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A0LXY7_GRAFK -force run

ID: 1407781876 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 902 (830)
Sequences: 221 (204.6)
Seq/Len: 0.266
Nf(neff/√len): 7.1

HHblits Results: (2013_03)
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: 0.266).

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
115_A160_S2.5900.91
46_V71_I2.5500.91
86_E114_K2.3600.86
113_N158_N2.1550.78
6_K10_F2.0290.71
38_M46_V2.0120.70
324_F333_V2.0100.70
573_N593_N2.0010.70
54_S59_F1.9140.65
614_F657_G1.6860.50
121_V127_A1.6440.48
514_S518_F1.6260.47
29_Q33_L1.6150.46
676_A715_L1.6130.46
414_A724_I1.5980.45
380_N423_N1.5940.45
489_L585_A1.5900.44
122_D126_N1.5860.44
49_K68_D1.5780.43
245_L295_F1.5460.41
640_P726_P1.5460.41
481_T517_D1.5370.41
114_K159_N1.5180.40
195_T247_F1.5030.39
114_K508_V1.4770.37
152_L784_L1.4760.37
480_K514_S1.4690.37
51_I66_I1.4640.36
563_T572_K1.4640.36
119_I427_K1.4380.35
169_S678_L1.4290.34
68_D86_E1.4270.34
380_N421_D1.4250.34
571_L618_L1.4150.33
164_Y389_G1.4040.33
117_V135_D1.4010.33
482_D510_S1.4010.33
64_L385_L1.3990.33
175_I178_L1.3980.32
66_I71_I1.3980.32
821_E836_R1.3940.32
30_L746_M1.3890.32
119_I129_Y1.3780.31
82_L131_I1.3730.31
813_V818_K1.3720.31
706_I797_I1.3670.31
5_L8_L1.3660.31
92_M178_L1.3620.30
612_P720_G1.3600.30
736_F752_L1.3560.30
7_I17_I1.3550.30
441_L489_L1.3510.30
368_F518_F1.3470.30
164_Y717_F1.3460.30
180_H195_T1.3420.29
789_T796_Q1.3420.29
245_L267_P1.3400.29
385_L392_N1.3340.29
68_D514_S1.3340.29
82_L576_G1.3330.29
344_N352_T1.3330.29
420_F700_F1.3240.28
13_L17_I1.3220.28
37_T40_D1.3190.28
361_F518_F1.3170.28
326_Y401_P1.3130.28
155_Y585_A1.3100.28
825_V831_I1.3090.28
232_T564_V1.3060.27
222_I508_V1.3060.27
2_K5_L1.3020.27
46_V491_N1.3010.27
814_A818_K1.2970.27
511_N514_S1.2910.27
389_G576_G1.2900.27
249_G293_G1.2810.26
97_L792_F1.2780.26
550_P745_D1.2750.26
57_R356_I1.2730.26
206_D580_I1.2720.26
827_A831_I1.2720.26
121_V164_Y1.2700.26
691_L695_D1.2680.26
442_K484_T1.2670.25
355_N425_I1.2670.25
823_K826_D1.2660.25
96_E495_F1.2660.25
144_E515_V1.2650.25
326_Y659_L1.2640.25
321_N486_S1.2640.25
71_I170_K1.2630.25
582_D623_L1.2620.25
93_S96_E1.2620.25
275_L576_G1.2600.25
577_L588_Q1.2600.25
742_H750_Y1.2560.25
243_L506_F1.2540.25
293_G303_G1.2540.25
51_I513_F1.2520.25
110_L134_E1.2510.25
486_S669_S1.2480.25
115_A489_L1.2470.25
117_V157_I1.2470.25
73_N552_F1.2440.24
113_N562_N1.2400.24
419_S436_S1.2380.24
193_L564_V1.2370.24
96_E663_L1.2350.24
54_S550_P1.2350.24
430_Y676_A1.2330.24
640_P727_M1.2330.24
264_F299_G1.2310.24
207_G831_I1.2300.24
482_D511_N1.2300.24
216_L384_D1.2270.24
769_L799_L1.2250.23
180_H247_F1.2240.23
655_L672_G1.2240.23
11_V21_V1.2240.23
807_N810_Q1.2220.23
152_L302_F1.2220.23
64_L585_A1.2220.23
108_D785_P1.2210.23
59_F491_N1.2160.23
13_L16_I1.2160.23
222_I741_S1.2160.23
5_L459_N1.2160.23
665_L757_P1.2150.23
35_K47_D1.2140.23
486_S515_V1.2120.23
203_L691_L1.2100.23
10_F15_I1.2040.22
787_G800_N1.2030.22
625_I749_N1.2010.22
23_P77_F1.2010.22
17_I21_V1.1960.22
489_L696_D1.1930.22
678_L786_I1.1910.22
159_N162_V1.1900.22
159_N465_N1.1890.22
670_L762_G1.1890.22
560_N585_A1.1880.22
690_L758_A1.1850.22
71_I703_F1.1850.22
769_L813_V1.1820.22
381_M708_L1.1810.21
551_S575_K1.1780.21
115_A361_F1.1760.21
178_L711_L1.1750.21
371_N392_N1.1750.21
118_N163_K1.1740.21
474_L628_S1.1730.21
479_G510_S1.1730.21
138_T142_N1.1700.21
112_L169_S1.1700.21
210_Y698_L1.1700.21
2_K788_I1.1690.21
15_I475_K1.1680.21
129_Y210_Y1.1680.21
425_I653_L1.1680.21
184_G430_Y1.1680.21
624_D702_N1.1650.21
462_L486_S1.1640.21
420_F460_A1.1640.21
299_G324_F1.1630.21
322_A519_M1.1630.21
669_S725_A1.1610.21
370_A391_V1.1590.21
85_G439_A1.1590.21
189_D287_E1.1570.20
133_V588_Q1.1570.20
118_N719_D1.1550.20
306_D328_D1.1530.20
451_I632_L1.1530.20
561_A669_S1.1520.20
180_H197_S1.1520.20
241_N640_P1.1510.20
105_K369_T1.1510.20
561_A702_N1.1490.20
813_V817_K1.1480.20
506_F557_L1.1480.20
821_E829_N1.1460.20
164_Y457_I1.1440.20
100_S117_V1.1420.20
297_L372_G1.1390.20
191_S222_I1.1390.20
85_G277_V1.1390.20
6_K160_S1.1390.20
5_L441_L1.1380.20
10_F112_L1.1370.20
721_M743_G1.1360.20
262_V425_I1.1350.20
495_F576_G1.1350.20
327_P569_L1.1330.19
574_A724_I1.1320.19
50_D178_L1.1310.19
6_K24_F1.1300.19
287_E596_N1.1290.19
163_K257_D1.1290.19
264_F756_V1.1290.19
240_V700_F1.1290.19
819_N831_I1.1280.19
135_D670_L1.1280.19
291_T750_Y1.1280.19
640_P720_G1.1260.19
98_F372_G1.1260.19
44_A640_P1.1250.19
64_L275_L1.1250.19
183_T744_F1.1240.19
182_G210_Y1.1240.19
396_I661_E1.1240.19
42_L380_N1.1230.19
462_L578_L1.1230.19
566_Y580_I1.1230.19
121_V129_Y1.1200.19
15_I440_S1.1200.19
184_G576_G1.1180.19
657_G672_G1.1160.19
828_I832_L1.1160.19
391_V508_V1.1150.19
486_S507_Q1.1150.19
214_N625_I1.1150.19
44_A131_I1.1150.19
401_P640_P1.1140.19
23_P676_A1.1130.19
810_Q821_E1.1120.19
356_I801_M1.1110.19
41_N434_K1.1100.19
157_I164_Y1.1090.18
73_N676_A1.1080.18
71_I83_A1.1070.18
182_G708_L1.1070.18
41_N489_L1.1060.18
361_F683_I1.1050.18
36_K719_D1.1050.18
62_A220_A1.1040.18
90_L157_I1.1040.18
42_L357_N1.1030.18
63_T629_F1.1030.18
272_K277_V1.1030.18
826_D835_K1.1020.18
117_V169_S1.1020.18
637_N640_P1.1020.18
703_F736_F1.1020.18
64_L168_S1.1010.18
528_S587_L1.1010.18
196_Y749_N1.1000.18
41_N70_S1.0990.18
123_S264_F1.0970.18
825_V829_N1.0960.18
32_D615_E1.0960.18
800_N809_T1.0950.18
680_T690_L1.0940.18
98_F632_L1.0940.18
260_M490_Q1.0940.18
213_Q718_T1.0930.18
479_G517_D1.0910.18
128_N166_D1.0900.18
322_A717_F1.0900.18
160_S749_N1.0890.18
308_T441_L1.0890.18
175_I469_V1.0890.18
241_N727_M1.0890.18
811_K814_A1.0880.18
40_D154_H1.0880.18
115_A327_P1.0860.18
42_L175_I1.0850.18
123_S769_L1.0840.18
98_F361_F1.0830.17
359_A649_L1.0830.17
393_L550_P1.0830.17
162_V788_I1.0810.17
41_N123_S1.0800.17
156_E585_A1.0800.17
170_K749_N1.0790.17
21_V292_N1.0780.17
274_F678_L1.0770.17
814_A825_V1.0770.17
97_L672_G1.0770.17
107_I135_D1.0770.17
5_L22_A1.0770.17
506_F569_L1.0760.17
432_N564_V1.0760.17
476_M483_I1.0760.17
182_G757_P1.0760.17
275_L278_I1.0760.17
125_G128_N1.0760.17
391_V745_D1.0760.17
18_L251_V1.0760.17
805_V814_A1.0750.17
53_L105_K1.0750.17
569_L744_F1.0750.17
16_I50_D1.0750.17
115_A687_K1.0750.17
164_Y249_G1.0730.17
368_F514_S1.0730.17
460_A471_V1.0710.17
459_N473_N1.0680.17
356_I796_Q1.0670.17
216_L570_E1.0670.17
326_Y576_G1.0660.17
40_D131_I1.0650.17
672_G689_D1.0640.17
456_Q598_S1.0640.17
576_G640_P1.0630.17
162_V618_L1.0630.17
246_T786_I1.0620.17
229_M385_L1.0620.17
812_V817_K1.0610.17
822_G825_V1.0610.17
249_G261_D1.0600.17
82_L510_S1.0600.17
326_Y640_P1.0590.17
83_A92_M1.0590.17
360_T678_L1.0580.17
660_N683_I1.0570.17
729_F754_L1.0570.17
567_D676_A1.0570.17
32_D162_V1.0570.17
346_T513_F1.0560.16
380_N610_T1.0560.16
156_E719_D1.0560.16
6_K11_V1.0560.16
12_I137_T1.0560.16
158_N412_L1.0540.16
510_S517_D1.0540.16
69_L150_L1.0540.16
6_K84_L1.0530.16
805_V823_K1.0520.16
65_V596_N1.0520.16
12_I15_I1.0520.16
165_D414_A1.0520.16
477_T492_L1.0510.16
657_G669_S1.0500.16
183_T513_F1.0500.16
9_G86_E1.0500.16
51_I514_S1.0490.16
82_L195_T1.0490.16
191_S635_M1.0480.16
818_K827_A1.0480.16
147_P339_D1.0480.16
241_N550_P1.0460.16
831_I835_K1.0460.16
293_G506_F1.0450.16
269_S506_F1.0450.16
374_I583_E1.0440.16
810_Q814_A1.0440.16
448_S622_S1.0440.16
118_N165_D1.0430.16
502_L660_N1.0430.16
596_N627_S1.0430.16
54_S710_K1.0430.16
729_F785_P1.0430.16
4_A553_L1.0430.16
385_L800_N1.0430.16
772_L776_S1.0410.16
521_A635_M1.0400.16
187_S729_F1.0400.16
452_P549_V1.0390.16
94_I169_S1.0380.16
635_M720_G1.0380.16
150_L696_D1.0380.16
59_F62_A1.0370.16
680_T708_L1.0370.16
50_D159_N1.0370.16
175_I743_G1.0370.16
82_L322_A1.0370.16
694_L750_Y1.0370.16
117_V161_R1.0350.16
146_T587_L1.0340.16
783_E808_L1.0340.16
607_T655_L1.0340.16
157_I708_L1.0340.16
699_N719_D1.0330.16
175_I581_R1.0330.16
26_F576_G1.0320.16
34_V575_K1.0320.16
420_F742_H1.0310.16
603_G710_K1.0310.16
166_D749_N1.0310.16
152_L468_N1.0300.16
58_S266_T1.0300.16
21_V107_I1.0300.16
271_F612_P1.0290.16
204_N209_N1.0290.16
569_L727_M1.0280.16
444_F672_G1.0280.16
157_I623_L1.0270.15
122_D588_Q1.0270.15
80_D550_P1.0270.15
724_I729_F1.0270.15
436_S590_I1.0250.15
557_L649_L1.0240.15
43_N298_N1.0240.15
655_L701_I1.0240.15
712_K722_V1.0240.15
506_F553_L1.0230.15
629_F748_M1.0230.15
629_F725_A1.0220.15
481_T510_S1.0220.15
382_L483_I1.0210.15
516_N554_D1.0210.15
305_T645_I1.0210.15
803_Q816_Q1.0210.15
5_L298_N1.0200.15
321_N395_N1.0200.15
77_F504_G1.0190.15
46_V66_I1.0190.15
282_Y389_G1.0180.15
73_N495_F1.0180.15
261_D302_F1.0180.15
21_V704_K1.0180.15
59_F225_D1.0170.15
12_I213_Q1.0170.15
340_M569_L1.0170.15
350_E379_E1.0170.15
587_L669_S1.0160.15
633_E729_F1.0160.15
338_L496_L1.0160.15
42_L460_A1.0150.15
827_A836_R1.0140.15
315_I374_I1.0130.15
370_A483_I1.0130.15
494_G561_A1.0120.15
507_Q662_D1.0120.15
328_D572_K1.0120.15
322_A441_L1.0120.15
271_F291_T1.0120.15
98_F492_L1.0110.15
356_I513_F1.0100.15
254_N257_D1.0100.15
152_L256_N1.0100.15
326_Y727_M1.0100.15
264_F457_I1.0090.15
129_Y346_T1.0090.15
557_L570_E1.0090.15
467_G628_S1.0080.15
90_L225_D1.0080.15
496_L724_I1.0080.15
48_F578_L1.0070.15
557_L752_L1.0050.15
97_L286_I1.0040.15
192_E198_E1.0030.15
469_V522_E1.0020.15
231_Y799_L1.0020.15
106_K561_A1.0020.15
777_L806_N1.0020.15
449_P476_M1.0010.15
5_L247_F1.0000.15
821_E835_K1.0000.15
64_L529_T1.0000.15
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: (17Jul14)
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  
1s5lU20.105335.90.984Contact Map
2j5lA1024.50.985Contact Map
1rxtA4013.80.987Contact Map
2lk9A10.026610.50.988Contact Map
3rwxA10.21738.50.988Contact Map
1spfA10.02887.90.988Contact Map
3jx8A60.26056.30.989Contact Map
1m56D20.02665.40.989Contact Map
2m3eA10.0415.10.989Contact Map
1qleD10.02664.60.989Contact 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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