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BI 110-785

ID: 1445201741 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 676 (648)
Sequences: 1103 (609)
Seq/Len: 1.702
Nf(neff/√len): 23.9

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: 1.702).

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_S3.1261.00
542_I606_A3.0801.00
97_A134_I2.8791.00
572_G595_P2.7301.00
517_E550_R2.5181.00
148_Y152_G2.4731.00
204_L208_L2.4511.00
405_T435_A2.4301.00
333_S337_D2.4131.00
484_S544_G2.3291.00
542_I561_A2.2540.99
517_E557_A2.2290.99
82_G91_S2.2200.99
604_L624_A2.1850.99
521_R534_F2.1590.99
542_I546_V2.1560.99
32_N394_T2.1350.99
604_L623_A2.1240.99
449_F512_A2.1130.99
74_Y117_A2.0630.99
574_G595_P2.0580.99
550_R555_C2.0570.99
517_E555_C2.0300.99
342_I361_A2.0210.99
566_L619_P2.0060.99
112_G117_A1.9940.98
80_D91_S1.9630.98
285_L451_S1.9620.98
298_W302_P1.9550.98
559_R562_C1.8980.98
439_L486_T1.8790.98
654_Y657_Y1.8720.97
122_R126_L1.8600.97
13_N670_S1.8240.97
480_V516_L1.8220.97
542_I558_I1.7620.96
563_H567_S1.7610.96
575_W623_A1.7520.96
50_A295_L1.7440.96
487_M490_L1.7440.96
484_S488_E1.7190.95
96_S125_I1.7040.95
520_Q524_G1.7020.95
284_C289_N1.6890.95
386_H437_N1.6690.94
369_Q388_G1.6680.94
556_V560_K1.6600.94
657_Y665_A1.6520.94
190_G266_M1.6410.93
515_F519_M1.6280.93
538_G561_A1.6270.93
329_G652_I1.6190.93
620_L624_A1.6150.93
494_K506_D1.6070.92
221_S226_A1.5930.92
576_G581_S1.5930.92
561_A606_A1.5920.92
91_S124_W1.5750.91
74_Y108_E1.5700.91
644_G654_Y1.5680.91
483_T512_A1.5510.91
444_N478_S1.5420.90
123_S127_E1.5390.90
83_W103_L1.5210.89
405_T442_L1.5190.89
550_R557_A1.5150.89
401_I449_F1.5080.89
24_S357_T1.5070.89
631_Q635_G1.5050.89
620_L623_A1.5030.89
195_G198_T1.5010.89
347_S668_E1.4970.88
566_L612_Q1.4950.88
626_L630_S1.4940.88
575_W603_V1.4930.88
285_L289_N1.4930.88
38_G485_A1.4890.88
130_G133_A1.4880.88
16_L663_I1.4850.88
532_V579_Y1.4740.87
487_M509_L1.4700.87
159_E265_A1.4590.87
241_L246_Y1.4570.87
104_R118_M1.4520.86
328_Q649_N1.4410.86
608_I672_R1.4310.85
146_G194_V1.4290.85
480_V521_R1.4200.85
124_W128_R1.4140.84
188_L299_V1.4110.84
570_L595_P1.4090.84
35_S333_S1.4080.84
562_C612_Q1.3970.83
108_E112_G1.3940.83
599_N643_M1.3870.83
335_L365_V1.3840.82
537_A582_C1.3840.82
654_Y662_P1.3790.82
24_S355_G1.3750.82
78_N84_G1.3720.82
93_M125_I1.3660.81
289_N452_Y1.3650.81
657_Y661_F1.3640.81
20_L345_I1.3590.81
98_L515_F1.3570.81
134_I138_G1.3560.81
341_S660_I1.3560.81
438_V442_L1.3540.81
218_W222_R1.3510.80
181_V288_V1.3500.80
654_Y665_A1.3460.80
375_P379_N1.3430.80
603_V623_A1.3410.80
519_M527_Y1.3340.79
276_E279_N1.3310.79
385_I441_S1.3280.79
604_L620_L1.3270.79
268_I271_E1.3270.79
654_Y661_F1.3270.79
53_V295_L1.3260.79
333_S643_M1.3190.78
70_C103_L1.3160.78
68_E71_R1.3120.78
548_A558_I1.3080.77
612_Q619_P1.3000.77
342_I411_A1.3000.77
366_K431_R1.2860.76
55_G196_P1.2860.76
636_D659_N1.2810.75
654_Y666_L1.2790.75
277_D310_H1.2780.75
170_H173_R1.2760.75
80_D124_W1.2760.75
630_S639_Q1.2750.75
644_G657_Y1.2740.75
312_Q315_P1.2730.74
267_K271_E1.2690.74
339_A345_I1.2650.74
15_T18_R1.2640.74
294_M314_I1.2630.74
291_V601_A1.2610.74
174_M182_Y1.2560.73
40_P135_T1.2490.72
402_S439_L1.2450.72
119_T123_S1.2420.72
33_W361_A1.2400.72
576_G606_A1.2380.72
267_K513_A1.2380.72
287_P467_A1.2350.71
101_V147_V1.2310.71
528_G536_Y1.2290.71
26_I35_S1.2290.71
342_I365_V1.2160.70
140_L156_L1.2150.69
36_D317_Y1.2140.69
34_A93_M1.2140.69
335_L368_S1.2040.68
448_G478_S1.1990.68
140_L185_M1.1970.68
87_I653_T1.1930.67
71_R75_N1.1920.67
457_S478_S1.1890.67
566_L617_P1.1890.67
467_A473_I1.1880.67
601_A632_L1.1830.67
437_N499_G1.1780.66
480_V519_M1.1730.66
23_Y663_I1.1730.66
487_M544_G1.1720.65
12_V670_S1.1720.65
562_C610_A1.1670.65
277_D290_K1.1660.65
283_I399_W1.1660.65
600_T607_L1.1630.65
270_M297_C1.1610.64
347_S608_I1.1610.64
359_R363_H1.1610.64
286_G290_K1.1600.64
514_N518_N1.1560.64
148_Y209_Y1.1550.64
225_C242_W1.1540.64
598_V643_M1.1490.63
37_L477_Y1.1490.63
596_H599_N1.1470.63
337_D392_F1.1470.63
282_Y310_H1.1460.63
491_A608_I1.1430.63
143_S153_N1.1410.62
580_L583_Q1.1380.62
210_T610_A1.1370.62
392_F531_G1.1370.62
202_L225_C1.1360.62
345_I572_G1.1360.62
455_T475_I1.1330.62
235_P241_L1.1330.62
523_D568_K1.1310.61
80_D84_G1.1310.61
139_K148_Y1.1300.61
71_R209_Y1.1250.61
480_V515_F1.1240.61
532_V644_G1.1140.60
457_S461_L1.1130.60
161_W183_L1.1120.59
662_P666_L1.1110.59
178_C182_Y1.1090.59
69_M512_A1.1090.59
347_S664_W1.1050.59
40_P648_K1.1050.59
97_A142_L1.1010.58
37_L287_P1.0970.58
40_P98_L1.0950.58
23_Y341_S1.0950.58
281_R396_D1.0900.57
97_A208_L1.0880.57
314_I353_T1.0880.57
400_L476_D1.0850.57
113_G119_T1.0840.57
397_H401_I1.0830.56
180_M185_M1.0800.56
436_V490_L1.0800.56
611_G620_L1.0800.56
177_H183_L1.0800.56
468_E473_I1.0790.56
370_I391_P1.0780.56
437_N500_H1.0760.56
451_S476_D1.0740.55
661_F665_A1.0740.55
97_A125_I1.0740.55
518_N560_K1.0710.55
270_M274_H1.0700.55
40_P329_G1.0690.55
580_L584_N1.0690.55
140_L292_L1.0680.55
37_L467_A1.0640.54
578_S587_Y1.0610.54
619_P623_A1.0600.54
653_T663_I1.0590.54
467_A470_F1.0590.54
177_H452_Y1.0560.54
176_C399_W1.0530.53
162_L208_L1.0510.53
618_A621_H1.0500.53
594_R641_E1.0490.53
449_F486_T1.0490.53
56_V102_A1.0490.53
108_E117_A1.0480.53
521_R529_C1.0460.53
101_V145_L1.0450.52
12_V16_L1.0440.52
600_T603_V1.0430.52
30_D394_T1.0430.52
339_A537_A1.0430.52
645_V651_M1.0420.52
111_N122_R1.0410.52
192_R622_R1.0410.52
339_A365_V1.0400.52
608_I623_A1.0400.52
274_H277_D1.0400.52
490_L549_G1.0390.52
178_C181_V1.0370.52
531_G654_Y1.0370.52
219_N461_L1.0360.51
544_G663_I1.0340.51
624_A669_Y1.0330.51
538_G603_V1.0330.51
38_G655_A1.0290.51
511_K623_A1.0280.51
548_A557_A1.0280.51
503_K511_K1.0280.51
36_D326_R1.0270.50
389_A400_L1.0240.50
290_K294_M1.0240.50
68_E325_M1.0220.50
338_T532_V1.0220.50
143_S271_E1.0180.50
503_K560_K1.0180.50
522_T633_E1.0180.50
283_I317_Y1.0170.49
455_T477_Y1.0170.49
409_L489_A1.0150.49
665_A669_Y1.0150.49
111_N518_N1.0150.49
276_E282_Y1.0140.49
147_V292_L1.0140.49
192_R268_I1.0140.49
138_G234_H1.0130.49
392_F448_G1.0130.49
520_Q523_D1.0130.49
23_Y565_L1.0130.49
465_N473_I1.0110.49
485_A599_N1.0110.49
621_H669_Y1.0090.49
262_R266_M1.0080.48
187_Y293_N1.0080.48
16_L26_I1.0060.48
469_T473_I1.0040.48
159_E164_P1.0040.48
218_W660_I1.0030.48
122_R207_E1.0020.48
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  
1w6kA10.97491000.238Contact Map
2sqcA20.91421000.333Contact Map
5bp8A101000.74Contact Map
1r76A10.42751000.764Contact Map
3q7aB10.46151000.816Contact Map
1gxmA20.36981000.822Contact Map
1n4qB60.39051000.836Contact Map
1hzfA10.36691000.84Contact Map
3draB10.38311000.841Contact Map
3dssB10.44531000.842Contact 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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