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OPENSEQ.org

BI 110-785

ID: 1445201223 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 676 (648)
Sequences: 1102 (610.7)
Seq/Len: 1.701
Nf(neff/√len): 24.0

HHblits Results: (2015_06)
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: 1.701).

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
446_N478_S3.1141.00
542_I606_A3.1061.00
97_A134_I2.8811.00
572_G595_P2.7561.00
517_E550_R2.5141.00
148_Y152_G2.4741.00
204_L208_L2.4641.00
405_T435_A2.4401.00
333_S337_D2.4141.00
484_S544_G2.3251.00
604_L623_A2.3001.00
521_R534_F2.2671.00
542_I561_A2.2480.99
604_L624_A2.2160.99
517_E557_A2.2110.99
82_G91_S2.2090.99
542_I546_V2.1690.99
32_N394_T2.1380.99
449_F512_A2.1040.99
574_G595_P2.0860.99
74_Y117_A2.0650.99
566_L619_P2.0220.99
285_L451_S2.0160.99
112_G117_A2.0130.99
517_E555_C1.9960.98
342_I361_A1.9820.98
550_R555_C1.9790.98
80_D91_S1.9490.98
13_N670_S1.9380.98
298_W302_P1.9330.98
439_L486_T1.9260.98
122_R126_L1.8770.97
654_Y657_Y1.8550.97
480_V516_L1.7840.96
484_S488_E1.7770.96
563_H567_S1.7690.96
542_I558_I1.7480.96
559_R562_C1.7310.95
575_W623_A1.7210.95
657_Y665_A1.7100.95
284_C289_N1.7100.95
520_Q524_G1.7080.95
50_A295_L1.7060.95
494_K506_D1.7040.95
96_S125_I1.7010.95
487_M490_L1.6910.95
515_F519_M1.6770.94
221_S226_A1.6700.94
369_Q388_G1.6650.94
620_L624_A1.6610.94
538_G561_A1.6600.94
386_H437_N1.6300.93
190_G266_M1.6220.93
329_G652_I1.6110.93
576_G581_S1.6000.92
620_L623_A1.5940.92
74_Y108_E1.5860.92
644_G654_Y1.5750.91
556_V560_K1.5740.91
561_A606_A1.5670.91
91_S124_W1.5610.91
24_S357_T1.5450.90
83_W103_L1.5420.90
444_N478_S1.5400.90
405_T442_L1.5290.90
550_R557_A1.5260.90
123_S127_E1.5200.89
566_L612_Q1.5190.89
631_Q635_G1.5180.89
195_G198_T1.5080.89
657_Y661_F1.4990.88
347_S668_E1.4970.88
38_G485_A1.4890.88
575_W603_V1.4880.88
130_G133_A1.4840.88
608_I672_R1.4810.88
285_L289_N1.4810.88
487_M509_L1.4770.87
483_T512_A1.4720.87
532_V579_Y1.4680.87
401_I449_F1.4670.87
626_L630_S1.4570.87
241_L246_Y1.4530.86
108_E112_G1.4460.86
159_E265_A1.4410.86
188_L299_V1.4340.85
146_G194_V1.4200.85
16_L663_I1.4180.84
328_Q649_N1.4160.84
35_S333_S1.4160.84
218_W222_R1.4010.83
104_R118_M1.4010.83
20_L345_I1.3960.83
335_L365_V1.3930.83
124_W128_R1.3860.83
480_V521_R1.3850.82
562_C612_Q1.3740.82
654_Y662_P1.3740.82
134_I138_G1.3740.82
98_L515_F1.3740.82
375_P379_N1.3730.82
24_S355_G1.3720.82
599_N643_M1.3700.82
33_W361_A1.3680.81
438_V442_L1.3670.81
93_M125_I1.3650.81
268_I271_E1.3650.81
78_N84_G1.3480.80
570_L595_P1.3480.80
181_V288_V1.3480.80
537_A582_C1.3470.80
604_L620_L1.3430.80
654_Y665_A1.3410.80
289_N452_Y1.3380.79
603_V623_A1.3310.79
385_I441_S1.3280.79
55_G196_P1.3250.78
333_S643_M1.3170.78
654_Y661_F1.3100.77
341_S660_I1.3090.77
70_C103_L1.2960.76
68_E71_R1.2940.76
342_I411_A1.2930.76
277_D310_H1.2820.75
276_E279_N1.2770.75
53_V295_L1.2770.75
366_K431_R1.2760.75
170_H173_R1.2760.75
612_Q619_P1.2760.75
548_A558_I1.2740.75
519_M527_Y1.2730.74
630_S639_Q1.2720.74
267_K271_E1.2700.74
339_A345_I1.2700.74
636_D659_N1.2690.74
644_G657_Y1.2660.74
654_Y666_L1.2630.74
26_I35_S1.2580.73
312_Q315_P1.2540.73
36_D317_Y1.2520.73
402_S439_L1.2510.73
267_K513_A1.2490.72
40_P135_T1.2470.72
174_M182_Y1.2460.72
294_M314_I1.2450.72
101_V147_V1.2430.72
287_P467_A1.2420.72
437_N499_G1.2390.72
15_T18_R1.2370.71
80_D124_W1.2330.71
514_N518_N1.2310.71
528_G536_Y1.2290.71
342_I365_V1.2250.70
87_I653_T1.2220.70
34_A93_M1.2150.69
576_G606_A1.2150.69
566_L617_P1.2140.69
448_G478_S1.2140.69
335_L368_S1.2030.68
23_Y663_I1.2030.68
71_R75_N1.2030.68
347_S608_I1.1980.68
140_L156_L1.1980.68
291_V601_A1.1890.67
467_A473_I1.1890.67
457_S478_S1.1840.67
282_Y310_H1.1840.67
119_T123_S1.1830.66
277_D290_K1.1820.66
96_S669_Y1.1790.66
487_M544_G1.1760.66
192_R622_R1.1670.65
140_L185_M1.1660.65
596_H599_N1.1660.65
283_I399_W1.1640.65
600_T607_L1.1610.64
225_C242_W1.1610.64
37_L477_Y1.1600.64
139_K148_Y1.1580.64
286_G290_K1.1570.64
148_Y209_Y1.1550.64
598_V643_M1.1530.64
12_V670_S1.1510.63
601_A632_L1.1490.63
143_S153_N1.1470.63
562_C610_A1.1470.63
337_D392_F1.1450.63
480_V519_M1.1430.63
69_M512_A1.1400.62
392_F531_G1.1380.62
235_P241_L1.1380.62
611_G620_L1.1350.62
202_L225_C1.1340.62
16_L26_I1.1310.61
480_V515_F1.1260.61
436_V490_L1.1240.61
455_T475_I1.1200.60
657_Y666_L1.1190.60
97_A142_L1.1180.60
71_R209_Y1.1170.60
347_S664_W1.1170.60
532_V644_G1.1150.60
619_P623_A1.1130.60
359_R363_H1.1110.59
178_C182_Y1.1080.59
80_D84_G1.1070.59
457_S461_L1.1070.59
523_D568_K1.1050.59
548_A557_A1.1020.58
177_H183_L1.0960.58
370_I391_P1.0950.58
40_P98_L1.0950.58
580_L584_N1.0940.58
449_F486_T1.0940.58
161_W183_L1.0940.58
270_M274_H1.0930.57
314_I353_T1.0930.57
210_T610_A1.0910.57
281_R396_D1.0910.57
624_A669_Y1.0890.57
580_L583_Q1.0880.57
400_L476_D1.0870.57
467_A470_F1.0860.57
23_Y341_S1.0840.57
40_P648_K1.0830.56
97_A125_I1.0830.56
491_A608_I1.0820.56
37_L287_P1.0780.56
270_M297_C1.0750.56
665_A669_Y1.0730.55
140_L292_L1.0730.55
40_P329_G1.0690.55
397_H401_I1.0680.55
177_H452_Y1.0650.55
451_S476_D1.0640.54
653_T663_I1.0630.54
162_L208_L1.0630.54
180_M185_M1.0620.54
437_N500_H1.0610.54
97_A208_L1.0600.54
219_N461_L1.0560.54
409_L489_A1.0560.54
108_E117_A1.0550.53
23_Y565_L1.0530.53
490_L549_G1.0520.53
12_V16_L1.0510.53
111_N122_R1.0490.53
389_A400_L1.0490.53
274_H277_D1.0460.52
521_R525_S1.0450.52
37_L467_A1.0450.52
30_D394_T1.0430.52
176_C399_W1.0430.52
113_G119_T1.0430.52
345_I572_G1.0420.52
621_H669_Y1.0420.52
645_V651_M1.0420.52
101_V145_L1.0420.52
518_N560_K1.0410.52
618_A621_H1.0380.52
487_M548_A1.0380.52
192_R268_I1.0370.52
256_W261_L1.0360.51
38_G655_A1.0360.51
661_F665_A1.0350.51
544_G663_I1.0340.51
521_R529_C1.0340.51
218_W660_I1.0330.51
339_A537_A1.0330.51
531_G654_Y1.0290.51
56_V102_A1.0280.51
535_T565_L1.0270.50
339_A365_V1.0270.50
138_G234_H1.0270.50
455_T477_Y1.0260.50
538_G603_V1.0250.50
503_K511_K1.0250.50
578_S587_Y1.0220.50
36_D326_R1.0220.50
262_R266_M1.0200.50
70_C75_N1.0200.50
68_E325_M1.0190.50
36_D542_I1.0190.50
594_R641_E1.0180.49
467_A643_M1.0180.49
616_D621_H1.0170.49
503_K560_K1.0170.49
392_F448_G1.0160.49
181_V471_G1.0150.49
93_M128_R1.0140.49
485_A599_N1.0120.49
600_T603_V1.0120.49
363_H427_L1.0120.49
290_K294_M1.0110.49
468_E473_I1.0100.49
520_Q523_D1.0070.48
178_C181_V1.0060.48
469_T473_I1.0040.48
276_E282_Y1.0030.48
143_S271_E1.0020.48
159_E164_P1.0010.48
111_N518_N1.0010.48
662_P665_A1.0000.48
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  
1w6kA10.97491000.243Contact Map
2sqcA20.91421000.339Contact Map
5bp8A101000.741Contact Map
1r76A10.42751000.766Contact Map
3q7aB10.46151000.815Contact Map
1gxmA20.36831000.823Contact Map
1n4qB60.39051000.836Contact Map
1hzfA10.36691000.841Contact Map
3draB10.38311000.841Contact Map
3dssB10.44381000.843Contact 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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