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VP4 -force run

ID: 1513623973 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 774 (771)
Sequences: 66 (24.4)
Seq/Len: 0.086
Nf(neff/√len): 0.9

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: 0.086).

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
226_P589_S2.3630.54
586_S589_S2.1560.44
226_P591_W2.0320.39
586_S591_W1.9980.37
629_L725_I1.9830.36
177_Y217_T1.9560.35
586_S590_A1.8920.32
226_P231_R1.8640.31
209_P649_I1.8430.30
226_P229_N1.7860.28
589_S592_T1.7750.28
226_P230_T1.7650.27
35_I514_M1.7210.26
226_P586_S1.7080.25
586_S592_T1.6430.23
60_T610_T1.6350.23
226_P232_N1.6250.22
238_I341_K1.6190.22
199_V547_N1.6000.21
682_A725_I1.5750.21
238_I538_V1.5680.20
226_P590_A1.5520.20
332_S689_F1.5510.20
142_D580_T1.5380.20
92_V226_P1.5370.20
35_I606_I1.5320.19
673_V679_V1.5280.19
514_M539_D1.5250.19
238_I762_K1.4820.18
345_I725_I1.4710.18
26_G464_I1.4450.17
536_S641_T1.4410.17
440_S561_V1.4370.17
476_S668_N1.4330.17
118_N584_V1.4300.16
341_K762_K1.4290.16
353_I629_L1.4230.16
495_D654_I1.4200.16
52_P668_N1.4170.16
180_T495_D1.4160.16
197_V553_K1.4130.16
581_M584_V1.4100.16
26_G220_I1.4090.16
35_I696_F1.4090.16
345_I440_S1.3940.16
159_L204_D1.3920.15
256_I406_S1.3890.15
304_N556_K1.3840.15
160_S622_M1.3700.15
222_N325_D1.3700.15
328_Y712_D1.3700.15
229_N232_N1.3680.15
55_I658_V1.3610.15
629_L682_A1.3580.15
92_V230_T1.3570.15
514_M538_V1.3570.15
312_V584_V1.3530.15
767_N770_M1.3490.14
278_N429_N1.3470.14
339_I652_N1.3460.14
545_A658_V1.3420.14
231_R589_S1.3400.14
115_E585_G1.3330.14
306_D429_N1.3290.14
128_L767_N1.3260.14
580_T650_T1.3260.14
404_L424_L1.3250.14
194_Y590_A1.3230.14
616_R704_Q1.3220.14
9_L765_I1.3150.14
151_S204_D1.3150.14
342_Y689_F1.3150.14
56_N171_G1.3120.14
479_D735_T1.3090.14
76_P592_T1.3070.13
100_N588_A1.3070.13
461_F580_T1.3070.13
587_T696_F1.3070.13
147_S151_S1.3050.13
186_T580_T1.3040.13
298_P752_E1.3010.13
194_Y586_S1.2970.13
194_Y589_S1.2940.13
189_Y284_S1.2920.13
363_R498_L1.2910.13
128_L579_Q1.2900.13
116_T647_V1.2870.13
25_V209_P1.2850.13
226_P233_V1.2840.13
587_T590_A1.2840.13
256_I757_E1.2800.13
514_M649_I1.2780.13
134_S345_I1.2740.13
440_S522_T1.2700.13
125_Q696_F1.2670.13
214_S503_E1.2670.13
541_A751_R1.2670.13
511_Q580_T1.2620.12
198_K306_D1.2600.12
282_V294_L1.2600.12
547_N680_F1.2590.12
341_K647_V1.2550.12
661_A684_T1.2530.12
160_S605_T1.2480.12
236_L495_D1.2460.12
403_I514_M1.2460.12
194_Y591_W1.2430.12
138_W456_N1.2420.12
163_K296_F1.2420.12
265_M682_A1.2420.12
93_A767_N1.2410.12
126_E740_F1.2350.12
52_P687_R1.2310.12
429_N680_F1.2310.12
595_V650_T1.2310.12
2_A773_R1.2280.12
656_E725_I1.2280.12
238_I325_D1.2270.12
554_R679_V1.2220.12
587_T596_T1.2220.12
627_E751_R1.2210.12
111_G556_K1.2200.12
209_P256_I1.2200.12
174_V440_S1.2180.12
209_P514_M1.2180.12
265_M617_L1.2170.12
561_V668_N1.2150.12
272_V676_N1.2120.11
56_N213_E1.2100.11
126_E167_V1.2080.11
250_V328_Y1.2080.11
229_N589_S1.2050.11
255_I679_V1.2010.11
651_P746_D1.2010.11
267_Y270_D1.1930.11
267_Y726_K1.1930.11
270_D726_K1.1930.11
26_G375_L1.1910.11
312_V499_G1.1900.11
100_N457_G1.1870.11
194_Y457_G1.1870.11
230_T589_S1.1870.11
590_A605_T1.1870.11
503_E623_T1.1840.11
20_D273_I1.1830.11
568_L705_K1.1830.11
14_Y81_W1.1820.11
243_I353_I1.1820.11
325_D540_A1.1790.11
238_I403_I1.1770.11
365_M702_D1.1770.11
587_T746_D1.1770.11
18_I551_R1.1760.11
147_S595_V1.1760.11
545_A716_I1.1760.11
109_E138_W1.1750.11
415_F679_V1.1750.11
522_T767_N1.1750.11
35_I403_I1.1730.11
229_N586_S1.1730.11
177_Y743_L1.1720.11
196_T605_T1.1720.11
25_V153_N1.1700.11
266_Q349_S1.1700.11
541_A605_T1.1690.11
155_H584_V1.1680.11
236_L773_R1.1680.11
162_N622_M1.1660.11
62_V610_T1.1630.11
5_I769_I1.1620.11
35_I539_D1.1620.11
124_K388_Q1.1590.10
587_T591_W1.1590.10
35_I418_F1.1580.10
545_A751_R1.1580.10
75_D195_S1.1560.10
207_I756_Q1.1560.10
265_M725_I1.1560.10
85_S431_S1.1550.10
122_F160_S1.1550.10
345_I559_E1.1540.10
394_W453_A1.1510.10
166_A680_F1.1480.10
220_I375_L1.1480.10
311_I429_N1.1480.10
241_R313_T1.1470.10
658_V704_Q1.1470.10
313_T648_Q1.1450.10
375_L464_I1.1450.10
500_E584_V1.1450.10
610_T703_V1.1450.10
65_I711_S1.1440.10
111_G304_N1.1420.10
131_S238_I1.1410.10
231_R591_W1.1400.10
306_D676_N1.1400.10
192_S670_S1.1380.10
353_I595_V1.1380.10
16_V627_E1.1370.10
77_P226_P1.1370.10
116_T238_I1.1370.10
160_S176_T1.1370.10
216_C498_L1.1370.10
115_E606_I1.1340.10
230_T586_S1.1340.10
576_S703_V1.1340.10
17_N575_V1.1310.10
120_N440_S1.1310.10
16_V762_K1.1300.10
26_G374_N1.1300.10
166_A272_V1.1270.10
457_G725_I1.1270.10
174_V282_V1.1250.10
211_A350_F1.1250.10
243_I339_I1.1250.10
485_M567_S1.1250.10
58_S138_W1.1240.10
22_I548_V1.1230.10
232_N586_S1.1180.10
440_S675_D1.1170.10
112_V117_R1.1160.10
112_V607_S1.1140.10
339_I566_D1.1140.10
35_I578_T1.1110.10
75_D105_V1.1110.10
198_K457_G1.1110.10
579_Q587_T1.1110.10
166_A645_K1.1090.10
296_F547_N1.1090.10
332_S342_Y1.1090.10
11_N659_T1.1070.10
266_Q351_V1.1070.10
282_V446_G1.1060.10
126_E214_S1.1040.10
292_A304_N1.1040.10
189_Y298_P1.1020.09
256_I398_S1.1020.09
26_G127_Q1.0990.09
79_D649_I1.0990.09
147_S353_I1.0990.09
593_S659_T1.0990.09
330_G496_R1.0970.09
564_L663_E1.0970.09
80_Y97_N1.0960.09
550_K746_D1.0960.09
72_T282_V1.0950.09
76_P229_N1.0950.09
168_M708_D1.0950.09
647_V762_K1.0930.09
33_V273_I1.0920.09
285_G532_S1.0920.09
35_I145_K1.0900.09
130_V440_S1.0900.09
211_A273_I1.0900.09
312_V674_I1.0900.09
77_P232_N1.0890.09
44_G166_A1.0880.09
100_N341_K1.0880.09
136_T585_G1.0880.09
418_F608_T1.0880.09
587_T605_T1.0860.09
76_P586_S1.0850.09
197_V339_I1.0850.09
339_I375_L1.0850.09
436_P580_T1.0830.09
11_N762_K1.0820.09
212_Q243_I1.0820.09
325_D389_L1.0810.09
431_S725_I1.0810.09
610_T748_R1.0810.09
365_M667_P1.0790.09
495_D679_V1.0790.09
166_A767_N1.0780.09
128_L587_T1.0750.09
579_Q597_N1.0750.09
310_E501_L1.0740.09
2_A312_V1.0720.09
656_E711_S1.0720.09
232_N589_S1.0710.09
265_M609_Q1.0710.09
300_N695_T1.0710.09
25_V111_G1.0690.09
26_G243_I1.0690.09
138_W653_T1.0690.09
495_D542_K1.0690.09
11_N120_N1.0680.09
35_I101_R1.0680.09
539_D649_I1.0680.09
174_V670_S1.0670.09
255_I547_N1.0650.09
26_G212_Q1.0640.09
142_D746_D1.0640.09
174_V393_D1.0640.09
239_T538_V1.0640.09
49_D255_I1.0610.09
265_M611_S1.0610.09
278_N388_Q1.0610.09
16_V436_P1.0600.09
255_I350_F1.0600.09
285_G634_I1.0600.09
522_T654_I1.0600.09
52_P476_S1.0580.09
456_N510_Q1.0580.09
152_Y500_E1.0570.09
174_V588_A1.0570.09
35_I311_I1.0550.09
60_T703_V1.0550.09
160_S213_E1.0540.09
464_I663_E1.0540.09
580_T595_V1.0540.09
76_P232_N1.0530.09
129_V200_N1.0510.09
345_I374_N1.0510.09
554_R590_A1.0510.09
21_E732_Y1.0500.09
274_R285_G1.0500.09
350_F692_R1.0480.09
241_R648_Q1.0470.09
92_V232_N1.0450.09
159_L189_Y1.0450.09
255_I388_Q1.0450.09
406_S696_F1.0440.09
563_E623_T1.0440.09
1_M9_L1.0430.09
1_M765_I1.0430.09
3_S9_L1.0430.09
3_S765_I1.0430.09
613_I682_A1.0430.09
142_D151_S1.0410.09
511_Q656_E1.0410.09
17_N495_D1.0400.09
160_S705_K1.0400.09
165_Y585_G1.0400.09
616_R630_N1.0400.09
166_A298_P1.0380.08
173_R374_N1.0380.08
464_I662_S1.0380.08
239_T341_K1.0370.08
332_S476_S1.0360.08
26_G339_I1.0340.08
72_T774_L1.0340.08
122_F171_G1.0340.08
580_T736_K1.0340.08
255_I282_V1.0330.08
8_Q765_I1.0310.08
11_N749_V1.0310.08
83_L258_K1.0310.08
522_T612_I1.0310.08
30_T575_V1.0300.08
105_V587_T1.0300.08
236_L388_Q1.0300.08
696_F746_D1.0300.08
130_V619_L1.0290.08
211_A674_I1.0290.08
403_I649_I1.0290.08
623_T703_V1.0290.08
86_P674_I1.0270.08
160_S545_A1.0270.08
167_V594_T1.0270.08
223_G474_V1.0270.08
103_L204_D1.0260.08
389_L680_F1.0260.08
55_I584_V1.0240.08
292_A711_S1.0240.08
321_N552_F1.0240.08
348_N394_W1.0240.08
567_S652_N1.0240.08
325_D611_S1.0230.08
345_I407_A1.0230.08
661_A741_N1.0230.08
183_N296_F1.0220.08
371_L631_F1.0220.08
545_A654_I1.0220.08
766_E773_R1.0220.08
62_V596_T1.0200.08
587_T592_T1.0200.08
397_M664_K1.0190.08
595_V656_E1.0190.08
658_V746_D1.0190.08
680_F683_G1.0190.08
35_I87_D1.0170.08
138_W656_E1.0170.08
256_I773_R1.0170.08
77_P229_N1.0160.08
106_I339_I1.0160.08
127_Q619_L1.0160.08
339_I488_V1.0160.08
612_I658_V1.0160.08
145_K150_G1.0150.08
446_G575_V1.0150.08
580_T596_T1.0150.08
149_D171_G1.0130.08
163_K547_N1.0130.08
249_Q374_N1.0130.08
507_T580_T1.0130.08
127_Q130_V1.0100.08
285_G391_V1.0100.08
545_A661_A1.0100.08
79_D174_V1.0090.08
22_I716_I1.0080.08
177_Y282_V1.0080.08
345_I682_A1.0080.08
372_A485_M1.0080.08
70_Q646_S1.0060.08
168_M189_Y1.0060.08
171_G213_E1.0060.08
547_N645_K1.0060.08
568_L756_Q1.0060.08
213_E605_T1.0050.08
657_I755_N1.0050.08
16_V659_T1.0030.08
76_P226_P1.0030.08
420_S662_S1.0030.08
118_N174_V1.0020.08
415_F673_V1.0020.08
18_I629_L1.0010.08
165_Y218_E1.0010.08
226_P592_T1.0010.08
255_I743_L1.0010.08
436_P461_F1.0010.08
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  
3iyuX30.95091000.057Contact Map
1slqA60.35141000.589Contact Map
2b4hA20.29331000.659Contact Map
1kqrA10.20671000.844Contact Map
2aenA80.21191000.852Contact Map
4drrA10.21061000.854Contact Map
2gboA20.047855.20.991Contact Map
4fp9B40.109844.90.991Contact Map
3i5cA20.153743.30.991Contact Map
4j40A2040.80.991Contact 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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