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OPENSEQ.org

spok1b again -force run

ID: 1490952127 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 600 (544)
Sequences: 527 (425.1)
Seq/Len: 0.969
Nf(neff/√len): 18.2

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: 0.969).

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
357_Q361_F2.8711.00
547_G569_L2.7221.00
219_D240_K2.5280.99
250_V316_L2.2310.98
112_T115_N2.0960.97
240_K244_K2.0490.96
291_A309_V2.0190.96
308_Y358_L2.0120.95
294_Q298_Y1.9340.94
591_E595_Y1.9000.93
240_K243_H1.8900.93
493_C497_C1.8800.93
129_K132_D1.7730.90
564_F579_G1.7280.88
259_L289_A1.7220.88
387_L390_W1.7200.88
495_Q498_L1.7100.87
76_P82_W1.6920.86
362_C370_A1.6870.86
357_Q360_S1.6850.86
495_Q499_L1.6310.84
310_A315_L1.6280.83
305_S319_Y1.6120.83
513_N517_H1.6040.82
318_L330_C1.6020.82
527_V532_F1.5980.82
123_H141_R1.5910.81
43_Y142_P1.5800.81
149_V152_T1.5770.81
217_Q220_G1.5760.81
494_T498_L1.5710.80
511_C517_H1.5640.80
33_L36_R1.5570.80
84_N88_V1.5350.78
497_C501_L1.5300.78
55_L63_S1.5270.78
303_G312_G1.5250.78
307_G317_L1.5170.77
508_D511_C1.5170.77
428_T431_K1.5050.76
512_P517_H1.5020.76
517_H525_H1.5000.76
508_D512_P1.4820.75
508_D513_N1.4780.74
497_C500_G1.4770.74
494_T497_C1.4770.74
296_F300_I1.4740.74
575_F580_T1.4710.74
595_Y598_L1.4500.72
82_W85_F1.4460.72
241_A244_K1.4410.72
468_R471_G1.4380.71
309_V320_V1.4330.71
402_L406_E1.4260.71
94_F101_C1.4250.70
40_F43_Y1.4210.70
307_G313_R1.4210.70
527_V535_M1.4160.70
375_S379_A1.4110.69
537_E577_G1.4070.69
316_L330_C1.4070.69
36_R42_E1.4070.69
39_T42_E1.3920.68
573_Y578_K1.3890.68
356_A362_C1.3820.67
317_L357_Q1.3800.67
311_A314_C1.3790.67
493_C498_L1.3690.66
569_L577_G1.3660.66
305_S320_V1.3640.66
292_L328_L1.3630.66
128_E240_K1.3630.66
551_V563_L1.3610.65
168_S172_R1.3610.65
335_P338_D1.3600.65
528_N535_M1.3600.65
167_F170_N1.3600.65
303_G306_Y1.3590.65
318_L327_T1.3570.65
573_Y591_E1.3530.65
532_F577_G1.3510.65
398_A401_G1.3440.64
560_M587_R1.3400.64
88_V92_H1.3340.63
70_V75_Y1.3330.63
219_D244_K1.3300.63
304_V307_G1.3250.62
578_K591_E1.3240.62
497_C508_D1.3150.61
76_P85_F1.3100.61
309_V316_L1.3060.61
499_L527_V1.2960.60
548_C579_G1.2890.59
219_D294_Q1.2730.58
492_Y497_C1.2690.57
308_Y315_L1.2680.57
219_D238_D1.2640.57
563_L568_L1.2630.57
591_E598_L1.2600.57
165_F594_V1.2580.56
327_T330_C1.2570.56
355_V361_F1.2570.56
498_L501_L1.2570.56
466_A471_G1.2550.56
295_V302_Y1.2500.56
109_S112_T1.2490.56
253_A257_E1.2490.56
146_I150_L1.2470.55
161_I170_N1.2460.55
293_T298_Y1.2420.55
147_L159_A1.2410.55
303_G494_T1.2390.55
560_M568_L1.2380.55
296_F326_Q1.2340.54
247_I314_C1.2340.54
310_A328_L1.2340.54
460_P463_S1.2320.54
289_A298_Y1.2270.54
294_Q299_M1.2250.53
572_G578_K1.2240.53
240_K298_Y1.2230.53
496_A566_L1.2200.53
563_L588_L1.2120.52
299_M303_G1.2110.52
317_L333_C1.2110.52
508_D517_H1.2110.52
238_D244_K1.2090.52
379_A383_A1.2070.52
108_E112_T1.2060.52
219_D298_Y1.2060.52
142_P146_I1.2030.51
383_A390_W1.2030.51
250_V332_P1.2000.51
560_M584_R1.1990.51
495_Q501_L1.1940.50
245_V253_A1.1940.50
492_Y575_F1.1920.50
491_Q514_V1.1910.50
335_P339_V1.1910.50
548_C577_G1.1870.50
401_G405_A1.1840.50
322_R379_A1.1830.49
112_T116_L1.1820.49
251_R334_L1.1800.49
558_G572_G1.1780.49
360_S365_S1.1780.49
580_T592_G1.1760.49
219_D243_H1.1740.49
493_C508_D1.1730.49
79_L94_F1.1720.48
573_Y595_Y1.1710.48
111_S115_N1.1700.48
297_D301_T1.1660.48
398_A406_E1.1630.48
51_L78_R1.1580.47
297_D310_A1.1570.47
497_C507_L1.1560.47
572_G591_E1.1540.47
247_I250_V1.1510.47
558_G573_Y1.1490.46
218_P224_R1.1490.46
61_S66_G1.1450.46
574_T578_K1.1440.46
385_A440_A1.1430.46
308_Y318_L1.1430.46
578_K595_Y1.1430.46
532_F567_E1.1390.45
493_C500_G1.1380.45
315_L358_L1.1350.45
90_H93_Y1.1340.45
292_L316_L1.1330.45
558_G561_G1.1300.45
329_Y362_C1.1300.45
42_E105_Q1.1280.44
543_S546_K1.1280.44
540_L565_K1.1270.44
108_E115_N1.1260.44
546_K577_G1.1260.44
558_G578_K1.1260.44
531_S534_D1.1220.44
309_V315_L1.1220.44
313_R317_L1.1200.44
289_A294_Q1.1180.44
237_Y241_A1.1180.44
295_V298_Y1.1180.44
122_D141_R1.1170.43
317_L361_F1.1130.43
236_I249_H1.1130.43
292_L358_L1.1120.43
246_A249_H1.1100.43
287_F290_M1.1090.43
288_I292_L1.1050.42
128_E219_D1.1020.42
161_I172_R1.1010.42
393_S402_L1.0980.42
567_E570_P1.0960.42
379_A390_W1.0950.41
580_T584_R1.0910.41
263_V293_T1.0890.41
359_V362_C1.0860.41
64_S127_N1.0860.41
300_I308_Y1.0850.41
495_Q575_F1.0810.40
565_K574_T1.0800.40
131_I222_G1.0760.40
127_N172_R1.0760.40
536_V548_C1.0730.40
310_A358_L1.0700.39
176_Q181_S1.0700.39
221_V242_A1.0700.39
157_G220_G1.0630.39
128_E238_D1.0620.39
548_C564_F1.0610.38
495_Q564_F1.0600.38
169_A174_L1.0600.38
321_D379_A1.0590.38
333_C336_A1.0580.38
153_H156_A1.0570.38
52_Y336_A1.0570.38
38_T42_E1.0550.38
218_P221_V1.0540.38
58_T66_G1.0540.38
399_Y402_L1.0500.38
550_M564_F1.0500.38
519_F551_V1.0480.37
581_V584_R1.0480.37
492_Y551_V1.0470.37
59_D63_S1.0470.37
290_M293_T1.0460.37
334_L350_L1.0460.37
129_K136_V1.0460.37
40_F156_A1.0450.37
539_Q547_G1.0440.37
339_V354_A1.0440.37
361_F597_R1.0420.37
159_A172_R1.0420.37
564_F577_G1.0420.37
543_S569_L1.0410.37
73_K82_W1.0410.37
536_V547_G1.0410.37
145_G223_I1.0390.37
73_K76_P1.0380.36
292_L333_C1.0370.36
116_L141_R1.0370.36
62_R70_V1.0350.36
74_Y94_F1.0340.36
359_V363_L1.0330.36
52_Y134_F1.0320.36
240_K294_Q1.0310.36
66_G244_K1.0310.36
485_D531_S1.0310.36
239_Y244_K1.0300.36
75_Y260_F1.0290.36
244_K294_Q1.0280.36
305_S372_E1.0250.35
238_D241_A1.0240.35
190_D193_L1.0230.35
529_A577_G1.0190.35
291_A316_L1.0190.35
238_D243_H1.0180.35
292_L297_D1.0130.34
231_Q247_I1.0120.34
234_A263_V1.0120.34
493_C511_C1.0120.34
462_A560_M1.0120.34
555_G581_V1.0100.34
563_L575_F1.0100.34
332_P359_V1.0080.34
494_T500_G1.0060.34
238_D294_Q1.0060.34
402_L421_Y1.0050.34
327_T331_H1.0040.34
497_C511_C1.0040.34
493_C501_L1.0030.34
52_Y139_V1.0020.33
532_F543_S1.0020.33
223_I356_A1.0020.33
112_T118_T1.0020.33
564_F576_V1.0020.33
527_V543_S1.0010.33
297_D328_L1.0000.33
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  
3jr1A20.121781.70.976Contact Map
4lgdA40.11577.80.977Contact Map
2olcA20.1183690.979Contact Map
3f7wA10.1117680.979Contact Map
2pywA20.12567.20.979Contact Map
3mwuA10.103367.10.979Contact Map
4md7E40.14567.10.979Contact Map
3lxlA10.166.50.979Contact Map
3warA10.148363.60.979Contact Map
3sg8A20.1133630.979Contact 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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