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C-A

ID: 1504645611 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 889 (887)
Sequences: 13859 (11760)
Seq/Len: 15.625
Nf(neff/√len): 394.9

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: 15.625).

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
597_P614_V4.6791.00
799_L838_G3.7461.00
509_R535_V3.7251.00
507_Q596_L3.4141.00
264_A295_A3.3981.00
616_S808_E3.1911.00
507_Q808_E3.0941.00
537_F546_R3.0901.00
552_Q602_Y2.9961.00
302_R310_T2.7941.00
839_R847_E2.6871.00
784_L800_Y2.6621.00
638_R663_A2.6421.00
489_V529_L2.6411.00
493_F529_L2.5871.00
741_Q759_I2.5161.00
498_K502_L2.5141.00
796_T849_L2.5131.00
61_T71_L2.4711.00
783_V838_G2.4641.00
464_V489_V2.4481.00
511_A555_V2.4251.00
756_N781_F2.4131.00
466_Q470_N2.3821.00
237_A247_A2.3721.00
255_V417_L2.3371.00
486_E490_K2.3351.00
504_C532_A2.3291.00
813_D816_L2.3211.00
495_V522_T2.2981.00
616_S619_A2.2971.00
508_D556_R2.2951.00
208_R403_P2.2851.00
194_R314_Q2.2831.00
259_W413_A2.2741.00
802_T831_L2.2671.00
304_F421_L2.2631.00
619_A752_S2.2471.00
680_E684_E2.2451.00
466_Q469_A2.2121.00
49_N53_A2.1951.00
506_A596_L2.1741.00
240_R305_Q2.1381.00
404_D408_D2.1321.00
493_F497_N2.1261.00
504_C508_D2.1181.00
858_I885_L2.1081.00
781_F801_I2.1041.00
187_D321_H2.1041.00
489_V587_P2.0841.00
51_L153_L2.0831.00
253_A296_V2.0631.00
395_W407_I2.0531.00
508_D532_A2.0421.00
548_A609_Q2.0321.00
457_Y465_K2.0311.00
783_V846_I2.0291.00
376_P379_F2.0221.00
509_R600_I1.9911.00
342_A345_P1.9871.00
495_V526_G1.9861.00
841_T847_E1.9701.00
474_P482_H1.9681.00
54_R149_E1.9671.00
520_Q645_L1.9461.00
668_N671_R1.9371.00
470_N473_R1.9321.00
133_M138_A1.9271.00
45_Q49_N1.9261.00
600_I811_A1.9211.00
780_G824_H1.9061.00
637_D688_T1.8991.00
780_G802_T1.8731.00
264_A297_D1.8611.00
695_A723_D1.8531.00
597_P808_E1.8381.00
115_L137_I1.8281.00
856_V865_L1.8191.00
33_E126_N1.8171.00
492_A529_L1.8151.00
841_T845_E1.8131.00
266_C293_L1.8131.00
326_G330_M1.8091.00
436_L440_Q1.8041.00
395_W411_F1.8011.00
824_H829_E1.7931.00
622_N778_N1.7921.00
798_E833_R1.7891.00
51_L150_F1.7791.00
550_L555_V1.7711.00
489_V493_F1.7661.00
223_I393_V1.7651.00
796_T837_L1.7591.00
33_E36_Y1.7531.00
61_T113_W1.7501.00
785_D789_R1.7501.00
509_R533_V1.7371.00
512_I523_A1.7341.00
595_D616_S1.7241.00
483_M522_T1.7241.00
477_F663_A1.7231.00
595_D618_R1.7231.00
691_N754_W1.7211.00
233_F244_P1.7111.00
505_K508_D1.7081.00
665_V687_I1.7051.00
458_C461_E1.6941.00
629_R777_A1.6891.00
869_E883_V1.6881.00
638_R687_I1.6791.00
148_A283_D1.6751.00
873_L880_A1.6651.00
491_R519_H1.6581.00
472_D486_E1.6551.00
619_A806_L1.6471.00
303_S306_E1.6431.00
68_Q72_E1.6391.00
478_D518_A1.6381.00
758_H845_E1.6311.00
593_N596_L1.6241.00
305_Q426_Q1.6221.00
671_R677_H1.6111.00
637_D716_R1.6081.00
146_L285_V1.6061.00
477_F685_H1.5881.00
378_V381_D1.5881.00
745_L754_W1.5871.00
758_H771_P1.5861.00
674_D677_H1.5851.00
637_D662_G1.5841.00
326_G329_V1.5781.00
781_F799_L1.5781.00
44_T150_F1.5771.00
474_P663_A1.5671.00
432_D436_L1.5661.00
649_L691_N1.5651.00
188_K324_F1.5621.00
526_G530_A1.5621.00
48_W118_I1.5581.00
50_L53_A1.5521.00
465_K469_A1.5501.00
55_H149_E1.5431.00
464_V529_L1.5431.00
253_A267_L1.5371.00
652_Y754_W1.5351.00
221_R408_D1.5341.00
667_P681_L1.5331.00
643_A649_L1.5331.00
95_R98_D1.5321.00
250_T307_R1.5281.00
543_E547_Q1.5261.00
548_A602_Y1.5251.00
459_L620_A1.5241.00
489_V492_A1.5191.00
523_A559_L1.5181.00
35_D126_N1.5181.00
251_A418_L1.5171.00
547_Q551_E1.5031.00
638_R665_V1.5001.00
873_L881_A1.4981.00
541_Q549_M1.4981.00
246_T312_Q1.4981.00
512_I524_V1.4931.00
497_N588_I1.4931.00
561_T564_I1.4931.00
329_V333_M1.4911.00
109_D112_R1.4911.00
681_L685_H1.4891.00
519_H561_T1.4821.00
198_L266_C1.4781.00
219_Q399_E1.4771.00
665_V681_L1.4771.00
653_D691_N1.4731.00
504_C510_V1.4701.00
822_L831_L1.4661.00
462_Q621_A1.4651.00
788_M800_Y1.4571.00
719_L745_L1.4561.00
235_Q239_K1.4521.00
623_T754_W1.4521.00
781_F838_G1.4491.00
691_N694_P1.4451.00
377_Q380_I1.4431.00
483_M518_A1.4381.00
168_F171_Y1.4331.00
259_W410_M1.4321.00
189_E193_Q1.4321.00
628_N660_V1.4301.00
188_K192_Q1.4251.00
313_K317_E1.4251.00
257_E298_L1.4251.00
299_D302_R1.4241.00
521_V654_I1.4151.00
478_D481_G1.4121.00
669_A672_Q1.4111.00
328_E331_R1.4060.99
535_V553_A1.4030.99
190_Y318_D1.4010.99
514_M523_A1.4000.99
40_D43_R1.3990.99
474_P477_F1.3990.99
652_Y691_N1.3980.99
346_V349_T1.3960.99
297_D302_R1.3960.99
415_A419_H1.3940.99
691_N745_L1.3940.99
215_D218_F1.3880.99
28_C31_Y1.3870.99
460_H617_H1.3870.99
592_A596_L1.3780.99
68_Q71_L1.3780.99
523_A527_A1.3730.99
552_Q609_Q1.3730.99
613_V807_A1.3720.99
642_L693_V1.3670.99
552_Q813_D1.3660.99
229_A419_H1.3640.99
296_V311_I1.3640.99
816_L820_R1.3610.99
254_A307_R1.3580.99
384_A393_V1.3580.99
463_I467_A1.3580.99
871_A874_K1.3510.99
464_V492_A1.3490.99
408_D412_D1.3480.99
434_I440_Q1.3480.99
463_I525_L1.3470.99
185_V189_E1.3460.99
560_T564_I1.3430.99
615_I807_A1.3420.99
39_L127_T1.3380.99
623_T652_Y1.3360.99
457_Y461_E1.3340.99
171_Y174_A1.3330.99
219_Q404_D1.3300.99
541_Q646_S1.3300.99
424_T427_V1.3290.99
814_P818_Q1.3270.99
250_T311_I1.3270.99
207_T406_M1.3250.99
551_E609_Q1.3240.99
755_S801_I1.3230.99
409_D413_A1.3200.99
62_I137_I1.3170.99
26_V29_H1.3160.99
624_I659_S1.3140.99
252_Y346_V1.3140.99
187_D323_L1.3050.99
721_S754_W1.3040.99
776_L779_Q1.2950.99
640_L667_P1.2920.99
276_P280_Q1.2890.99
460_H592_A1.2890.99
476_V518_A1.2860.99
444_R447_V1.2820.99
345_P349_T1.2820.99
226_D229_A1.2790.99
41_H120_V1.2730.99
350_S354_L1.2680.99
188_K332_E1.2650.99
865_L883_V1.2620.99
251_A421_L1.2620.99
641_G666_Y1.2600.99
691_N721_S1.2590.99
327_V330_M1.2570.99
837_L852_E1.2570.99
50_L153_L1.2560.99
751_A801_I1.2550.99
479_S668_N1.2540.99
397_V407_I1.2530.99
56_D167_T1.2520.99
824_H831_L1.2490.99
800_Y833_R1.2430.98
244_P391_L1.2410.98
298_L302_R1.2410.98
69_R72_E1.2360.98
807_A821_F1.2360.98
44_T129_L1.2340.98
50_L157_S1.2270.98
717_L743_V1.2260.98
474_P484_T1.2240.98
349_T352_I1.2240.98
533_V597_P1.2230.98
634_N637_D1.2220.98
649_L754_W1.2220.98
31_Y36_Y1.2220.98
293_L329_V1.2200.98
232_T419_H1.2190.98
255_V414_F1.2180.98
640_L682_M1.2170.98
782_R824_H1.2170.98
325_S329_V1.2160.98
507_Q597_P1.2120.98
433_V437_P1.2120.98
234_K386_D1.2100.98
793_V840_Y1.2070.98
623_T753_I1.2060.98
437_P440_Q1.2060.98
82_T119_G1.2060.98
515_D561_T1.2030.98
477_F482_H1.2010.98
85_S122_K1.2000.98
476_V521_V1.1970.98
648_D748_A1.1960.98
484_T487_E1.1950.98
379_F382_C1.1940.98
223_I411_F1.1940.98
838_G848_F1.1930.98
553_A602_Y1.1890.98
192_Q332_E1.1890.98
433_V440_Q1.1880.98
193_Q196_D1.1880.98
726_P729_L1.1870.98
324_F332_E1.1870.98
649_L721_S1.1860.98
240_R309_R1.1820.98
98_D102_K1.1810.98
194_R317_E1.1800.98
403_P406_M1.1790.98
774_L845_E1.1770.98
28_C36_Y1.1770.98
657_P662_G1.1760.98
785_D791_C1.1740.98
463_I489_V1.1740.98
249_M267_L1.1740.98
402_F407_I1.1690.97
236_R422_A1.1690.97
99_I121_T1.1660.97
254_A417_L1.1630.97
343_L346_V1.1580.97
190_Y194_R1.1570.97
623_T752_S1.1560.97
792_P795_V1.1560.97
534_Y651_V1.1550.97
481_G491_R1.1450.97
652_Y745_L1.1450.97
725_I744_S1.1440.97
657_P664_L1.1430.97
103_M132_S1.1430.97
751_A755_S1.1430.97
689_V717_L1.1430.97
462_Q625_A1.1410.97
623_T653_D1.1380.97
643_A691_N1.1380.97
447_V840_Y1.1380.97
623_T721_S1.1380.97
614_V811_A1.1370.97
221_R404_D1.1350.97
9_V12_A1.1340.97
649_L652_Y1.1340.97
103_M119_G1.1260.97
257_E260_S1.1230.97
743_V759_I1.1210.97
633_V662_G1.1190.96
548_A552_Q1.1190.96
492_A526_G1.1180.96
464_V493_F1.1130.96
335_R338_G1.1120.96
627_I652_Y1.1100.96
783_V799_L1.1100.96
866_G869_E1.1100.96
440_Q443_E1.1090.96
351_A354_L1.1090.96
103_M106_R1.1060.96
57_M60_A1.1040.96
467_A489_V1.1040.96
331_R334_A1.1030.96
148_A152_M1.1020.96
628_N656_G1.1010.96
615_I752_S1.1010.96
528_L598_A1.1000.96
637_D689_V1.0990.96
207_T210_H1.0970.96
226_D419_H1.0960.96
498_K501_E1.0950.96
242_L246_T1.0940.96
511_A550_L1.0930.96
83_D122_K1.0920.96
721_S752_S1.0910.96
623_T691_N1.0910.96
224_R392_Q1.0900.96
502_L557_F1.0900.96
653_D754_W1.0890.96
62_I136_L1.0850.96
329_V332_E1.0840.96
692_S697_M1.0810.95
618_R804_H1.0800.95
439_W443_E1.0800.95
651_V753_I1.0800.95
376_P380_I1.0780.95
782_R802_T1.0770.95
434_I437_P1.0770.95
854_N869_E1.0760.95
800_Y822_L1.0730.95
233_F247_A1.0730.95
118_I129_L1.0690.95
640_L681_L1.0680.95
232_T423_R1.0680.95
377_Q381_D1.0660.95
215_D400_G1.0650.95
858_I863_I1.0630.95
40_D154_Y1.0630.95
19_D22_G1.0620.95
221_R411_F1.0620.95
730_P733_M1.0580.95
599_Y615_I1.0580.95
691_N696_L1.0550.95
435_T440_Q1.0540.95
544_L609_Q1.0520.95
442_A446_S1.0520.95
242_L308_A1.0500.94
224_R390_G1.0460.94
776_L805_G1.0460.94
620_A753_I1.0450.94
236_R240_R1.0430.94
653_D745_L1.0430.94
720_L725_I1.0420.94
524_V654_I1.0410.94
727_L731_D1.0410.94
433_V436_L1.0380.94
39_L44_T1.0360.94
783_V791_C1.0340.94
268_N344_M1.0330.94
491_R494_A1.0330.94
432_D435_T1.0320.94
504_C530_A1.0320.94
43_R157_S1.0310.94
544_L548_A1.0300.94
23_Y28_C1.0300.94
481_G518_A1.0300.94
511_A537_F1.0270.94
315_L319_L1.0260.94
67_E71_L1.0250.93
642_L692_S1.0220.93
650_S654_I1.0220.93
536_P749_T1.0220.93
633_V637_D1.0200.93
544_L547_Q1.0190.93
376_P381_D1.0180.93
306_E309_R1.0170.93
639_V657_P1.0160.93
249_M253_A1.0160.93
623_T627_I1.0160.93
13_Y287_D1.0150.93
443_E447_V1.0140.93
855_Q864_E1.0130.93
432_D437_P1.0110.93
780_G829_E1.0100.93
110_T136_L1.0100.93
751_A806_L1.0100.93
624_I656_G1.0100.93
328_E332_E1.0090.93
470_N486_E1.0090.93
717_L741_Q1.0090.93
491_R522_T1.0080.93
839_R849_L1.0070.93
782_R831_L1.0050.93
461_E464_V1.0030.93
327_V331_R1.0020.92
319_L322_R1.0010.92
533_V600_I1.0000.92
686_G714_A1.0000.92
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  
2vsqA10.97981000.141Contact Map
4dg8A10.49041000.519Contact Map
1amuA20.49381000.556Contact Map
4iz6A20.49721000.56Contact Map
3tsyA10.45561000.562Contact Map
4d4iA101000.567Contact Map
3wvnA20.42521000.568Contact Map
4gr5A40.51411000.569Contact Map
3vnrA10.47921000.57Contact Map
3g7sA20.48261000.571Contact 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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