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Fan Yang

ID: 1501039344 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 960 (748)
Sequences: 1387 (918.2)
Seq/Len: 1.854
Nf(neff/√len): 33.6

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: 1.854).

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 > 50% 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
321_R326_E3.4071.00
566_K576_F3.2721.00
425_E428_K3.1151.00
709_Q731_N2.9161.00
573_E577_E2.8421.00
568_E583_K2.6591.00
412_F416_M2.5641.00
736_R739_A2.4551.00
625_C630_C2.4501.00
734_E741_K2.3831.00
330_L756_D2.1920.99
561_A565_T2.1810.99
654_E658_P2.1780.99
455_R458_Y2.1770.99
318_D437_R2.1680.99
714_T717_V2.1220.99
730_N734_E2.0880.99
654_E734_E2.0830.99
734_E738_D2.0640.99
338_Y342_L2.0270.99
305_W315_Q2.0190.99
731_N734_E1.9660.99
738_D741_K1.9520.98
317_I333_A1.9160.98
561_A564_L1.8770.98
705_E734_E1.8420.98
315_Q336_G1.8380.98
338_Y709_Q1.8300.97
480_K489_A1.8190.97
421_A425_E1.7950.97
305_W316_P1.7860.97
630_C633_E1.7800.97
348_V415_F1.7450.96
161_P164_V1.7420.96
593_Y711_G1.7390.96
639_S643_L1.7200.96
140_L158_I1.7200.96
452_D574_K1.7180.96
651_N654_E1.6960.95
327_K338_Y1.6920.95
699_L702_E1.6850.95
730_N739_A1.6840.95
382_C386_C1.6840.95
468_R471_S1.6670.95
709_Q727_A1.6650.95
406_N409_T1.6220.94
720_F723_A1.6060.93
574_K578_E1.5980.93
316_P336_G1.5870.93
702_E705_E1.5730.92
873_N876_M1.5580.92
557_Y565_T1.5550.92
731_N738_D1.5540.92
642_M646_Q1.5490.92
316_P323_Y1.5260.91
621_R624_E1.5250.91
654_E705_E1.5200.91
331_Y338_Y1.5170.91
598_Y603_K1.5170.91
730_N741_K1.5160.91
754_A758_G1.4960.90
633_E638_L1.4950.90
434_L438_W1.4940.90
587_L591_N1.4810.89
176_M245_T1.4800.89
707_I764_L1.4760.89
642_M645_K1.4740.89
608_G613_Y1.4710.89
343_I728_L1.4600.88
772_V775_N1.4580.88
652_L657_I1.4560.88
315_Q320_V1.4530.88
164_V168_E1.4490.88
301_L316_P1.4420.87
492_T567_I1.4410.87
603_K633_E1.4400.87
379_C382_C1.4390.87
421_A424_M1.4380.87
709_Q730_N1.4370.87
335_L339_T1.4330.87
569_V576_F1.4320.87
730_N736_R1.4290.87
562_R566_K1.4290.87
279_A282_P1.4230.86
890_P893_I1.4210.86
339_T731_N1.4140.86
646_Q654_E1.4120.86
562_R576_F1.4040.85
565_T576_F1.4000.85
489_A567_I1.3900.85
899_K903_L1.3860.84
613_Y621_R1.3800.84
663_F667_L1.3790.84
904_M907_L1.3740.84
737_L756_D1.3730.84
748_R757_I1.3710.84
332_F335_L1.3700.84
709_Q722_L1.3680.83
841_Y856_D1.3630.83
717_V724_P1.3580.83
242_D245_T1.3530.82
883_D888_D1.3440.82
646_Q658_P1.3410.82
327_K336_G1.3390.82
595_P598_Y1.3390.82
860_V863_A1.3370.81
337_A426_H1.3350.81
247_S751_A1.3270.81
574_K756_D1.3270.81
570_P579_R1.3240.81
708_I716_F1.3230.80
316_P320_V1.3200.80
331_Y335_L1.3190.80
168_E249_I1.3150.80
641_I645_K1.3140.80
542_A547_L1.3130.80
571_K588_K1.3130.80
333_A434_L1.3110.80
644_G647_L1.3080.79
630_C634_L1.3070.79
646_Q650_N1.3040.79
660_M664_I1.3020.79
405_D409_T1.3020.79
730_N738_D1.2990.79
642_M727_A1.2950.78
378_M389_W1.2860.78
843_E854_S1.2860.78
251_Y255_K1.2850.78
726_F730_N1.2830.78
867_F871_F1.2790.77
690_D693_L1.2720.77
729_L733_I1.2710.77
563_W567_I1.2700.77
304_E319_L1.2670.76
327_K577_E1.2660.76
588_K595_P1.2640.76
543_V547_L1.2620.76
433_R892_D1.2570.76
589_F597_F1.2570.76
550_I557_Y1.2520.75
543_V546_N1.2520.75
336_G339_T1.2480.75
709_Q738_D1.2460.75
711_G736_R1.2440.74
534_I538_V1.2440.74
323_Y331_Y1.2420.74
643_L646_Q1.2400.74
423_F427_W1.2370.74
572_T583_K1.2370.74
879_S883_D1.2360.74
637_Q646_Q1.2340.74
724_P736_R1.2330.74
717_V743_V1.2320.73
702_E706_M1.2310.73
331_Y342_L1.2260.73
637_Q641_I1.2260.73
415_F419_W1.2260.73
578_E756_D1.2240.73
452_D457_E1.2210.73
588_K712_F1.2200.72
335_L338_Y1.2190.72
328_V335_L1.2180.72
588_K598_Y1.2160.72
565_T579_R1.2130.72
341_M426_H1.2130.72
425_E561_A1.2080.71
654_E741_K1.2050.71
332_F342_L1.2030.71
625_C629_G1.2020.71
720_F734_E1.1990.71
584_A599_V1.1980.70
595_P637_Q1.1970.70
771_A775_N1.1960.70
806_N809_L1.1940.70
776_A783_S1.1910.70
727_A731_N1.1880.70
334_W706_M1.1870.69
807_H841_Y1.1870.69
331_Y738_D1.1870.69
572_T575_S1.1840.69
540_A544_I1.1840.69
633_E641_I1.1830.69
723_A739_A1.1810.69
369_M398_A1.1800.69
698_G702_E1.1800.69
345_A415_F1.1800.69
455_R460_A1.1790.69
397_T400_A1.1790.69
709_Q734_E1.1780.69
813_N835_I1.1770.69
593_Y603_K1.1770.69
741_K758_G1.1750.68
470_E473_N1.1740.68
577_E581_T1.1690.68
284_H305_W1.1680.68
600_A634_L1.1680.68
709_Q716_F1.1670.68
452_D455_R1.1650.67
905_V908_F1.1640.67
357_C360_V1.1630.67
727_A741_K1.1590.67
748_R758_G1.1560.66
713_V739_A1.1550.66
844_P847_S1.1540.66
664_I667_L1.1540.66
435_N440_L1.1530.66
429_R438_W1.1520.66
538_V544_I1.1510.66
281_Y287_D1.1480.66
583_K587_L1.1480.66
638_L642_M1.1480.66
236_D239_S1.1470.66
720_F731_N1.1450.65
170_E174_L1.1410.65
132_E142_L1.1400.65
754_A757_I1.1370.65
579_R583_K1.1360.65
367_M371_D1.1350.64
712_F719_S1.1340.64
160_A164_V1.1330.64
565_T581_T1.1290.64
366_S369_M1.1280.64
720_F726_F1.1270.64
370_C386_C1.1220.63
381_L398_A1.1220.63
698_G701_P1.1190.63
134_N140_L1.1180.63
339_T713_V1.1180.63
820_G823_P1.1150.62
597_F600_A1.1150.62
568_E571_K1.1100.62
633_E644_G1.1060.61
325_G329_G1.1060.61
542_A546_N1.1050.61
731_N741_K1.1040.61
421_A428_K1.1030.61
425_E429_R1.1030.61
722_L725_L1.1000.61
381_L394_A1.0990.61
143_E157_K1.0980.61
630_C641_I1.0970.61
812_F817_F1.0950.60
599_V603_K1.0940.60
396_A399_R1.0930.60
571_K583_K1.0920.60
795_Y856_D1.0910.60
379_C386_C1.0880.60
377_T390_K1.0880.60
736_R748_R1.0850.59
638_L641_I1.0850.59
589_F595_P1.0850.59
654_E730_N1.0850.59
766_G770_L1.0840.59
552_L556_V1.0790.59
587_L601_F1.0780.59
162_W234_L1.0770.58
690_D696_F1.0760.58
272_L285_D1.0750.58
727_A730_N1.0750.58
640_I643_L1.0740.58
143_E159_H1.0720.58
571_K575_S1.0710.58
348_V411_F1.0700.58
912_E915_K1.0700.58
634_L637_Q1.0700.58
435_N441_T1.0690.58
315_Q739_A1.0690.58
271_L276_V1.0670.57
588_K599_V1.0660.57
556_V560_I1.0660.57
710_F730_N1.0660.57
508_V553_L1.0650.57
332_F338_Y1.0650.57
232_F240_F1.0650.57
386_C395_C1.0630.57
630_C645_K1.0630.57
571_K591_N1.0630.57
170_E179_K1.0620.57
786_I790_V1.0620.57
306_A315_Q1.0600.57
367_M372_Q1.0600.57
132_E277_Y1.0590.56
170_E232_F1.0590.56
717_V730_N1.0570.56
895_Q907_L1.0570.56
613_Y623_E1.0560.56
430_K434_L1.0540.56
880_D883_D1.0540.56
887_P890_P1.0530.56
651_N655_I1.0530.56
705_E738_D1.0530.56
713_V726_F1.0510.56
637_Q645_K1.0510.56
784_D804_F1.0510.56
715_L719_S1.0510.56
283_L305_W1.0500.56
578_E593_Y1.0500.56
301_L305_W1.0480.55
811_S835_I1.0480.55
140_L143_E1.0480.55
651_N705_E1.0480.55
710_F714_T1.0460.55
300_L304_E1.0460.55
602_F606_F1.0450.55
554_D591_N1.0440.55
713_V727_A1.0430.55
606_F617_F1.0420.55
323_Y334_W1.0410.55
421_A886_I1.0390.54
687_Y690_D1.0380.54
588_K603_K1.0370.54
818_Q822_A1.0370.54
343_I422_T1.0360.54
747_R770_L1.0360.54
573_E740_K1.0350.54
218_K221_S1.0340.54
423_F428_K1.0330.54
512_I515_R1.0310.53
715_L767_V1.0300.53
711_G716_F1.0300.53
714_T718_A1.0290.53
376_I390_K1.0280.53
652_L656_G1.0280.53
716_F721_P1.0250.53
155_F159_H1.0240.53
807_H856_D1.0230.53
410_V458_Y1.0220.52
420_A719_S1.0210.52
717_V737_L1.0200.52
325_G331_Y1.0190.52
718_A735_I1.0190.52
629_G642_M1.0190.52
379_C395_C1.0170.52
587_L595_P1.0170.52
719_S734_E1.0150.52
865_L869_I1.0140.52
321_R329_G1.0140.52
721_P731_N1.0140.52
546_N557_Y1.0130.51
172_L175_K1.0130.51
162_W166_C1.0120.51
372_Q392_S1.0120.51
811_S855_K1.0110.51
599_V710_F1.0110.51
716_F720_F1.0110.51
515_R546_N1.0100.51
906_E912_E1.0070.51
706_M730_N1.0070.51
252_E256_R1.0070.51
873_N879_S1.0070.51
591_N600_A1.0060.51
899_K902_V1.0050.51
370_C379_C1.0050.51
586_L704_M1.0020.50
391_M395_C1.0020.50
424_M428_K1.0020.50
904_M908_F1.0010.50
301_L315_Q1.0010.50
727_A739_A1.0010.50
325_G332_F1.0000.50
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  
4wisA20.64581000.46Contact Map
3wu2I20.038529.90.988Contact Map
4y3uB10.03124.30.992Contact Map
1n7lA10.055240.992Contact Map
4dixA20.07540.992Contact Map
2rhqB10.09273.90.992Contact Map
4b1qP10.02813.80.992Contact Map
1repC10.057330.993Contact Map
2baiA10.033330.993Contact Map
3cmqA10.09792.90.993Contact 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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