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mexb

ID: 1499799432 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 1000 (993)
Sequences: 4580 (2704)
Seq/Len: 4.612
Nf(neff/√len): 85.8

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: 4.612).

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
957_G960_E4.9421.00
309_T312_N4.6381.00
244_E247_E4.6271.00
591_V625_G4.2011.00
304_K334_S4.1491.00
169_T305_A4.0911.00
247_E263_K4.0431.00
62_V88_M3.9921.00
142_V158_I3.8021.00
154_L321_M3.5701.00
47_V88_M3.5031.00
65_I69_M3.3881.00
311_A314_E3.3631.00
165_P309_T3.3601.00
76_R93_T3.3261.00
735_A745_I3.3091.00
193_L198_L3.2741.00
680_F828_G3.2161.00
248_N263_K3.2011.00
75_L92_V3.1551.00
729_E807_K3.1381.00
58_Q822_P3.1101.00
345_G349_L3.0681.00
741_S744_D3.0531.00
759_N770_V2.9771.00
307_R328_D2.9761.00
282_N608_S2.9691.00
186_I207_I2.8951.00
65_I90_I2.8801.00
691_G694_V2.8741.00
251_L265_V2.8441.00
3_K7_D2.8331.00
450_S479_A2.8221.00
69_M90_I2.8101.00
314_E322_K2.7671.00
247_E268_V2.6801.00
209_A736_S2.6011.00
193_L265_V2.6001.00
948_A962_A2.5781.00
61_V122_V2.5541.00
62_V82_S2.5321.00
598_L651_A2.5021.00
633_P636_E2.5021.00
730_I735_A2.4241.00
731_D805_T2.4181.00
10_I888_A2.4121.00
188_L203_V2.4101.00
301_D305_A2.4091.00
182_Y270_L2.3761.00
262_L268_V2.3761.00
14_V885_L2.3561.00
189_D192_K2.3311.00
588_Q592_D2.3151.00
731_D734_K2.2761.00
388_F472_I2.2501.00
342_K346_E2.2241.00
280_Q588_Q2.2171.00
243_A247_E2.1971.00
371_A484_V2.1871.00
382_V476_S2.1671.00
188_L200_P2.1661.00
34_Q569_Q2.1591.00
415_N418_R2.1481.00
578_T582_S2.1451.00
267_D775_R2.1291.00
696_L700_N2.1161.00
408_D939_K2.0961.00
183_S771_Y2.0861.00
45_V69_M2.0851.00
280_Q595_R2.0841.00
786_S801_N2.0831.00
712_L715_V2.0821.00
76_R95_E2.0721.00
977_S981_I2.0571.00
605_S642_N2.0431.00
586_R589_V2.0381.00
561_T837_G2.0371.00
783_D786_S2.0361.00
3_K432_R2.0311.00
55_E59_D2.0291.00
694_V697_Q2.0201.00
730_I745_I2.0201.00
684_L702_F2.0171.00
4_F11_F2.0031.00
338_H342_K1.9991.00
429_E433_K1.9831.00
62_V80_S1.9831.00
781_N784_D1.9781.00
740_V790_V1.9741.00
45_V65_I1.9721.00
606_V629_I1.9581.00
339_E998_Q1.9581.00
77_Y819_N1.9571.00
699_R717_P1.9531.00
587_T625_G1.9511.00
740_V803_F1.9141.00
698_A854_V1.9051.00
82_S88_M1.8991.00
378_G480_L1.8991.00
572_L651_A1.8951.00
69_M92_V1.8791.00
613_T625_G1.8751.00
642_N650_R1.8681.00
57_V61_V1.8591.00
74_N98_T1.8491.00
20_M377_L1.8431.00
650_R654_H1.8401.00
199_T791_R1.8201.00
205_S208_Q1.8131.00
115_T124_R1.8131.00
735_A740_V1.8041.00
204_S772_L1.7891.00
242_T245_Q1.7881.00
120_Q124_R1.7871.00
78_I92_V1.7851.00
426_S429_E1.7851.00
951_L956_K1.7741.00
729_E805_T1.7681.00
728_L804_A1.7651.00
8_R892_E1.7621.00
65_I114_A1.7541.00
43_I104_Q1.7531.00
591_V613_T1.7461.00
145_T322_K1.7431.00
697_Q701_K1.7431.00
597_Y654_H1.7331.00
190_P778_A1.7331.00
592_D595_R1.7300.99
844_E866_R1.7260.99
202_D791_R1.7250.99
956_K964_E1.7210.99
479_A483_I1.7180.99
181_Q273_Q1.7140.99
594_M655_F1.7140.99
985_V989_I1.7110.99
189_D267_D1.7090.99
593_S597_Y1.7070.99
47_V62_V1.7050.99
903_V941_A1.7050.99
339_E342_K1.6870.99
7_D428_R1.6870.99
75_L78_I1.6860.99
562_A923_D1.6860.99
68_Q114_A1.6830.99
241_Q245_Q1.6650.99
706_A843_V1.6650.99
297_A302_T1.6610.99
305_A308_Q1.6490.99
379_T477_A1.6360.99
574_A629_I1.6330.99
835_S838_D1.6320.99
203_V265_V1.6240.99
419_V437_Q1.6130.99
974_V978_L1.6070.99
19_I378_G1.6060.99
445_I482_V1.6050.99
193_L196_Y1.6010.99
607_S632_K1.5990.99
24_G28_L1.5940.99
775_R778_A1.5930.99
207_I249_I1.5840.99
609_V627_A1.5810.99
745_I803_F1.5770.99
591_V611_T1.5720.99
188_L193_L1.5670.99
245_Q248_N1.5640.99
53_S56_T1.5620.99
951_L964_E1.5480.99
472_I476_S1.5410.99
533_S537_H1.5400.99
244_E248_N1.5400.99
262_L266_A1.5380.99
537_H540_P1.5340.99
13_W894_W1.5290.98
593_S596_E1.5270.98
703_L715_V1.5260.98
423_E433_K1.5160.98
714_R829_E1.5130.98
884_F888_A1.5120.98
572_L648_A1.5110.98
170_K305_A1.5060.98
172_V291_I1.5050.98
703_L707_A1.5010.98
305_A309_T1.5000.98
11_F889_A1.4990.98
169_T309_T1.4990.98
632_K636_E1.4910.98
175_F289_I1.4860.98
187_W269_G1.4850.98
605_S632_K1.4840.98
112_Q115_T1.4830.98
196_Y260_V1.4820.98
142_V323_V1.4820.98
185_R773_Q1.4800.98
643_S646_E1.4790.98
307_R325_Y1.4780.98
14_V889_A1.4770.98
896_I949_K1.4720.98
582_S586_R1.4640.98
528_E967_R1.4560.98
418_R968_M1.4540.98
218_Q231_N1.4540.98
13_W17_L1.4520.98
301_D304_K1.4510.98
92_V107_V1.4500.98
328_D331_P1.4480.98
156_N160_S1.4470.98
576_V625_G1.4430.98
686_D854_V1.4420.98
576_V594_M1.4340.97
915_T926_F1.4340.97
834_L838_D1.4320.97
712_L839_A1.4280.97
651_A655_F1.4260.97
683_F823_A1.4260.97
694_V698_A1.4240.97
66_E817_R1.4220.97
578_T587_T1.4180.97
172_V302_T1.4120.97
702_F847_V1.4110.97
834_L842_A1.4100.97
26_S384_A1.4080.97
711_A834_L1.4080.97
98_T106_Q1.4040.97
699_R824_M1.4030.97
370_I492_L1.4010.97
199_T202_D1.4000.97
441_A950_E1.4000.97
57_V82_S1.3990.97
62_V90_I1.3970.97
473_T477_A1.3950.97
7_D432_R1.3940.97
142_V154_L1.3940.97
592_D596_E1.3880.97
334_S338_H1.3860.97
163_Q167_S1.3850.97
140_V325_Y1.3850.97
606_V609_V1.3840.97
45_V92_V1.3820.97
99_D102_I1.3750.96
598_L606_V1.3730.96
198_L202_D1.3720.96
22_A381_G1.3710.96
204_S208_Q1.3710.96
590_V593_S1.3690.96
547_V551_G1.3680.96
158_I162_I1.3680.96
352_F369_T1.3680.96
701_K705_L1.3610.96
74_N95_E1.3590.96
684_L699_R1.3540.96
425_L433_K1.3530.96
923_D926_F1.3500.96
542_L546_V1.3490.96
202_D205_S1.3460.96
594_M658_F1.3430.96
310_I323_V1.3400.96
791_R797_M1.3380.96
711_A842_A1.3380.96
143_V322_K1.3350.96
593_S660_D1.3350.96
231_N276_S1.3340.96
43_I107_V1.3320.96
115_T123_Q1.3320.96
142_V162_I1.3310.96
595_R609_V1.3300.95
47_V65_I1.3290.95
684_L826_I1.3240.95
698_A850_L1.3170.95
240_L246_F1.3160.95
254_N258_S1.3140.95
549_V553_I1.3130.95
162_I313_L1.3080.95
148_S320_G1.3060.95
137_L303_A1.3020.95
273_Q769_R1.3020.95
482_V979_A1.2950.95
680_F843_V1.2950.95
681_D825_E1.2940.95
562_A921_S1.2920.94
727_K809_E1.2900.94
970_L974_V1.2890.94
647_L650_R1.2870.94
896_I899_S1.2870.94
840_M862_S1.2840.94
304_K308_Q1.2830.94
982_L985_V1.2820.94
727_K807_K1.2800.94
433_K436_G1.2750.94
642_N647_L1.2740.94
47_V122_V1.2740.94
446_A482_V1.2710.94
141_G281_F1.2710.94
46_Q89_T1.2660.94
576_V591_V1.2600.93
412_V435_M1.2590.93
26_S381_G1.2590.93
29_S384_A1.2580.93
734_K737_A1.2510.93
841_A844_E1.2500.93
705_L846_I1.2480.93
158_I289_I1.2450.93
317_M323_V1.2430.93
157_Y321_M1.2410.93
740_V745_I1.2390.93
698_A701_K1.2360.93
699_R703_L1.2340.93
68_Q113_L1.2330.92
166_L175_F1.2320.92
349_L353_L1.2300.92
239_R762_I1.2280.92
280_Q592_D1.2270.92
790_V803_F1.2270.92
303_A330_T1.2260.92
102_I105_V1.2240.92
712_L828_G1.2210.92
309_T313_L1.2200.92
522_S526_G1.2200.92
58_Q815_L1.2190.92
528_E532_A1.2170.92
415_N437_Q1.2160.92
959_V963_I1.2150.92
799_P802_A1.2140.92
702_F826_I1.2080.91
77_Y93_T1.2030.91
383_L388_F1.2030.91
207_I758_V1.2030.91
449_L939_K1.2020.91
361_N417_E1.2000.91
685_Q857_S1.1950.91
145_T148_S1.1930.91
65_I111_L1.1870.90
79_S93_T1.1860.90
725_Q811_G1.1850.90
218_Q276_S1.1840.90
379_T476_S1.1840.90
572_L629_I1.1830.90
98_T103_A1.1810.90
408_D979_A1.1810.90
50_P123_Q1.1810.90
307_R330_T1.1800.90
818_Y859_T1.1780.90
42_A91_T1.1780.90
94_F107_V1.1770.90
744_D747_S1.1730.90
234_I753_W1.1730.90
95_E98_T1.1710.90
785_L806_G1.1690.90
842_A846_I1.1640.89
416_V493_C1.1620.89
728_L806_G1.1610.89
140_V289_I1.1590.89
27_I390_I1.1590.89
163_Q177_V1.1560.89
839_A842_A1.1560.89
838_D841_A1.1560.89
1_M5_F1.1550.89
842_A845_E1.1520.89
382_V386_F1.1520.89
529_R533_S1.1500.89
792_N796_E1.1490.89
193_L203_V1.1480.88
573_F628_F1.1430.88
216_S749_V1.1430.88
602_E605_S1.1420.88
550_A553_I1.1410.88
784_D787_K1.1410.88
184_M761_F1.1390.88
885_L889_A1.1370.88
439_Q443_V1.1360.88
200_P751_I1.1350.88
574_A598_L1.1350.88
921_S926_F1.1340.88
522_S525_H1.1340.88
157_Y161_N1.1340.88
700_N703_L1.1300.87
304_K307_R1.1300.87
58_Q817_R1.1280.87
404_L980_F1.1270.87
449_L478_M1.1260.87
139_V290_A1.1230.87
701_K704_M1.1220.87
543_L550_A1.1210.87
684_L854_V1.1210.87
5_F12_A1.1200.87
81_E91_T1.1200.87
903_V906_L1.1180.87
590_V658_F1.1160.86
815_L822_P1.1140.86
649_K652_Q1.1130.86
703_L826_I1.1130.86
428_R432_R1.1130.86
31_P389_S1.1100.86
595_R611_T1.1100.86
192_K196_Y1.1090.86
518_R522_S1.1090.86
593_S658_F1.1070.86
69_M75_L1.1070.86
956_K960_E1.1060.86
155_S180_S1.1030.86
169_T302_T1.1020.86
206_A249_I1.1020.86
47_V82_S1.1020.86
2_S435_M1.1000.85
278_N588_Q1.0990.85
445_I979_A1.0970.85
386_F476_S1.0970.85
278_N613_T1.0970.85
920_L999_H1.0960.85
383_L472_I1.0940.85
432_R436_G1.0940.85
465_V468_R1.0920.85
911_A930_L1.0910.85
706_A712_L1.0870.84
834_L839_A1.0870.84
146_D320_G1.0870.84
958_I962_A1.0860.84
922_N926_F1.0840.84
313_L317_M1.0840.84
683_F818_Y1.0830.84
734_K738_L1.0830.84
442_L482_V1.0810.84
703_L717_P1.0800.84
150_T153_D1.0790.84
47_V125_Q1.0780.84
693_E696_L1.0760.84
110_K113_L1.0760.84
6_I432_R1.0750.84
898_F902_L1.0720.83
758_V772_L1.0720.83
145_T320_G1.0720.83
347_A351_V1.0710.83
415_N419_V1.0710.83
578_T590_V1.0710.83
203_V772_L1.0680.83
462_S563_F1.0680.83
163_Q175_F1.0650.83
367_I492_L1.0650.83
591_V627_A1.0650.83
873_P877_A1.0650.83
70_N820_G1.0640.83
279_A288_G1.0630.83
246_F262_L1.0590.82
745_I800_F1.0590.82
419_V433_K1.0570.82
16_A19_I1.0560.82
48_S87_S1.0560.82
602_E647_L1.0550.82
211_N759_N1.0540.82
700_N704_M1.0530.82
192_K734_K1.0520.82
388_F475_V1.0510.82
388_F469_Q1.0510.82
530_G533_S1.0500.82
41_P94_F1.0490.82
602_E654_H1.0480.81
719_G824_M1.0480.81
382_V480_L1.0480.81
288_G610_F1.0470.81
76_R863_Y1.0440.81
144_S320_G1.0440.81
977_S980_F1.0430.81
597_Y651_A1.0420.81
702_F846_I1.0400.81
709_N842_A1.0400.81
201_G744_D1.0380.81
178_F290_A1.0360.80
30_L390_I1.0360.80
447_M886_C1.0350.80
205_S209_A1.0330.80
201_G205_S1.0310.80
69_M78_I1.0300.80
69_M107_V1.0290.80
352_F372_V1.0290.80
417_E421_A1.0280.80
291_I306_I1.0280.80
879_S931_L1.0280.80
914_A918_R1.0270.80
250_L259_Q1.0270.80
841_A845_E1.0260.79
551_G555_M1.0260.79
940_N977_S1.0230.79
830_P839_A1.0230.79
214_I746_N1.0220.79
404_L979_A1.0220.79
594_M627_A1.0200.79
281_F286_A1.0150.78
558_R916_S1.0150.78
876_Y934_I1.0140.78
30_L380_F1.0130.78
145_T284_S1.0130.78
335_A338_H1.0110.78
526_G530_G1.0090.78
366_L496_M1.0080.78
978_L982_L1.0070.78
2_S6_I1.0060.78
492_L496_M1.0060.78
413_V434_S1.0050.78
166_L309_T1.0050.78
3_K436_G1.0050.78
198_L251_L1.0040.77
952_H958_I1.0040.77
360_Q517_N1.0030.77
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  
4k0jA60.931000.282Contact Map
4mt1A10.9741000.343Contact Map
3ne5A10.9611000.353Contact Map
3w9iA60.9951000.353Contact Map
4dx5A30.9961000.366Contact Map
4r86A20.2891000.76Contact Map
3aqpA20.6651000.779Contact Map
2ew9A10.149760.984Contact Map
4n8nA40.170.70.985Contact Map
4q2lA10.0661.20.986Contact 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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