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pafa

ID: 1505351539 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 546 (541)
Sequences: 1171 (838.9)
Seq/Len: 2.165
Nf(neff/√len): 36.1

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: 2.165).

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
147_G175_T5.1611.00
276_L301_L4.6541.00
329_L333_F4.3541.00
158_G170_A3.6151.00
414_L419_V3.5741.00
284_D339_K3.4821.00
143_T296_F3.1881.00
518_D537_G2.9451.00
84_T137_L2.8491.00
67_L540_I2.8351.00
436_V467_I2.8291.00
280_D331_D2.7441.00
237_W364_A2.6731.00
244_K251_Y2.6521.00
433_V469_I2.5581.00
55_G330_A2.5531.00
512_Q542_E2.4991.00
142_V524_S2.4631.00
196_E202_N2.4001.00
35_L347_V2.3821.00
281_A285_G2.3791.00
301_L332_F2.3751.00
221_L323_L2.2271.00
346_L526_L2.2031.00
139_S534_G2.1771.00
388_F422_Y2.1341.00
51_K222_L2.1241.00
283_I335_K2.0900.99
307_V321_T2.0690.99
51_K229_E2.0470.99
85_S95_H2.0450.99
222_L226_Q2.0130.99
118_T135_R1.9730.99
86_I350_S1.9660.99
94_I534_G1.9530.99
234_N247_P1.9450.99
336_L345_Y1.9450.99
55_G334_N1.9410.99
154_S291_D1.9370.99
276_L332_F1.9310.99
57_F329_L1.9210.99
290_A339_K1.9160.99
370_G475_Y1.9090.99
333_F347_V1.9050.99
273_T328_D1.8910.99
211_A262_K1.8550.98
346_L504_G1.8480.98
383_K426_E1.8320.98
109_K115_S1.8300.98
280_D335_K1.8100.98
424_M467_I1.8060.98
409_L414_L1.7780.98
33_V336_L1.7760.98
239_G482_K1.7660.98
408_V412_S1.7600.97
140_T145_Q1.7600.97
287_Q290_A1.7580.97
387_K422_Y1.7560.97
54_E58_K1.7510.97
76_P458_G1.7420.97
420_R438_S1.7250.97
404_F419_V1.7190.97
160_S187_F1.7070.97
59_R337_D1.6920.97
87_F298_T1.6830.96
121_P124_T1.6790.96
39_Q308_G1.6720.96
59_R333_F1.6580.96
406_R416_L1.6550.96
75_V489_W1.6540.96
315_S318_V1.6480.96
34_G348_F1.6360.96
199_K203_D1.6280.95
201_V278_M1.6270.95
85_S516_M1.6000.95
157_V282_A1.5950.95
63_T501_M1.5810.94
330_A334_N1.5770.94
70_V498_L1.5590.94
390_A393_I1.5580.94
60_M499_L1.5560.94
142_V296_F1.5550.94
67_L514_Y1.5410.93
415_K418_D1.5400.93
70_V514_Y1.5370.93
284_D335_K1.5320.93
287_Q291_D1.5250.93
277_Q280_D1.5200.93
86_I519_I1.5190.93
51_K319_E1.5140.93
51_K226_Q1.5090.92
71_H494_S1.5080.92
88_T141_T1.5040.92
170_A177_A1.5030.92
157_V286_N1.4960.92
331_D335_K1.4700.91
55_G329_L1.4640.91
108_G395_A1.4600.91
289_G295_D1.4480.90
305_D309_H1.4450.90
79_T352_D1.4440.90
409_L419_V1.4420.90
138_W460_N1.4370.90
254_L268_T1.4370.90
432_S475_Y1.4220.89
52_Y57_F1.4170.89
337_D345_Y1.4150.89
309_H486_H1.3940.88
147_G156_V1.3890.88
51_K323_L1.3860.88
362_M367_M1.3850.87
40_M322_Y1.3830.87
60_M333_F1.3820.87
173_N367_M1.3720.87
271_G303_S1.3680.87
336_L347_V1.3670.87
277_Q331_D1.3610.86
178_F286_N1.3540.86
134_P294_T1.3470.85
385_K391_D1.3430.85
157_V178_F1.3370.85
176_G194_T1.3330.85
329_L332_F1.3290.84
438_S441_E1.3250.84
72_I496_I1.3190.84
36_V86_I1.3010.83
233_D238_E1.2980.82
37_V349_L1.2970.82
376_M427_L1.2960.82
79_T305_D1.2940.82
90_S94_I1.2930.82
382_V386_Q1.2920.82
320_D324_R1.2910.82
174_P177_A1.2810.81
305_D486_H1.2790.81
124_T127_N1.2690.80
155_K291_D1.2640.80
372_F471_S1.2550.79
208_N211_A1.2540.79
72_I516_M1.2540.79
162_K309_H1.2540.79
342_K345_Y1.2500.79
420_R424_M1.2470.79
391_D408_V1.2460.79
222_L327_R1.2460.79
360_G371_F1.2450.79
146_L296_F1.2440.79
145_Q530_Q1.2420.78
79_T309_H1.2400.78
65_Y510_S1.2350.78
189_T194_T1.2320.78
498_L514_Y1.2300.77
83_H309_H1.2270.77
276_L280_D1.2260.77
404_F423_V1.2250.77
424_M441_E1.2240.77
234_N248_T1.2210.77
79_T100_N1.2200.77
79_T353_H1.2190.77
427_L469_I1.2090.76
521_P535_A1.2070.76
424_M428_K1.2060.76
190_S193_Y1.2010.75
498_L540_I1.1870.74
473_D533_S1.1840.74
220_T224_I1.1810.73
79_T83_H1.1790.73
132_H167_I1.1720.73
335_K339_K1.1720.73
500_F543_V1.1710.72
154_S293_I1.1690.72
160_S275_T1.1660.72
309_H352_D1.1640.72
333_F337_D1.1610.72
112_Y163_D1.1600.71
502_G505_I1.1590.71
423_V467_I1.1580.71
44_Y48_Y1.1490.70
59_R347_V1.1470.70
60_M64_G1.1460.70
427_L436_V1.1410.70
153_T228_T1.1400.70
37_V325_L1.1360.69
87_F348_F1.1320.69
78_V81_I1.1310.69
58_K62_N1.1300.69
393_I414_L1.1290.68
441_E444_E1.1260.68
40_M44_Y1.1260.68
83_H100_N1.1250.68
313_P355_A1.1250.68
410_A413_K1.1250.68
165_A300_N1.1240.68
90_S95_H1.1230.68
100_N486_H1.1230.68
105_K466_D1.1190.67
304_T321_T1.1190.67
266_R306_Y1.1180.67
83_H162_K1.1180.67
524_S529_I1.1090.66
143_T156_V1.1070.66
334_N338_K1.1060.66
276_L328_D1.1030.66
220_T316_I1.1010.66
337_D341_G1.0990.65
42_W66_S1.0980.65
309_H353_H1.0950.65
105_K403_Y1.0890.64
380_M426_E1.0880.64
103_Y107_L1.0870.64
31_L295_D1.0850.64
100_N309_H1.0850.64
504_G526_L1.0810.64
353_H486_H1.0800.63
234_N246_T1.0790.63
281_A284_D1.0780.63
273_T277_Q1.0770.63
244_K255_A1.0740.63
33_V347_V1.0730.63
51_K228_T1.0650.62
406_R466_D1.0640.62
252_T256_K1.0590.61
160_S300_N1.0570.61
114_T132_H1.0540.61
420_R439_T1.0540.61
401_Q465_G1.0520.60
66_S499_L1.0510.60
12_L18_L1.0500.60
56_G330_A1.0500.60
162_K486_H1.0470.60
158_G167_I1.0460.60
100_N305_D1.0450.60
167_I170_A1.0440.60
65_Y508_G1.0420.59
416_L420_R1.0410.59
341_G344_N1.0370.59
240_L482_K1.0370.59
353_H493_D1.0360.59
231_S235_V1.0330.58
276_L331_D1.0330.58
164_R486_H1.0320.58
447_I456_I1.0300.58
38_D100_N1.0280.58
93_S435_Y1.0260.58
420_R440_E1.0250.57
514_Y540_I1.0240.57
524_S535_A1.0220.57
235_V364_A1.0210.57
434_L472_K1.0190.57
49_Y58_K1.0190.57
104_D111_V1.0170.57
79_T162_K1.0130.56
217_G255_A1.0120.56
112_Y170_A1.0120.56
79_T164_R1.0080.56
510_S514_Y1.0080.56
164_R309_H1.0070.55
77_T487_S1.0060.55
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  
3q3qA10.91031000.442Contact Map
3szyA10.70881000.63Contact Map
1ei6A40.69231000.648Contact Map
2gsoA20.67771000.657Contact Map
3nkqA10.69781000.659Contact Map
4gtwA20.72711000.666Contact Map
4lr2A10.6741000.674Contact Map
2qzuA10.60621000.771Contact Map
2w5vA20.60261000.776Contact Map
3b5qA20.52381000.781Contact 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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