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lads

ID: 1425375820 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 795 (773)
Sequences: 943 (800.3)
Seq/Len: 1.220
Nf(neff/√len): 28.8

Jackhmmer Results: (2015_01_07)
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: 1.220).

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
38_E73_S3.2931.00
576_D580_G2.9061.00
108_L155_L2.8251.00
398_L402_S2.8001.00
717_L729_T2.7361.00
549_F595_Q2.7251.00
550_T577_T2.7181.00
398_L401_S2.5301.00
409_N412_L2.5161.00
576_D634_G2.4911.00
695_R712_P2.4140.99
534_K537_Q2.3590.99
492_F530_G2.3050.99
618_V623_G2.2780.99
627_H637_F2.2200.99
420_D481_Q2.2090.99
394_R398_L2.2070.99
391_K395_A2.1810.98
674_E680_Q2.1800.98
391_K394_R2.1490.98
730_C764_M2.0700.98
629_S632_G2.0670.98
555_V559_V2.0620.98
615_R619_E2.0460.97
590_Y625_L2.0340.97
549_F604_Y2.0260.97
538_A617_L1.9980.97
626_T638_L1.9950.97
429_E432_T1.9940.97
669_T693_R1.9820.97
597_D602_R1.9720.97
265_R278_D1.9620.96
395_A398_L1.9490.96
572_V639_L1.9390.96
545_N576_D1.9380.96
530_G621_L1.9180.96
550_T553_G1.9060.96
618_V639_L1.9030.96
716_L745_L1.8960.95
630_R633_Q1.8860.95
394_R402_S1.8620.95
580_G634_G1.8560.95
746_A764_M1.8170.94
580_G608_G1.7940.93
545_N608_G1.7840.93
759_C764_M1.7820.93
746_A759_C1.7660.93
586_G627_H1.7520.92
537_Q613_L1.7450.92
576_D635_S1.7430.92
476_A534_K1.7430.92
680_Q696_T1.7340.92
408_L412_L1.7310.92
673_V729_T1.7150.91
545_N606_G1.7110.91
441_L460_A1.7070.91
545_N580_G1.6960.91
479_E607_L1.6860.90
717_L746_A1.6610.89
580_G629_S1.6500.89
473_D534_K1.6240.88
720_Q750_H1.6170.88
170_W175_Y1.6150.88
675_D721_M1.6140.87
700_G724_M1.6140.87
74_V156_R1.6110.87
764_M784_W1.5990.87
750_H759_C1.5850.86
673_V703_A1.5740.86
487_P621_L1.5740.86
717_L730_C1.5740.86
674_E696_T1.5610.85
416_N419_K1.5560.85
133_P142_E1.5470.84
697_A706_L1.5420.84
438_I464_A1.5340.84
609_I613_L1.5330.84
402_S405_L1.5260.83
394_R401_S1.5120.82
678_I682_V1.5110.82
701_S723_V1.4980.82
37_F49_I1.4940.81
718_D770_K1.4890.81
670_V692_Y1.4890.81
79_L153_V1.4770.80
46_I154_Y1.4740.80
675_D718_D1.4730.80
595_Q605_G1.4720.80
110_L153_V1.4700.80
576_D629_S1.4680.80
675_D770_K1.4670.80
377_G380_S1.4650.80
629_S635_S1.4640.80
669_T712_P1.4620.79
575_I636_R1.4580.79
427_T432_T1.4570.79
524_L570_L1.4570.79
184_Y187_G1.4560.79
580_G635_S1.4440.78
409_N413_A1.4430.78
46_I49_I1.4380.78
412_L416_N1.4280.77
329_G333_A1.4270.77
582_D585_A1.4200.77
541_Y610_G1.4190.76
139_Y142_E1.4150.76
578_G634_G1.4150.76
395_A401_S1.4110.76
669_T695_R1.4080.76
430_L470_M1.4020.75
619_E624_E1.3970.75
545_N610_G1.3960.75
38_E75_F1.3950.75
111_P117_Y1.3910.74
45_D48_D1.3890.74
444_M453_L1.3880.74
590_Y611_L1.3870.74
720_Q764_M1.3830.74
776_E780_L1.3760.73
538_A639_L1.3740.73
46_I50_T1.3740.73
129_F132_R1.3740.73
581_F585_A1.3730.73
74_V77_L1.3630.72
104_D125_D1.3620.72
679_N749_A1.3560.72
432_T467_M1.3560.72
555_V561_A1.3530.72
721_M724_M1.3490.71
37_F40_V1.3480.71
204_F213_L1.3470.71
562_G571_R1.3460.71
590_Y627_H1.3440.71
699_N702_E1.3420.71
107_D120_A1.3410.71
618_V625_L1.3390.70
428_H606_G1.3380.70
449_M453_L1.3310.70
412_L466_D1.3290.70
493_S496_G1.3280.69
734_R765_S1.3280.69
550_T634_G1.3220.69
595_Q604_Y1.3190.69
675_D722_P1.3180.69
674_E699_N1.3120.68
423_L613_L1.3110.68
745_L784_W1.3090.68
379_L382_A1.3080.68
595_Q614_C1.3070.68
428_H541_Y1.3060.68
352_L357_Y1.3050.68
432_T592_R1.3040.67
695_R706_L1.3010.67
576_D608_G1.2970.67
427_T467_M1.2950.67
107_D156_R1.2930.67
719_C746_A1.2890.66
726_G770_K1.2870.66
98_L103_L1.2870.66
528_L644_T1.2870.66
599_S605_G1.2840.66
425_T595_Q1.2780.65
460_A467_M1.2780.65
466_D621_L1.2700.64
487_P534_K1.2680.64
378_L382_A1.2650.64
405_L409_N1.2650.64
721_M770_K1.2640.64
437_V464_A1.2560.63
665_P690_L1.2540.63
233_G238_W1.2520.63
108_L141_F1.2470.62
123_T141_F1.2460.62
431_R472_N1.2460.62
698_D702_E1.2440.62
378_L381_L1.2420.62
395_A402_S1.2410.62
700_G721_M1.2350.61
537_Q609_I1.2340.61
538_A618_V1.2220.60
430_L550_T1.2210.60
364_T371_G1.2210.60
748_T763_G1.2210.60
679_N734_R1.2200.60
590_Y608_G1.2190.60
514_L547_I1.2180.60
74_V158_E1.2140.59
541_Y614_C1.2130.59
428_H433_P1.2130.59
415_S418_L1.2130.59
699_N723_V1.2110.59
475_L609_I1.2090.59
550_T576_D1.2070.59
422_F427_T1.2030.58
548_K595_Q1.2020.58
668_C692_Y1.2010.58
580_G593_F1.2010.58
363_L366_Y1.2010.58
424_A430_L1.2000.58
766_D780_L1.2000.58
81_L153_V1.1970.58
547_I785_L1.1960.58
704_L707_L1.1960.58
553_G577_T1.1920.57
42_G74_V1.1910.57
325_A332_V1.1910.57
560_A575_I1.1890.57
380_S383_L1.1890.57
539_L572_V1.1890.57
428_H608_G1.1890.57
525_P613_L1.1890.57
105_K158_E1.1880.57
428_H749_A1.1770.56
707_L729_T1.1760.56
447_V453_L1.1760.56
582_D631_P1.1750.56
734_R742_L1.1730.55
541_Y609_I1.1730.55
125_D129_F1.1730.55
378_L384_A1.1710.55
676_N683_T1.1700.55
39_D42_G1.1660.55
78_R152_R1.1640.55
672_V683_T1.1630.54
440_S483_G1.1620.54
361_M364_T1.1610.54
557_L561_A1.1580.54
548_K576_D1.1550.54
719_C759_C1.1550.54
391_K398_L1.1550.54
606_G610_G1.1530.53
450_D453_L1.1480.53
490_E532_A1.1480.53
704_L729_T1.1440.53
432_T439_G1.1420.52
708_A736_L1.1420.52
419_K531_D1.1410.52
376_V382_A1.1400.52
599_S604_Y1.1400.52
558_R575_I1.1370.52
401_S405_L1.1340.52
729_T746_A1.1320.51
538_A615_R1.1320.51
724_M729_T1.1280.51
678_I730_C1.1260.51
124_G127_L1.1250.51
430_L474_I1.1240.51
590_Y593_F1.1240.51
730_C744_V1.1220.50
375_E380_S1.1190.50
502_R516_F1.1160.50
348_I539_L1.1160.50
103_L106_L1.1140.50
443_L456_Y1.1130.50
580_G590_Y1.1120.49
52_R57_S1.1100.49
468_M621_L1.1090.49
545_N629_S1.1090.49
665_P692_Y1.1080.49
375_E379_L1.1070.49
443_L621_L1.1060.49
576_D590_Y1.1020.48
750_H764_M1.0980.48
730_C783_D1.0950.48
200_N212_Y1.0930.48
479_E541_Y1.0930.48
673_V699_N1.0910.47
139_Y144_G1.0910.47
730_C762_A1.0880.47
531_D550_T1.0880.47
545_N548_K1.0870.47
541_Y608_G1.0870.47
746_A750_H1.0860.47
487_P537_Q1.0840.47
550_T580_G1.0820.47
49_I58_F1.0770.46
700_G726_G1.0770.46
388_N391_K1.0760.46
596_A599_S1.0750.46
293_L543_V1.0740.46
760_L766_D1.0730.46
412_L420_D1.0720.46
668_C785_L1.0710.45
548_K580_G1.0700.45
742_L780_L1.0700.45
428_H431_R1.0700.45
600_L605_G1.0690.45
38_E42_G1.0660.45
548_K610_G1.0660.45
432_T436_G1.0660.45
371_G380_S1.0640.45
719_C764_M1.0630.45
197_L220_A1.0620.45
323_I327_L1.0610.44
425_T602_R1.0610.44
716_L729_T1.0570.44
439_G443_L1.0570.44
436_G440_S1.0550.44
505_Y547_I1.0550.44
716_L784_W1.0540.44
680_Q698_D1.0540.44
545_N609_I1.0540.44
578_G635_S1.0530.44
573_E638_L1.0520.44
474_I477_L1.0500.43
780_L783_D1.0500.43
576_D611_L1.0470.43
679_N682_V1.0470.43
623_G642_Q1.0470.43
570_L643_L1.0460.43
402_S406_E1.0440.43
66_L73_S1.0440.43
35_D78_R1.0430.43
369_Q382_A1.0420.43
436_G463_S1.0400.42
376_V381_L1.0390.42
270_T278_D1.0380.42
727_F759_C1.0370.42
679_N746_A1.0370.42
608_G634_G1.0360.42
475_L606_G1.0360.42
541_Y606_G1.0350.42
683_T747_L1.0340.42
679_N764_M1.0340.42
556_T559_V1.0330.42
422_F531_D1.0310.42
25_V28_L1.0310.42
667_E693_R1.0300.41
764_M780_L1.0270.41
597_D604_Y1.0270.41
428_H432_T1.0270.41
721_M749_A1.0270.41
704_L742_L1.0270.41
371_G375_E1.0260.41
590_Y637_F1.0250.41
123_T139_Y1.0240.41
579_I604_Y1.0240.41
39_D156_R1.0230.41
774_F778_Q1.0230.41
599_S602_R1.0220.41
546_A576_D1.0220.41
487_P531_D1.0210.41
544_D549_F1.0210.41
576_D606_G1.0210.41
690_L764_M1.0200.41
671_L697_A1.0200.41
109_Y122_R1.0190.40
366_Y371_G1.0190.40
731_R762_A1.0190.40
686_M774_F1.0180.40
549_F579_I1.0180.40
730_C746_A1.0170.40
545_N634_G1.0170.40
619_E639_L1.0170.40
504_Q537_Q1.0170.40
674_E729_T1.0170.40
439_G463_S1.0160.40
98_L108_L1.0160.40
430_L467_M1.0150.40
721_M726_G1.0150.40
576_D632_G1.0150.40
746_A784_W1.0150.40
571_R640_R1.0130.40
759_C784_W1.0120.40
592_R612_A1.0120.40
437_V460_A1.0120.40
425_T429_E1.0110.40
101_P132_R1.0100.40
723_V729_T1.0100.40
675_D679_N1.0090.40
388_N394_R1.0090.40
578_G629_S1.0090.40
538_A621_L1.0090.40
437_V456_Y1.0080.39
428_H545_N1.0070.39
36_V68_A1.0070.39
371_G384_A1.0070.39
720_Q759_C1.0050.39
703_A731_R1.0050.39
707_L737_P1.0010.39
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: (31Jan15)
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  
3a0rA10.41511000.712Contact Map
4i5sA20.36861000.734Contact Map
4q20A20.29061000.753Contact Map
4e01A10.35971000.754Contact Map
2c2aA10.29561000.754Contact Map
4mpcA10.40251000.754Contact Map
3jz3A20.20251000.754Contact Map
4gczA20.44281000.758Contact Map
4bixA20.28811000.76Contact Map
2e0aA20.39871000.768Contact 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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