.69
329_G473_I1.1580.69
268_I271_E1.1570.69
284_C288_V1.1570.69
625_R629_N1.1560.69
37_L43_L1.1560.69
101_V145_L1.1550.69
339_A408_G1.1550.69
384_H441_S1.1540.69
312_Q316_D1.1540.69
286_G290_K1.1530.69
362_H415_L1.1500.68
263_E267_K1.1480.68
175_W647_N1.1480.68
436_V490_L1.1470.68
161_W269_A1.1460.68
523_D568_K1.1440.68
176_C285_L1.1430.68
645_V651_M1.1420.68
473_I647_N1.1410.68
348_T549_G1.1400.67
484_S488_E1.1390.67
501_R504_E1.1380.67
589_N593_N1.1380.67
48_V522_T1.1380.67
464_I583_Q1.1370.67
212_P215_E1.1360.67
402_S486_T1.1350.67
578_S587_Y1.1320.67
604_L608_I1.1320.67
438_V442_L1.1310.67
576_G581_S1.1290.66
38_G655_A1.1270.66
502_T506_D1.1260.66
210_T610_A1.1240.66
618_A621_H1.1240.66
70_C106_L1.1230.66
620_L623_A1.1230.66
180_M285_L1.1220.66
143_S153_N1.1220.66
71_R75_N1.1180.65
40_P135_T1.1180.65
382_F454_L1.1170.65
93_M128_R1.1140.65
617_P621_H1.1110.65
266_M270_M1.1080.64
576_G589_N1.1080.64
70_C103_L1.1060.64
385_I437_N1.1050.64
636_D658_R1.1000.63
205_R208_L1.1000.63
37_L46_G1.0970.63
40_P98_L1.0910.63
636_D659_N1.0910.63
55_G61_L1.0900.62
141_W287_P1.0900.62
15_T464_I1.0900.62
276_E288_V1.0870.62
642_I651_M1.0860.62
162_L339_A1.0860.62
12_V628_I1.0860.62
122_R207_E1.0850.62
624_A669_Y1.0850.62
52_Y200_M1.0850.62
278_E284_C1.0830.62
283_I310_H1.0820.62
36_D330_Y1.0790.61
601_A632_L1.0770.61
274_H281_R1.0760.61
181_V646_F1.0750.61
159_E265_A1.0750.61
274_H277_D1.0740.61
277_D281_R1.0730.61
238_Q243_G1.0730.61
41_M99_N1.0730.61
15_T628_I1.0720.60
335_L365_V1.0710.60
273_I282_Y1.0710.60
41_M76_H1.0700.60
78_N84_G1.0690.60
402_S450_A1.0680.60
280_S286_G1.0670.60
553_N622_R1.0660.60
98_L135_T1.0640.60
389_A400_L1.0620.59
68_E325_M1.0620.59
377_D396_D1.0620.59
37_L330_Y1.0600.59
97_A131_A1.0600.59
413_L667_G1.0590.59
69_M512_A1.0580.59
352_D560_K1.0580.59
43_L46_G1.0530.58
296_C299_V1.0510.58
119_T122_R1.0450.58
534_F588_T1.0450.58
353_T356_S1.0440.57
400_L476_D1.0440.57
519_M527_Y1.0410.57
38_G485_A1.0410.57
442_L456_R1.0410.57
190_G262_R1.0410.57
62_S65_H1.0400.57
288_V293_N1.0400.57
237_M571_P1.0390.57
290_K293_N1.0380.57
287_P329_G1.0370.57
335_L368_S1.0350.56
109_D112_G1.0330.56
283_I317_Y1.0330.56
116_G119_T1.0290.56
580_L584_N1.0290.56
55_G196_P1.0260.55
277_D284_C1.0260.55
83_W103_L1.0240.55
450_A486_T1.0210.55
638_P658_R1.0200.55
453_E456_R1.0190.55
657_Y661_F1.0180.55
566_L612_Q1.0180.55
135_T649_N1.0180.55
340_F660_I1.0180.55
96_S669_Y1.0170.54
537_A582_C1.0170.54
385_I438_V1.0140.54
345_I599_N1.0130.54
73_I561_A1.0130.54
291_V297_C1.0130.54
140_L292_L1.0110.54
294_M297_C1.0110.54
273_I283_I1.0100.54
339_A345_I1.0090.54
292_L296_C1.0090.54
116_G120_K1.0060.53
167_L170_H1.0050.53
347_S667_G1.0050.53
576_G606_A1.0040.53
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  
1w6kA10.97491000.278Contact Map
2sqcA20.91721000.349Contact Map
5bp8A101000.757Contact Map
1r76A10.4291000.775Contact Map
3q7aB10.46151000.823Contact Map
1gxmA20.36981000.832Contact Map
1n4qB60.38461000.848Contact Map
3draB10.38761000.849Contact Map
1hzfA10.36981000.85Contact Map
3dssB10.44231000.856Contact 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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