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hNav15-DIII-IV

ID: 1500065841 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 822 (672)
Sequences: 2759 (1638)
Seq/Len: 4.106
Nf(neff/√len): 63.2

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: 4.106).

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
477_Y560_T5.9331.00
331_V383_V2.9751.00
59_E63_K2.8961.00
381_C392_Y2.7401.00
154_F258_I2.7091.00
331_V336_F2.6861.00
432_R435_R2.5291.00
355_T362_K2.4361.00
380_E384_K2.4261.00
393_F402_F2.3861.00
381_C402_F2.3331.00
166_F234_A2.3281.00
72_Y81_D2.3181.00
234_A256_F2.3081.00
57_V89_L2.2791.00
482_M506_S2.2681.00
60_M72_Y2.1741.00
78_C81_D2.1051.00
398_N401_D2.0991.00
481_G557_F2.0891.00
158_G255_Y2.0581.00
72_Y78_C2.0491.00
225_K520_D2.0441.00
159_V211_V2.0001.00
372_L376_I1.9941.00
60_M64_W1.9841.00
360_P364_N1.9701.00
294_T297_Q1.9391.00
225_K517_A1.9101.00
64_W69_F1.8981.00
438_R441_R1.8961.00
392_Y402_F1.8891.00
358_Q363_I1.8311.00
218_L259_F1.8251.00
327_I383_V1.8221.00
155_S211_V1.8131.00
224_F260_I1.7921.00
336_F380_E1.7820.99
561_Y565_S1.7810.99
51_M55_V1.7680.99
14_E21_I1.7570.99
434_A438_R1.7440.99
477_Y481_G1.7370.99
293_M297_Q1.7280.99
72_Y77_W1.7170.99
169_C190_C1.7130.99
77_W81_D1.7100.99
297_Q300_Y1.7050.99
392_Y398_N1.6950.99
208_F256_F1.6930.99
17_I21_I1.6930.99
526_I558_F1.6510.99
381_C384_K1.6500.99
378_T409_I1.6460.99
8_V62_L1.6430.99
81_D85_V1.6340.99
56_F59_E1.6310.99
572_M581_F1.6080.99
557_F561_Y1.6080.99
17_I55_V1.6050.99
336_F347_N1.5970.99
293_M300_Y1.5940.99
432_R436_I1.5770.98
393_F399_I1.5760.98
371_L375_A1.5700.98
71_K74_T1.5690.98
109_R112_R1.5670.98
220_Q223_T1.5670.98
72_Y82_F1.5640.98
373_F380_E1.5590.98
534_C548_C1.5560.98
251_Y255_Y1.5330.98
515_T519_W1.5320.98
116_P122_R1.5230.98
337_D344_I1.5010.98
435_R438_R1.5010.98
63_K72_Y1.5000.98
340_I376_I1.4970.98
359_S362_K1.4820.97
498_F512_Q1.4810.97
1_R4_C1.4730.97
571_N575_A1.4730.97
73_F82_F1.4630.97
433_L436_I1.4540.97
324_Q389_R1.4500.97
69_F82_F1.4440.97
327_I386_A1.4440.97
487_Y501_Q1.4350.97
347_N373_F1.4340.97
353_V362_K1.4340.97
392_Y401_D1.4340.97
203_K209_D1.4290.97
476_I483_A1.4290.97
343_L377_F1.4260.97
392_Y397_W1.4240.97
108_L112_R1.4140.96
164_G209_D1.4140.96
245_Q248_Y1.4140.96
384_K388_L1.4120.96
385_L393_F1.4120.96
576_I580_N1.4080.96
158_G162_F1.4040.96
608_D611_A1.4020.96
60_M82_F1.3970.96
380_E401_D1.3940.96
162_F252_M1.3930.96
429_R434_A1.3880.96
354_E358_Q1.3840.96
50_K54_Y1.3820.96
115_R118_R1.3820.96
330_I484_N1.3790.96
325_G329_D1.3770.96
510_L561_Y1.3750.96
69_F73_F1.3720.95
112_R116_P1.3720.95
500_F506_S1.3670.95
13_F17_I1.3570.95
58_L62_L1.3570.95
12_W15_T1.3560.95
425_P429_R1.3520.95
326_F330_I1.3500.95
267_T274_V1.3470.95
300_Y303_A1.3460.95
478_S506_S1.3380.95
525_P528_N1.3370.95
438_R442_L1.3310.94
440_L443_I1.3240.94
571_N578_L1.3170.94
126_M275_I1.3060.94
235_V253_Y1.3020.94
343_L376_I1.3000.93
380_E387_A1.3000.93
85_V88_S1.2980.93
4_C65_V1.2950.93
13_F21_I1.2950.93
225_K228_M1.2940.93
355_T359_S1.2870.93
217_A230_I1.2850.93
312_P319_P1.2830.93
490_W501_Q1.2660.92
517_A520_D1.2610.92
478_S481_G1.2540.92
63_K78_C1.2530.92
109_R114_L1.2520.92
340_I344_I1.2500.92
523_L558_F1.2490.92
70_K73_F1.2470.91
73_F79_W1.2450.91
519_W523_L1.2380.91
159_V163_A1.2370.91
502_T505_N1.2360.91
59_E81_D1.2310.91
427_L430_V1.2280.91
429_R433_L1.2280.91
63_K68_G1.2230.90
558_F561_Y1.2230.90
558_F565_S1.2220.90
23_L27_A1.2220.90
482_M485_F1.2220.90
527_L555_I1.2200.90
377_F408_S1.2200.90
558_F566_F1.2190.90
271_F278_N1.2180.90
207_N213_A1.2170.90
336_F340_I1.2160.90
384_K392_Y1.2120.90
296_E299_K1.2110.90
554_G558_F1.2100.90
25_S30_F1.2100.90
384_K398_N1.2070.90
482_M503_F1.2060.90
318_R329_D1.2050.90
498_F509_C1.1990.89
5_Y9_E1.1870.89
428_F432_R1.1850.88
430_V438_R1.1840.88
640_S666_R1.1800.88
383_V387_A1.1790.88
450_R453_L1.1780.88
373_F377_F1.1750.88
80_L85_V1.1730.88
349_V353_V1.1730.88
256_F265_F1.1720.88
63_K81_D1.1720.88
503_F507_M1.1710.88
554_G557_F1.1710.88
347_N351_M1.1670.87
571_N581_F1.1650.87
142_N146_V1.1610.87
150_F153_I1.1560.87
60_M63_K1.1520.87
377_F384_K1.1500.86
21_I28_L1.1430.86
155_S214_G1.1400.86
293_M298_K1.1400.86
399_I403_V1.1400.86
572_M578_L1.1390.86
154_F158_G1.1380.86
187_K191_E1.1340.85
132_A136_A1.1300.85
331_V387_A1.1300.85
378_T405_V1.1300.85
344_I348_M1.1300.85
572_M577_I1.1280.85
561_Y566_F1.1270.85
59_E72_Y1.1260.85
267_T273_G1.1260.85
115_R120_L1.1250.85
255_Y259_F1.1180.84
374_V408_S1.1160.84
572_M575_A1.1150.84
10_H19_F1.1110.84
443_I456_L1.1100.84
593_S596_D1.1090.84
355_T358_Q1.1090.84
21_I24_S1.1070.83
14_E28_L1.1050.83
443_I446_A1.1030.83
113_A118_R1.1030.83
478_S483_A1.1020.83
59_E66_A1.0990.83
368_K372_L1.0980.83
155_S215_Y1.0950.83
348_M351_M1.0940.82
214_G219_L1.0940.82
575_A578_L1.0940.82
435_R440_L1.0940.82
88_S112_R1.0930.82
368_K375_A1.0920.82
344_I351_M1.0910.82
384_K401_D1.0870.82
440_L446_A1.0860.82
332_T388_L1.0840.82
52_F59_E1.0840.82
426_T429_R1.0820.81
370_N373_F1.0800.81
171_N199_L1.0790.81
295_E299_K1.0760.81
482_M486_A1.0750.81
616_E619_V1.0740.81
270_L274_V1.0740.81
59_E68_G1.0700.80
116_P120_L1.0690.80
297_Q301_Y1.0640.80
295_E298_K1.0620.80
269_N272_I1.0610.80
209_D214_G1.0600.80
342_F410_V1.0590.80
113_A116_P1.0580.79
178_P181_Y1.0550.79
369_I373_F1.0550.79
212_G478_S1.0530.79
658_D664_T1.0530.79
566_F570_V1.0510.79
500_F510_L1.0500.79
220_Q524_S1.0490.79
351_M370_N1.0480.79
430_V434_A1.0460.78
253_Y257_V1.0450.78
344_I347_N1.0440.78
130_V133_L1.0430.78
381_C385_L1.0420.78
575_A580_N1.0420.78
481_G484_N1.0400.78
210_N213_A1.0390.78
76_A79_W1.0380.78
604_W608_D1.0360.77
474_M510_L1.0350.77
225_K231_M1.0340.77
606_K626_A1.0300.77
397_W405_V1.0300.77
25_S49_D1.0290.77
293_M296_E1.0290.77
13_F59_E1.0280.77
291_I294_T1.0270.77
25_S28_L1.0270.77
512_Q522_L1.0270.77
481_G500_F1.0260.76
434_A437_G1.0250.76
90_V379_G1.0230.76
330_I383_V1.0230.76
53_T88_S1.0230.76
64_W73_F1.0220.76
33_I38_R1.0210.76
573_Y580_N1.0200.76
61_L65_V1.0190.76
339_T342_F1.0190.76
347_N370_N1.0180.76
166_F169_C1.0180.76
375_A379_G1.0180.76
146_V151_W1.0170.76
577_I580_N1.0130.75
21_I25_S1.0120.75
296_E300_Y1.0100.75
398_N404_V1.0100.75
49_D56_F1.0080.75
377_F380_E1.0070.75
72_Y85_V1.0060.74
120_L126_M1.0060.74
661_F664_T1.0050.74
649_V652_D1.0030.74
227_W517_A1.0030.74
292_F297_Q1.0000.74
219_L225_K1.0000.74
608_D615_I1.0000.74
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  
4dxwA40.26891000.805Contact Map
3rvyA20.26641000.811Contact Map
4bgnA20.26031000.815Contact Map
4jpzB20.17271000.827Contact Map
4dckA10.18611000.843Contact Map
3j9pD40.60951000.845Contact Map
2r9rB20.41481000.847Contact Map
3behA40.27131000.849Contact Map
4cbcA40.111999.90.873Contact Map
4ltoA40.166799.90.874Contact 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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