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OPENSEQ.org

bla

ID: 1486730333 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 642 (601)
Sequences: 1111 (654.4)
Seq/Len: 1.849
Nf(neff/√len): 26.7

HHblits Results: (2016_02)
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: 1.849).

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
79_R103_E2.5561.00
46_V72_L2.3251.00
59_I83_I2.2911.00
91_L95_V2.2661.00
123_F126_L2.1310.99
335_I357_F2.1190.99
455_K478_Q2.1180.99
389_N415_N2.0570.99
435_L454_V1.9880.99
535_C563_C1.9640.99
410_L432_L1.9590.99
112_L131_N1.9130.98
131_N531_N1.9120.98
86_N110_N1.8910.98
96_F151_L1.8390.98
110_N507_N1.8030.97
59_I62_N1.7950.97
103_E124_K1.7910.97
38_R41_A1.7900.97
408_Q433_L1.7870.97
432_L435_L1.7650.97
224_E487_L1.7650.97
105_L123_F1.7380.96
55_T79_R1.7160.96
38_R54_T1.7030.96
357_F381_L1.6700.95
62_N110_N1.6540.95
91_L487_L1.6430.94
91_L523_I1.6390.94
478_Q500_S1.6270.94
387_Q413_S1.6240.94
537_C584_C1.6070.93
36_V54_T1.5860.93
47_P51_P1.5780.93
67_L95_V1.5770.93
142_F145_M1.5670.92
412_I415_N1.5650.92
105_L126_L1.5630.92
99_N102_L1.5530.92
342_D364_N1.5520.92
43_L47_P1.5520.92
340_V384_L1.5520.92
432_L454_V1.5470.92
47_P531_N1.5390.91
453_K476_A1.5090.90
46_V59_I1.4890.89
96_F584_C1.4880.89
404_M533_F1.4830.89
86_N462_N1.4750.89
66_E91_L1.4740.89
78_L480_L1.4630.88
460_H481_N1.4600.88
76_P442_L1.4500.88
482_I504_I1.4460.88
96_F120_T1.4280.87
148_L151_L1.4170.86
88_I110_N1.4080.86
145_M480_L1.4050.85
70_S160_K1.4040.85
483_A503_I1.3890.85
153_L386_L1.3870.84
78_L102_L1.3820.84
255_N258_L1.3810.84
36_V41_A1.3680.83
457_L474_L1.3670.83
563_C584_C1.3650.83
176_L199_L1.3560.83
436_N458_D1.3540.82
86_N507_N1.3540.82
426_C429_T1.3520.82
537_C542_F1.3520.82
529_G556_G1.3420.82
378_L384_L1.3380.81
407_L432_L1.3340.81
88_I550_S1.3280.81
415_N507_N1.3210.80
71_D112_L1.3200.80
72_L447_F1.3160.80
531_N537_C1.3160.80
404_M410_L1.3140.80
62_N86_N1.3040.79
477_L480_L1.3030.79
57_L341_S1.3020.79
294_L299_F1.3020.79
467_I495_S1.3000.79
369_D574_L1.3000.79
128_L131_N1.2980.79
384_L410_L1.2970.79
487_L530_N1.2960.78
321_F324_S1.2900.78
110_N131_N1.2890.78
231_V566_P1.2890.78
85_H109_H1.2720.77
507_N531_N1.2670.76
504_I532_P1.2630.76
110_N129_S1.2570.75
285_I288_V1.2390.74
292_G324_S1.2360.74
381_L384_L1.2340.74
67_L576_D1.2330.73
58_D192_Q1.2320.73
280_I285_I1.2280.73
363_S483_A1.2280.73
354_T357_F1.2270.73
122_N380_K1.2260.73
81_L123_F1.2220.73
595_A600_L1.2190.72
38_R47_P1.2170.72
102_L105_L1.2130.72
362_F386_L1.2120.72
401_T404_M1.2060.71
220_A367_L1.2010.71
542_F561_Y1.1990.70
306_L314_V1.1980.70
48_Q501_V1.1980.70
603_S609_L1.1940.70
86_N102_L1.1940.70
531_N542_F1.1790.69
99_N454_V1.1780.69
72_L443_T1.1770.68
490_L519_S1.1700.68
410_L435_L1.1690.68
213_L280_I1.1650.67
194_F480_L1.1620.67
160_K434_I1.1610.67
528_A533_F1.1600.67
39_S368_T1.1570.67
340_V378_L1.1560.66
566_P571_G1.1550.66
384_L584_C1.1550.66
61_Q85_H1.1550.66
433_L455_K1.1550.66
503_I509_V1.1540.66
415_N462_N1.1530.66
509_V531_N1.1510.66
58_D82_I1.1500.66
526_I532_P1.1490.66
57_L485_N1.1490.66
476_A479_E1.1490.66
485_N507_N1.1480.66
50_L348_M1.1470.66
377_H442_L1.1460.65
521_H561_Y1.1440.65
280_I357_F1.1440.65
399_N454_V1.1430.65
60_S106_D1.1410.65
54_T78_L1.1390.65
384_L533_F1.1390.65
306_L309_L1.1390.65
47_P566_P1.1390.65
69_T91_L1.1370.65
83_I102_L1.1360.64
367_L442_L1.1290.64
65_A124_K1.1290.64
76_P115_V1.1290.64
69_T109_H1.1280.64
72_L377_H1.1280.64
191_L485_N1.1250.63
71_D566_P1.1250.63
107_L110_N1.1250.63
432_L438_S1.1240.63
46_V71_D1.1240.63
158_L379_I1.1230.63
487_L490_L1.1220.63
487_L574_L1.1220.63
485_N531_N1.1200.63
54_T75_L1.1180.63
513_S516_F1.1140.62
360_L490_L1.1110.62
412_I421_E1.1110.62
242_R245_S1.1090.62
142_F480_L1.1080.62
420_D442_L1.1060.61
110_N415_N1.1050.61
389_N394_L1.1050.61
159_Q162_S1.1050.61
345_M543_V1.1040.61
411_D414_Q1.1040.61
543_V574_L1.1030.61
64_I485_N1.1020.61
358_L530_N1.1020.61
59_I64_I1.0990.61
38_R401_T1.0970.60
453_K548_Q1.0970.60
477_L535_C1.0960.60
127_D364_N1.0960.60
615_W619_M1.0960.60
614_P622_Q1.0920.60
411_D458_D1.0910.60
361_D385_S1.0900.60
311_V314_V1.0890.60
62_N507_N1.0880.59
462_N485_N1.0870.59
627_R630_T1.0850.59
283_F335_I1.0840.59
387_Q400_M1.0830.59
59_I107_L1.0830.59
91_L202_I1.0820.59
41_A54_T1.0800.59
115_V118_H1.0800.59
122_N536_T1.0800.59
82_I543_V1.0790.59
601_T605_T1.0770.58
290_L366_L1.0760.58
147_Q506_H1.0760.58
360_L457_L1.0740.58
623_W627_R1.0730.58
461_N484_F1.0730.58
164_R309_L1.0680.57
401_T412_I1.0670.57
60_S411_D1.0660.57
610_Y617_L1.0660.57
620_L626_T1.0660.57
625_Q628_L1.0650.57
50_L536_T1.0640.57
53_R75_L1.0630.57
340_V357_F1.0630.57
105_L480_L1.0620.57
340_V482_I1.0610.57
204_P607_L1.0610.57
67_L96_F1.0610.57
131_N507_N1.0610.57
72_L387_Q1.0590.56
221_V412_I1.0590.56
67_L259_N1.0580.56
105_L110_N1.0540.56
49_D92_D1.0540.56
610_Y624_T1.0510.56
625_Q629_R1.0500.55
314_V335_I1.0500.55
608_C619_M1.0500.55
142_F418_R1.0490.55
623_W628_L1.0480.55
311_V316_S1.0460.55
339_T361_D1.0460.55
78_L110_N1.0440.55
57_L377_H1.0440.55
391_L492_G1.0440.55
153_L382_E1.0430.55
58_D62_N1.0420.55
389_N462_N1.0410.54
183_G435_L1.0410.54
68_Q98_F1.0400.54
334_N524_R1.0400.54
623_W626_T1.0400.54
592_T595_A1.0390.54
51_P284_S1.0380.54
608_C614_P1.0360.54
407_L410_L1.0360.54
459_L598_L1.0340.54
37_D508_S1.0330.54
99_N391_L1.0320.53
286_S436_N1.0320.53
601_T606_F1.0320.53
46_V225_L1.0300.53
47_P58_D1.0280.53
67_L106_D1.0280.53
597_M600_L1.0280.53
72_L83_I1.0270.53
483_A529_G1.0260.53
73_Q79_R1.0260.53
395_A502_L1.0250.53
470_D599_V1.0240.53
537_C563_C1.0240.53
484_F506_H1.0220.52
59_I510_F1.0220.52
106_D417_L1.0210.52
225_L396_Y1.0200.52
72_L499_L1.0200.52
364_N518_Q1.0200.52
412_I438_S1.0200.52
511_H538_E1.0190.52
54_T139_C1.0190.52
289_K292_G1.0190.52
616_Y619_M1.0190.52
154_S413_S1.0180.52
412_I417_L1.0180.52
217_V241_L1.0180.52
490_L570_K1.0180.52
220_A225_L1.0180.52
594_G597_M1.0170.52
120_T365_N1.0170.52
481_N503_I1.0150.52
56_T525_S1.0150.52
115_V362_F1.0150.52
46_V416_S1.0140.52
385_S446_V1.0140.52
605_T610_Y1.0140.52
64_I86_N1.0130.51
54_T57_L1.0120.51
155_A190_S1.0110.51
359_H385_S1.0110.51
607_L617_L1.0090.51
86_N129_S1.0080.51
608_C616_Y1.0080.51
341_S477_L1.0080.51
47_P361_D1.0080.51
595_A598_L1.0070.51
601_T604_V1.0050.51
112_L491_P1.0040.50
53_R140_N1.0040.50
43_L62_N1.0030.50
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  
3j0aA20.88631000.505Contact Map
1ziwA10.78191000.527Contact Map
2z7xB10.79441000.527Contact Map
2z81A10.82711000.536Contact Map
3vq2A20.79441000.547Contact Map
3t6qA20.82241000.548Contact Map
4g8aA20.82711000.55Contact Map
3a79B10.79911000.56Contact Map
3wn4A10.84741000.566Contact Map
3wpcA20.86921000.573Contact 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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