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OPENSEQ.org

Lisa N Kinch

ID: 1503695255 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 911 (851)
Sequences: 890 (394.2)
Seq/Len: 1.046
Nf(neff/√len): 13.5

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: 1.046).

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
408_A737_A2.7451.00
504_V509_G2.3380.99
845_A849_V2.2070.98
495_F714_G2.0450.96
717_A723_W2.0070.96
397_I453_L1.9890.96
494_G717_A1.9710.95
381_G385_D1.9070.94
436_G439_E1.8820.94
621_D629_T1.8740.93
409_V765_L1.8630.93
642_N645_A1.8630.93
661_I665_F1.8570.93
829_K882_E1.8070.92
878_F882_E1.8070.92
883_L887_D1.8010.92
452_A763_G1.7260.89
420_A444_T1.6920.88
376_G380_G1.6870.88
396_D399_D1.6800.87
120_L123_L1.6600.87
407_A422_T1.6270.85
584_F613_S1.6170.85
452_A764_L1.6060.84
415_A423_F1.6030.84
264_F289_M1.5890.83
415_A424_G1.5860.83
690_S694_R1.5790.83
494_G723_W1.5670.82
93_A96_R1.5660.82
820_P834_H1.5650.82
518_R522_E1.5540.81
411_F414_F1.5540.81
331_A335_L1.5380.80
729_V732_V1.5370.80
788_L800_L1.5280.80
613_S617_M1.5260.80
439_E466_G1.5250.79
834_H837_T1.5250.79
432_R480_E1.5210.79
467_P788_L1.5120.79
498_I714_G1.5070.78
621_D631_K1.5040.78
472_E490_R1.5010.78
837_T840_Q1.5000.78
383_V387_R1.4940.78
393_Y396_D1.4810.77
878_F886_L1.4720.76
388_R413_Y1.4720.76
414_F417_L1.4720.76
94_W106_S1.4610.75
682_S690_S1.4560.75
584_F617_M1.4560.75
413_Y426_L1.4530.75
520_T533_I1.4500.74
528_I679_F1.4390.74
517_S791_I1.4360.73
879_R882_E1.4360.73
848_W851_K1.4360.73
492_W574_S1.4350.73
580_G617_M1.4320.73
389_R392_Y1.4280.73
848_W852_S1.4280.73
464_F468_L1.4270.73
394_L398_T1.4260.73
411_F423_F1.4230.73
332_L335_L1.4150.72
429_E433_N1.4140.72
395_S399_D1.4090.71
411_F426_L1.4070.71
597_F601_L1.4040.71
270_G278_Y1.3990.71
332_L339_Q1.3900.70
773_S793_L1.3800.69
335_L339_Q1.3800.69
102_L107_L1.3800.69
86_E94_W1.3740.69
811_L824_Y1.3690.68
677_L681_E1.3660.68
139_F153_L1.3620.68
724_L730_R1.3600.68
271_P286_A1.3530.67
93_A97_P1.3470.66
784_P790_G1.3400.66
832_R882_E1.3390.66
678_I685_T1.3380.66
278_Y289_M1.3320.65
94_W97_P1.3310.65
372_L375_T1.3290.65
837_T844_L1.3260.65
527_L531_I1.3260.65
535_E592_K1.3250.65
726_A729_V1.3230.64
304_R308_L1.3220.64
759_Q817_K1.3180.64
466_G531_I1.3130.64
343_L346_R1.3030.63
153_L156_A1.3010.63
405_V762_S1.2960.62
788_L792_F1.2950.62
411_F421_I1.2950.62
503_L718_L1.2890.61
518_R528_I1.2860.61
415_A425_G1.2850.61
393_Y399_D1.2840.61
381_G389_R1.2820.61
573_L580_G1.2820.61
324_T327_P1.2810.61
521_Q536_T1.2810.61
694_R702_F1.2790.61
723_W729_V1.2780.60
666_A670_P1.2760.60
840_Q860_P1.2750.60
767_A770_V1.2730.60
263_R283_R1.2700.60
75_W80_R1.2700.60
456_A701_G1.2690.60
78_A100_S1.2670.59
729_V733_T1.2670.59
865_L868_P1.2640.59
544_F571_A1.2640.59
819_H825_V1.2640.59
819_H833_M1.2630.59
333_L338_V1.2630.59
397_I764_L1.2590.59
726_A735_A1.2580.59
723_W726_A1.2580.59
321_L326_A1.2580.59
389_R393_Y1.2570.59
808_R811_L1.2570.59
685_T690_S1.2560.58
490_R521_Q1.2560.58
504_V675_F1.2550.58
904_Y910_P1.2540.58
673_L677_L1.2500.58
508_E525_S1.2490.58
461_V467_P1.2440.57
411_F424_G1.2420.57
379_F506_A1.2410.57
92_G96_R1.2390.57
721_M756_V1.2380.57
104_F108_L1.2370.57
819_H830_T1.2320.56
382_L704_L1.2310.56
520_T527_L1.2280.56
449_I764_L1.2270.56
385_D388_R1.2250.56
790_G794_Y1.2240.56
411_F415_A1.2230.55
682_S694_R1.2220.55
614_I847_L1.2210.55
83_Q88_L1.2190.55
98_H110_L1.2180.55
381_G388_R1.2170.55
730_R733_T1.2160.55
683_Q686_T1.2140.55
687_L690_S1.2070.54
413_Y773_S1.2060.54
820_P828_V1.2020.54
415_A421_I1.2010.53
582_F585_A1.2000.53
266_F289_M1.2000.53
485_E488_V1.1960.53
94_W110_L1.1960.53
809_I841_I1.1940.53
687_L702_F1.1930.53
107_L110_L1.1930.53
278_Y286_A1.1930.53
421_I462_V1.1910.52
447_Q501_V1.1900.52
450_L476_F1.1880.52
391_P703_H1.1870.52
513_V522_E1.1860.52
725_S729_V1.1840.52
106_S111_R1.1830.52
385_D396_D1.1810.52
502_V707_L1.1790.51
94_W102_L1.1780.51
576_V812_L1.1770.51
687_L691_K1.1760.51
289_M299_Y1.1750.51
783_I794_Y1.1750.51
437_V674_V1.1740.51
416_A426_L1.1730.51
112_R115_T1.1720.51
413_Y425_G1.1710.51
598_P601_L1.1710.51
412_I708_L1.1700.51
479_C535_E1.1700.51
703_H771_G1.1680.50
799_S802_G1.1680.50
788_L804_Q1.1600.50
788_L795_M1.1560.49
698_K705_D1.1560.49
532_F535_E1.1530.49
616_I620_V1.1530.49
705_D734_H1.1520.49
580_G629_T1.1500.49
81_W85_E1.1500.49
440_L486_Y1.1480.48
333_L339_Q1.1480.48
659_F663_M1.1470.48
844_L847_L1.1470.48
706_L726_A1.1450.48
385_D393_Y1.1440.48
532_F538_S1.1440.48
93_A99_L1.1430.48
510_S703_H1.1410.48
843_C851_K1.1410.48
414_F419_P1.1400.48
330_Q333_L1.1400.48
811_L837_T1.1400.48
372_L376_G1.1380.47
83_Q97_P1.1380.47
94_W98_H1.1380.47
691_K795_M1.1370.47
468_L513_V1.1370.47
160_K250_A1.1340.47
97_P102_L1.1340.47
810_L856_S1.1340.47
331_A338_V1.1340.47
94_W99_L1.1320.47
493_I708_L1.1320.47
102_L106_S1.1320.47
537_F541_I1.1310.47
863_L866_T1.1310.47
902_D910_P1.1300.47
330_Q335_L1.1300.47
472_E505_V1.1270.46
337_P340_R1.1260.46
220_I231_V1.1230.46
81_W94_W1.1210.46
738_L748_G1.1210.46
269_L287_T1.1200.46
304_R315_L1.1200.46
608_F614_I1.1200.46
517_S524_F1.1200.46
466_G469_L1.1190.46
475_F489_G1.1170.46
406_L447_Q1.1160.45
404_Q422_T1.1150.45
411_F416_A1.1130.45
809_I813_F1.1120.45
315_L320_V1.1120.45
94_W111_R1.1120.45
332_L340_R1.1120.45
399_D415_A1.1110.45
422_T635_P1.1110.45
298_A323_P1.1100.45
294_F298_A1.1100.45
771_G804_Q1.1100.45
95_G104_F1.1060.45
436_G473_E1.1050.44
834_H847_L1.1050.44
83_Q89_G1.1020.44
408_A692_P1.1020.44
399_D424_G1.0990.44
97_P100_S1.0980.44
690_S702_F1.0970.44
333_L343_L1.0960.44
485_E579_A1.0930.43
688_I698_K1.0930.43
420_A436_G1.0930.43
119_V132_A1.0910.43
478_F482_N1.0910.43
519_Y527_L1.0910.43
727_T731_S1.0900.43
96_R100_S1.0900.43
758_E762_S1.0900.43
439_E531_I1.0900.43
63_E78_A1.0900.43
485_E664_M1.0870.43
297_D310_S1.0870.43
870_R883_L1.0870.43
605_I836_F1.0870.43
775_L781_S1.0850.43
452_A455_G1.0850.43
473_E618_V1.0840.42
332_L338_V1.0840.42
310_S319_L1.0820.42
723_W727_T1.0820.42
532_F800_L1.0820.42
85_E102_L1.0820.42
165_G168_E1.0820.42
380_G508_E1.0800.42
301_A316_D1.0800.42
339_Q343_L1.0790.42
99_L110_L1.0770.42
424_G494_G1.0770.42
527_L535_E1.0770.42
702_F735_A1.0770.42
811_L814_K1.0770.42
900_G903_E1.0760.42
510_S520_T1.0750.42
467_P800_L1.0740.42
593_N599_G1.0740.42
614_I635_P1.0730.41
813_F855_A1.0720.41
244_F289_M1.0720.41
660_P802_G1.0710.41
787_V792_F1.0710.41
741_M753_I1.0700.41
443_S700_S1.0690.41
71_Q124_Q1.0690.41
856_S866_T1.0680.41
733_T766_V1.0680.41
571_A681_E1.0670.41
791_I798_T1.0670.41
490_R610_V1.0670.41
878_F883_L1.0660.41
471_F843_C1.0660.41
455_G460_L1.0660.41
708_L864_I1.0640.41
596_Y616_I1.0640.41
445_A771_G1.0640.41
316_D320_V1.0640.41
469_L472_E1.0640.41
61_L78_A1.0630.41
64_L98_H1.0630.41
82_V98_H1.0630.41
229_V240_P1.0620.40
784_P796_G1.0620.40
400_A416_A1.0620.40
608_F632_L1.0620.40
104_F112_R1.0610.40
83_Q96_R1.0600.40
101_H104_F1.0590.40
807_D824_Y1.0590.40
308_L321_L1.0570.40
804_Q808_R1.0570.40
616_I665_F1.0530.40
83_Q87_N1.0530.40
462_V504_V1.0520.40
304_R307_L1.0520.40
64_L86_E1.0510.39
741_M757_K1.0500.39
728_T763_G1.0490.39
808_R840_Q1.0480.39
412_I416_A1.0470.39
494_G520_T1.0450.39
525_S689_V1.0450.39
436_G531_I1.0440.39
335_L338_V1.0420.39
795_M851_K1.0420.39
456_A467_P1.0420.39
784_P792_F1.0410.39
707_L740_V1.0410.39
490_R548_P1.0400.39
677_L698_K1.0400.39
333_L342_L1.0390.38
399_D404_Q1.0390.38
786_A797_V1.0380.38
409_V769_L1.0380.38
692_P719_F1.0370.38
609_G719_F1.0360.38
237_L269_L1.0350.38
688_I704_L1.0350.38
77_E86_E1.0350.38
434_Q642_N1.0350.38
381_G387_R1.0350.38
280_Q283_R1.0340.38
632_L635_P1.0340.38
264_F288_L1.0340.38
870_R887_D1.0330.38
86_E97_P1.0330.38
739_T819_H1.0330.38
631_K634_V1.0330.38
331_A339_Q1.0320.38
817_K856_S1.0310.38
335_L342_L1.0310.38
497_L535_E1.0300.38
299_Y304_R1.0290.38
280_Q287_T1.0290.38
529_S650_I1.0280.37
493_I693_E1.0270.37
689_V694_R1.0260.37
100_S103_T1.0260.37
522_E888_A1.0250.37
84_L89_G1.0250.37
512_L844_L1.0250.37
761_I772_L1.0250.37
807_D811_L1.0250.37
464_F521_Q1.0240.37
681_E697_V1.0240.37
466_G472_E1.0240.37
718_L769_L1.0230.37
307_L314_F1.0230.37
331_A340_R1.0230.37
776_M779_I1.0230.37
394_L397_I1.0210.37
810_L875_P1.0210.37
432_R476_F1.0210.37
450_L715_V1.0210.37
685_T704_L1.0210.37
386_I391_P1.0200.37
698_K703_H1.0200.37
450_L453_L1.0200.37
106_S109_E1.0190.37
505_V509_G1.0190.37
528_I802_G1.0190.37
118_T144_Q1.0180.37
399_D422_T1.0180.37
435_M723_W1.0180.37
588_L612_I1.0180.37
584_F750_A1.0180.37
298_A322_P1.0170.36
689_V735_A1.0170.36
510_S528_I1.0160.36
685_T689_V1.0160.36
94_W107_L1.0160.36
146_R149_D1.0160.36
535_E763_G1.0150.36
773_S776_M1.0150.36
706_L731_S1.0140.36
602_R607_D1.0130.36
675_F681_E1.0130.36
789_F796_G1.0130.36
676_I685_T1.0120.36
688_I863_L1.0110.36
466_G471_F1.0110.36
226_A236_F1.0110.36
521_Q682_S1.0110.36
269_L282_G1.0110.36
592_K598_P1.0110.36
104_F111_R1.0100.36
81_W102_L1.0100.36
510_S518_R1.0080.36
124_Q290_S1.0080.36
728_T732_V1.0070.36
133_N150_R1.0070.36
224_S243_G1.0070.36
330_Q340_R1.0050.35
599_G605_I1.0050.35
695_K698_K1.0050.35
418_S729_V1.0050.35
535_E538_S1.0050.35
88_L100_S1.0050.35
444_T474_A1.0040.35
377_Q380_G1.0040.35
81_W86_E1.0040.35
89_G93_A1.0030.35
617_M847_L1.0030.35
689_V726_A1.0020.35
93_A98_H1.0020.35
439_E496_W1.0010.35
52_P55_H1.0010.35
98_H106_S1.0010.35
505_V515_F1.0000.35
513_V519_Y1.0000.35
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  
1hynP40.33151000.742Contact Map
4ky9A20.30741000.772Contact Map
1bzkA10.046199.70.944Contact Map
1bnxA10.036299.40.955Contact Map
3qe7A10.429299.20.958Contact Map
3urrA20.166899.10.96Contact Map
2a0jA10.160399.10.96Contact Map
1bh7A10.034990.963Contact Map
2oq3A10.160398.60.967Contact Map
3oxpA20.161498.50.968Contact 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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