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OPENSEQ.org

d30PEX5S

ID: 1509381588 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 572 (572)
Sequences: 651 (507.4)
Seq/Len: 1.138
Nf(neff/√len): 21.2

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: 1.138).

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
118_W121_E3.7871.00
233_L237_F2.9281.00
301_P327_Q2.8321.00
254_L258_L2.7661.00
140_W143_E2.5281.00
357_R360_E2.4330.99
255_Q258_L2.4130.99
118_W122_F2.0890.97
220_W224_F2.0480.97
105_R109_V2.0470.97
251_W255_Q2.0460.97
351_A494_T1.9550.96
305_G321_F1.9450.96
343_A351_A1.8380.94
254_L257_E1.8300.93
159_W162_E1.8230.93
251_W254_L1.7440.91
319_L323_A1.7170.90
63_V67_L1.7070.90
105_R108_G1.6930.89
201_F205_V1.6890.89
255_Q259_E1.6860.89
343_A494_T1.6580.88
210_L214_E1.6130.86
348_E486_L1.5570.83
370_M456_G1.5560.83
271_W275_Y1.5550.83
140_W144_F1.5490.83
522_R530_I1.5450.83
436_E440_A1.5410.82
488_W507_A1.5360.82
306_L337_Y1.5250.82
258_L261_M1.5240.81
87_L90_E1.5230.81
172_W175_E1.5220.81
251_W257_E1.5210.81
351_A470_A1.5060.80
500_Q503_E1.4780.79
28_K481_R1.4710.78
257_E261_M1.4620.78
304_E307_R1.4570.77
269_H272_L1.4530.77
342_Q345_N1.4510.77
115_S119_A1.4430.76
529_C541_H1.4340.76
235_M238_E1.4260.75
298_H301_P1.4240.75
343_A470_A1.4140.74
325_V331_H1.4140.74
389_L495_L1.4130.74
321_F518_Y1.4100.74
106_A109_V1.4080.74
237_F241_K1.4080.74
302_F337_Y1.4020.73
172_W176_P1.4000.73
139_D147_E1.3960.73
519_I522_R1.3910.73
258_L263_K1.3900.72
469_K498_G1.3890.72
221_V224_F1.3890.72
16_P531_N1.3850.72
210_L213_S1.3730.71
121_E125_A1.3720.71
545_A566_I1.3670.71
567_W571_R1.3670.71
385_A495_L1.3620.70
177_E180_A1.3550.70
116_E119_A1.3460.69
526_G542_F1.3360.68
397_P400_A1.3330.68
441_A446_P1.3230.67
318_V462_N1.3220.67
452_D481_R1.3200.67
302_F331_H1.3180.67
536_R540_E1.3160.66
252_D260_E1.3150.66
238_E241_K1.2890.64
198_A201_F1.2880.64
300_Q303_E1.2870.64
525_L528_S1.2870.64
471_V475_T1.2830.64
300_Q548_M1.2760.63
336_Q358_C1.2660.62
250_F254_L1.2650.62
79_P82_F1.2650.62
390_R528_S1.2620.62
215_G221_V1.2620.62
254_L262_A1.2600.61
137_E140_W1.2590.61
367_T468_D1.2570.61
213_S216_T1.2550.61
220_W223_Q1.2540.61
12_G18_M1.2530.61
137_E141_S1.2500.61
141_S145_I1.2460.60
289_F377_T1.2460.60
257_E262_A1.2460.60
487_L494_T1.2460.60
355_L474_F1.2430.60
234_D237_F1.2420.60
493_A496_A1.2390.60
465_G542_F1.2360.59
184_W188_Y1.2350.59
141_S144_F1.2340.59
116_E120_Q1.2320.59
462_N532_L1.2320.59
159_W163_Y1.2310.59
439_L443_R1.2260.58
47_S50_A1.2260.58
529_C537_E1.2230.58
431_F435_K1.2180.58
481_R484_D1.2120.57
313_D316_N1.2120.57
434_V456_G1.2110.57
347_Q549_Q1.2050.56
258_L262_A1.2030.56
250_F257_E1.1990.56
379_E495_L1.1980.56
520_R524_N1.1930.55
428_D519_I1.1930.55
255_Q262_A1.1930.55
234_D238_E1.1920.55
311_E548_M1.1910.55
377_T459_V1.1910.55
253_K257_E1.1900.55
4_R7_V1.1890.55
215_G220_W1.1880.55
373_A478_L1.1880.55
494_T499_N1.1880.55
345_N522_R1.1710.53
441_A456_G1.1700.53
469_K522_R1.1670.53
307_R311_E1.1640.52
366_Q398_A1.1630.52
63_V501_S1.1620.52
328_D331_H1.1580.52
513_E548_M1.1580.52
529_C538_A1.1570.52
87_L92_Q1.1570.52
250_F255_Q1.1550.52
118_W125_A1.1530.51
302_F333_E1.1520.51
178_G181_T1.1520.51
301_P304_E1.1510.51
305_G317_A1.1510.51
305_G528_S1.1510.51
491_L507_A1.1500.51
321_F368_A1.1500.51
235_M241_K1.1490.51
454_Q473_C1.1490.51
139_D146_S1.1480.51
534_A549_Q1.1460.51
442_V453_V1.1450.51
19_K22_G1.1430.50
104_Q109_V1.1420.50
198_A209_K1.1400.50
427_S465_G1.1380.50
318_V400_A1.1370.50
114_L117_N1.1370.50
99_F102_A1.1360.50
357_R513_E1.1360.50
342_Q346_E1.1350.50
459_V526_G1.1340.50
176_P180_A1.1330.49
194_L198_A1.1320.49
82_F91_M1.1310.49
247_D250_F1.1280.49
254_L261_M1.1270.49
510_R513_E1.1260.49
305_G320_L1.1250.49
342_Q399_Y1.1250.49
467_Y551_K1.1230.48
302_F321_F1.1200.48
223_Q226_R1.1200.48
217_S220_W1.1190.48
377_T386_C1.1140.48
162_E165_E1.1130.48
315_P318_V1.1090.47
470_A494_T1.1040.47
139_D143_E1.1010.46
464_S467_Y1.1000.46
293_N319_L1.0990.46
181_T185_Y1.0990.46
255_Q270_P1.0980.46
440_A443_R1.0960.46
208_P212_N1.0960.46
79_P87_L1.0950.46
261_M264_R1.0940.46
377_T431_F1.0930.46
305_G446_P1.0910.45
103_P106_A1.0910.45
138_T148_V1.0910.45
201_F204_K1.0880.45
271_W274_D1.0870.45
231_S239_R1.0860.45
461_F472_D1.0860.45
251_W262_A1.0860.45
176_P179_T1.0850.45
308_R316_N1.0850.45
344_E371_A1.0850.45
394_R405_P1.0850.45
224_F227_P1.0830.45
471_V501_S1.0810.44
315_P519_I1.0800.44
299_P535_H1.0800.44
232_A237_F1.0760.44
316_N550_R1.0740.44
233_L241_K1.0720.44
222_D226_R1.0720.44
199_S204_K1.0690.43
276_D279_T1.0690.43
344_E549_Q1.0690.43
173_L176_P1.0670.43
29_A315_P1.0650.43
221_V226_R1.0620.43
248_V252_D1.0610.43
488_W542_F1.0580.42
455_C494_T1.0560.42
256_A260_E1.0540.42
362_K505_V1.0540.42
195_Q198_A1.0530.42
350_L449_I1.0510.42
22_G435_K1.0510.42
306_L309_L1.0500.42
399_Y469_K1.0480.41
373_A473_C1.0480.41
317_A488_W1.0470.41
11_C15_N1.0460.41
302_F306_L1.0450.41
462_N527_I1.0450.41
82_F87_L1.0430.41
28_K31_R1.0400.41
501_S518_Y1.0400.41
496_A522_R1.0390.41
525_L538_A1.0380.40
355_L538_A1.0380.40
352_I385_A1.0350.40
119_A122_F1.0350.40
351_A487_L1.0340.40
160_A163_Y1.0290.40
247_D251_W1.0290.40
250_F258_L1.0260.39
253_K262_A1.0250.39
182_D188_Y1.0250.39
454_Q472_D1.0230.39
291_E476_A1.0230.39
270_P273_S1.0230.39
449_I453_V1.0230.39
232_A241_K1.0210.39
467_Y553_R1.0200.39
107_P110_A1.0190.39
245_E248_V1.0190.39
120_Q125_A1.0180.39
252_D256_A1.0180.39
379_E501_S1.0180.39
374_V464_S1.0170.39
490_K503_E1.0160.38
274_D277_D1.0150.38
351_A464_S1.0150.38
293_N323_A1.0150.38
21_A503_E1.0140.38
348_E400_A1.0130.38
526_G529_C1.0130.38
490_K499_N1.0120.38
194_L202_V1.0110.38
517_G529_C1.0110.38
348_E502_E1.0080.38
517_G526_G1.0070.38
221_V225_T1.0050.37
389_L507_A1.0050.37
360_E432_L1.0050.37
498_G501_S1.0040.37
342_Q522_R1.0040.37
302_F305_G1.0030.37
253_K260_E1.0030.37
334_A453_V1.0030.37
200_D204_K1.0020.37
27_D31_R1.0020.37
257_E264_R1.0000.37
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  
4eqfA10.44061000.772Contact Map
1fchA20.47551000.772Contact Map
3cv0A10.47031000.82Contact Map
3dssA10.45981000.826Contact Map
3draA10.48251000.833Contact Map
1w3bA20.46151000.836Contact Map
3q7aA10.47551000.842Contact Map
4l9pA10.48781000.843Contact Map
4ynvA201000.848Contact Map
1dceA20.437199.90.853Contact 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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