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OPENSEQ.org

2decoli

ID: 1409913778 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 544 (535)
Sequences: 1006 (831.7)
Seq/Len: 1.880
Nf(neff/√len): 36.0

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: 1.880).

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
382_Q411_D2.9341.00
271_V274_A2.7951.00
256_F265_L2.7541.00
268_R316_I2.5971.00
417_I428_A2.4921.00
274_A323_V2.4781.00
266_D314_N2.3921.00
492_S500_Q2.3411.00
235_G252_P2.3361.00
175_V189_S2.2641.00
160_D164_P2.2291.00
382_Q409_L2.2061.00
333_R357_E2.1920.99
524_L538_L2.1690.99
14_V42_A2.0830.99
318_H337_D2.0330.99
474_S493_G2.0110.99
266_D312_N2.0010.99
370_R388_E1.9950.99
270_D318_H1.9440.98
234_K253_D1.9100.98
58_I87_A1.8940.98
40_G60_L1.8160.97
174_G188_P1.7610.97
499_L516_L1.7460.96
388_E405_R1.7430.96
128_N154_N1.7220.96
499_L518_Y1.7110.96
314_N339_N1.6770.95
56_G89_L1.6760.95
194_N203_A1.6680.95
380_P391_R1.6650.95
334_L353_I1.6420.94
213_I238_V1.6340.94
265_L311_I1.6060.94
521_M524_L1.6040.94
16_L19_F1.5870.93
421_P435_G1.5810.93
349_L380_P1.5660.92
473_V493_G1.5660.92
172_V175_V1.5540.92
369_V387_I1.5430.92
371_K386_N1.5240.91
148_A176_D1.5170.91
230_R255_V1.5120.91
239_R432_L1.5090.91
503_Y537_D1.4990.90
86_T97_G1.4760.89
284_S374_L1.4470.88
176_D185_D1.4320.87
254_V267_G1.4180.86
159_G164_P1.4150.86
252_P272_P1.4140.86
331_K493_G1.4110.86
342_Q347_L1.3880.85
217_G231_V1.3860.85
134_L336_G1.3860.85
376_F379_P1.3780.84
183_P243_P1.3770.84
361_H366_D1.3710.84
264_T312_N1.3680.84
367_L403_G1.3640.83
125_G157_L1.3590.83
495_V516_L1.3500.83
252_P508_F1.3470.82
112_V125_G1.3460.82
251_S272_P1.3350.82
362_A367_L1.3340.82
148_A471_F1.3320.81
157_L166_L1.3270.81
218_D230_R1.3210.81
171_Q192_A1.3180.80
323_V507_I1.3140.80
17_N163_S1.3100.80
360_F413_P1.3100.80
406_V422_A1.3070.80
215_L233_A1.3040.79
252_P282_P1.2980.79
449_T452_L1.2920.79
108_F315_L1.2860.78
451_M455_L1.2770.77
189_S206_V1.2740.77
20_D37_I1.2710.77
15_N41_K1.2700.77
252_P269_V1.2690.77
428_A505_V1.2640.76
367_L517_R1.2640.76
320_G333_R1.2600.76
495_V499_L1.2600.76
494_Y500_Q1.2530.76
158_G167_F1.2450.75
85_L98_W1.2440.75
367_L418_F1.2320.74
124_G157_L1.2300.74
206_V495_V1.2300.74
534_Q539_L1.2270.73
430_S472_G1.2270.73
390_I418_F1.2200.73
315_L338_L1.2200.73
246_V527_E1.2150.72
184_F367_L1.2110.72
403_G418_F1.2100.72
336_G367_L1.2080.72
413_P433_L1.2070.72
417_I505_V1.2050.71
273_W322_N1.2030.71
418_F503_Y1.2000.71
200_S221_W1.2000.71
162_Q210_Q1.1960.71
265_L315_L1.1910.70
183_P241_T1.1880.70
199_R218_D1.1870.70
387_I450_S1.1870.70
402_A432_L1.1850.70
138_N147_A1.1820.69
246_V380_P1.1800.69
254_V265_L1.1770.69
49_T54_P1.1760.69
156_R516_L1.1730.69
200_S219_A1.1720.68
62_G65_V1.1720.68
203_A214_Y1.1700.68
332_A355_I1.1700.68
415_A429_L1.1650.68
126_N156_R1.1650.68
35_S66_Q1.1640.68
124_G156_R1.1600.67
327_A413_P1.1600.67
157_L406_V1.1590.67
275_R322_N1.1590.67
21_L36_G1.1580.67
240_I340_V1.1560.67
44_V307_A1.1550.67
325_I387_I1.1540.67
340_V349_L1.1520.67
329_G367_L1.1430.66
442_Q449_T1.1420.66
108_F216_N1.1420.66
166_L503_Y1.1410.65
66_Q135_A1.1390.65
59_T86_T1.1360.65
170_L241_T1.1350.65
374_L387_I1.1340.65
389_A404_V1.1340.65
54_P238_V1.1330.65
383_P421_P1.1330.65
532_V539_L1.1300.64
407_T489_V1.1290.64
40_G499_L1.1280.64
456_G463_I1.1260.64
364_G391_R1.1250.64
319_V336_G1.1250.64
408_G419_S1.1240.64
316_I339_N1.1180.63
124_G130_R1.1160.63
372_G452_L1.1120.63
482_G504_G1.1080.62
315_L364_G1.1060.62
17_N64_N1.1050.62
230_R257_E1.1030.62
196_N526_L1.1020.61
85_L171_Q1.1020.61
401_I423_M1.0960.61
193_V420_D1.0950.61
208_T238_V1.0950.61
252_P431_Y1.0940.61
407_T416_E1.0940.61
501_V504_G1.0940.61
194_N201_T1.0930.61
504_G515_T1.0910.60
405_R416_E1.0910.60
439_E478_L1.0900.60
252_P504_G1.0880.60
352_Q373_E1.0870.60
494_Y497_P1.0830.59
376_F383_P1.0830.59
19_F39_T1.0820.59
238_V484_G1.0810.59
267_G383_P1.0800.59
85_L353_I1.0780.59
362_A528_A1.0760.59
97_G100_I1.0750.59
332_A433_L1.0740.59
365_Q436_Q1.0740.59
112_V482_G1.0720.58
184_F463_I1.0690.58
328_F367_L1.0680.58
126_N154_N1.0680.58
22_A124_G1.0670.58
127_V444_D1.0670.58
279_H336_G1.0670.58
312_N406_V1.0650.58
158_G491_V1.0630.57
372_G389_A1.0630.57
203_A216_N1.0630.57
379_P527_E1.0600.57
446_A449_T1.0570.57
27_F41_K1.0550.56
193_V253_D1.0540.56
158_G236_S1.0530.56
365_Q391_R1.0530.56
434_R444_D1.0510.56
44_V53_L1.0470.56
365_Q450_S1.0470.56
196_N199_R1.0440.55
347_L516_L1.0440.55
427_A431_Y1.0430.55
232_T255_V1.0410.55
64_N265_L1.0400.55
452_L519_R1.0370.55
190_Q199_R1.0360.54
56_G80_F1.0350.54
385_L406_V1.0330.54
60_L207_R1.0320.54
42_A45_A1.0320.54
11_R55_Q1.0320.54
438_L441_D1.0270.53
423_M431_Y1.0270.53
417_I429_L1.0240.53
190_Q395_A1.0230.53
165_Q198_M1.0220.53
71_V74_A1.0210.53
402_A413_P1.0200.53
498_G518_Y1.0200.53
387_I406_V1.0200.53
155_L507_I1.0190.53
367_L391_R1.0180.52
123_L164_P1.0160.52
157_L165_Q1.0160.52
334_L367_L1.0160.52
476_L491_V1.0150.52
78_V120_R1.0150.52
307_A315_L1.0140.52
384_Y409_L1.0120.52
376_F435_G1.0120.52
317_V396_T1.0110.52
487_S490_V1.0110.52
177_I426_Q1.0090.51
378_G413_P1.0090.51
432_L465_G1.0080.51
503_Y512_A1.0070.51
206_V213_I1.0070.51
17_N44_V1.0060.51
151_V261_N1.0060.51
170_L382_Q1.0050.51
370_R390_I1.0050.51
205_T269_V1.0040.51
268_R318_H1.0040.51
360_F402_A1.0040.51
332_A352_Q1.0010.51
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  
3hpeA20.273919.50.972Contact Map
3lycA160.415415.80.974Contact Map
4c69X10.424614.10.974Contact Map
1wubA10.290411.20.975Contact Map
3petA20.382410.40.976Contact Map
3ap9A10.27218.40.977Contact Map
2d6mA20.27216.40.978Contact Map
2fgsA10.27215.90.978Contact Map
1y0gA40.27764.90.979Contact Map
2jmmA10.15074.90.979Contact 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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