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OPENSEQ.org

b -force run

ID: 1512032649 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 661 (625)
Sequences: 606 (452.3)
Seq/Len: 0.970
Nf(neff/√len): 18.1

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: 0.970).

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
197_C208_C2.3750.99
298_V360_V2.2470.98
298_V549_V2.2430.98
237_V360_V2.1840.98
298_V421_V2.1720.97
55_L176_V2.1120.97
176_V298_V2.0900.97
321_W327_C2.0880.96
437_S446_S2.0200.96
197_C202_W2.0100.95
114_M298_V2.0030.95
176_V360_V1.9870.95
237_V421_V1.9850.95
156_P527_P1.9630.95
55_L360_V1.9590.94
222_G405_G1.9470.94
114_M549_V1.9260.94
144_P265_P1.9070.93
176_V237_V1.8890.93
636_C641_L1.8880.93
298_V482_I1.8810.93
237_V298_V1.8680.92
76_C91_C1.8630.92
360_V421_V1.8620.92
133_V314_I1.8620.92
314_I323_E1.8610.92
65_T85_P1.8520.92
253_I262_P1.8320.91
421_V549_V1.8300.91
239_F362_Y1.7680.89
195_V204_L1.7510.89
59_C76_C1.7360.88
55_L298_V1.7330.88
139_G201_G1.7260.88
367_G556_H1.7150.87
387_P576_P1.7110.87
98_N122_Y1.7100.87
278_P340_P1.7070.87
360_V549_V1.7040.87
302_C316_C1.7040.87
206_P325_P1.7040.87
55_L237_V1.6960.87
208_C213_C1.6860.86
237_V549_V1.6830.86
482_I549_V1.6780.86
98_N119_A1.6760.86
302_C327_C1.6700.85
114_M360_V1.6610.85
325_P448_P1.6600.85
114_M237_V1.6580.85
114_M176_V1.6420.84
553_C578_C1.6420.84
118_C135_C1.6390.84
253_I437_S1.6320.84
421_V482_I1.6300.84
277_P527_P1.6250.83
176_V421_V1.6220.83
202_W208_C1.6180.83
156_P399_P1.6140.83
96_L99_G1.6110.83
357_G418_G1.6060.82
306_F557_H1.6040.82
244_N305_N1.5920.82
265_P387_P1.5830.81
216_L239_F1.5800.81
360_V482_I1.5720.80
235_D480_D1.5690.80
265_P448_P1.5680.80
116_Y551_Y1.5650.80
138_D200_Y1.5640.80
216_L339_P1.5620.80
180_C197_C1.5520.79
122_Y245_Y1.5480.79
195_V314_I1.5380.78
85_P265_P1.5380.78
636_C646_C1.5330.78
197_C213_C1.5320.78
260_W267_C1.5260.78
505_C515_C1.5250.78
146_C389_C1.5180.77
160_N184_Y1.5110.77
144_P448_P1.5030.76
174_D480_D1.4990.76
565_A574_T1.4970.76
360_V612_I1.4950.76
553_C567_C1.4940.75
176_V549_V1.4920.75
418_G609_G1.4760.74
126_G188_G1.4730.74
247_L370_L1.4710.74
114_M421_V1.4670.74
237_V482_I1.4640.73
421_V612_I1.4620.73
239_F265_P1.4620.73
135_C140_W1.4620.73
140_W146_C1.4480.72
116_Y239_F1.4400.72
641_L646_C1.4390.72
178_Y300_I1.4390.72
55_L114_M1.4390.72
418_G479_G1.4350.71
53_K296_E1.4290.71
387_P513_P1.4290.71
59_C87_C1.4250.70
219_I222_G1.4230.70
367_G428_Y1.4210.70
530_I533_G1.4210.70
344_N365_K1.4160.70
142_S262_P1.4130.70
244_N619_D1.4110.69
442_G570_G1.4100.69
59_C81_W1.4060.69
415_Y543_Y1.3990.68
239_F423_Y1.3950.68
423_Y448_P1.3930.68
144_P387_P1.3860.67
325_P431_L1.3820.67
397_K525_T1.3790.67
180_C208_C1.3780.67
255_C267_C1.3730.66
292_Y415_Y1.3590.65
99_G144_P1.3530.65
274_C327_C1.3470.64
368_Y557_H1.3360.63
283_S405_G1.3260.62
249_G310_G1.3180.62
135_C146_C1.3110.61
56_S82_S1.3090.61
30_V57_F1.3080.61
567_C578_C1.3040.60
116_Y362_Y1.3020.60
133_V195_V1.3010.60
237_V612_I1.2980.60
486_C505_C1.2950.60
382_K443_K1.2950.60
480_D547_S1.2920.59
423_Y551_Y1.2910.59
148_K269_G1.2900.59
616_C636_C1.2850.59
383_W389_C1.2840.59
195_V253_I1.2810.58
116_Y300_I1.2690.57
302_C321_W1.2650.57
570_G578_C1.2650.57
57_F300_I1.2620.57
245_Y358_D1.2610.57
585_S614_F1.2610.57
245_Y429_Y1.2530.56
549_V612_I1.2530.56
156_P178_Y1.2520.56
325_P513_P1.2510.56
527_P551_Y1.2510.56
423_Y437_S1.2500.56
33_G63_Y1.2500.56
111_Q357_G1.2380.55
614_F644_P1.2350.54
55_L549_V1.2340.54
32_N60_L1.2340.54
160_N181_A1.2290.54
85_P448_P1.2270.54
636_C639_G1.2230.53
139_G259_G1.2230.53
76_C81_W1.2220.53
178_Y362_Y1.2210.53
65_T247_L1.2170.53
153_C156_P1.2160.53
55_L482_I1.2160.53
74_T83_P1.2140.52
118_C146_C1.2120.52
121_G183_G1.2100.52
428_Y456_V1.2090.52
76_C87_C1.2080.52
114_M612_I1.2030.51
314_I376_I1.2020.51
400_P528_P1.2000.51
25_C28_P1.1980.51
176_V482_I1.1980.51
261_Y384_T1.1980.51
124_T186_T1.1890.50
203_S511_K1.1850.50
201_G258_F1.1840.50
316_C327_C1.1820.49
80_G139_G1.1780.49
216_L399_P1.1770.49
161_G206_P1.1770.49
234_G295_G1.1760.49
274_C321_W1.1740.49
110_I233_E1.1720.48
231_Y354_Y1.1700.48
381_G525_T1.1660.48
547_S610_E1.1660.48
537_S549_V1.1640.48
74_T253_I1.1640.48
178_Y206_P1.1640.48
112_E296_E1.1630.48
572_W578_C1.1630.48
314_I437_S1.1600.47
91_C524_C1.1600.47
280_P402_V1.1600.47
235_D296_E1.1580.47
387_P448_P1.1580.47
295_G357_G1.1550.47
381_G389_C1.1540.47
550_E613_E1.1530.47
170_F415_Y1.1520.47
169_T230_T1.1500.46
439_C486_C1.1500.46
267_C274_C1.1480.46
505_C508_G1.1470.46
318_D405_G1.1460.46
423_Y484_F1.1460.46
55_L421_V1.1450.46
265_P325_P1.1430.46
249_G433_G1.1420.46
486_C510_V1.1410.46
108_Y170_F1.1400.46
124_T144_P1.1390.45
94_P99_G1.1380.45
277_P339_P1.1350.45
417_T545_N1.1320.45
186_T189_G1.1310.45
321_W444_W1.1310.45
180_C202_W1.1300.45
316_C321_W1.1300.45
405_G537_S1.1290.45
587_T593_N1.1290.45
206_P448_P1.1290.45
64_T102_S1.1230.44
378_C389_C1.1230.44
222_G247_L1.1220.44
49_M170_F1.1190.44
226_P237_V1.1160.43
161_G222_G1.1140.43
153_C197_C1.1110.43
305_N619_D1.1100.43
110_I137_S1.1070.43
133_V376_I1.1070.43
142_S323_E1.1050.42
510_V515_C1.1040.42
483_D550_E1.1030.42
277_P490_Y1.1020.42
245_Y305_N1.0960.42
637_D640_Q1.0940.41
533_G559_L1.0930.41
399_P421_V1.0920.41
327_C578_C1.0900.41
172_V199_T1.0900.41
429_Y620_T1.0900.41
553_C561_G1.0880.41
358_D480_D1.0870.41
339_P399_P1.0870.41
116_Y325_P1.0860.41
296_E480_D1.0850.41
116_Y178_Y1.0820.40
325_P387_P1.0810.40
482_I612_I1.0810.40
299_H313_E1.0810.40
287_T360_V1.0790.40
91_C146_C1.0790.40
144_P325_P1.0780.40
370_L387_P1.0770.40
448_P513_P1.0760.40
559_L576_P1.0760.40
85_P387_P1.0730.40
172_V356_N1.0720.39
486_C515_C1.0710.39
30_V74_T1.0690.39
239_F551_Y1.0690.39
359_K375_E1.0680.39
277_P399_P1.0680.39
364_C389_C1.0680.39
383_W572_W1.0680.39
582_C616_C1.0620.39
153_C396_C1.0580.38
96_L461_M1.0580.38
402_V423_Y1.0560.38
253_I261_Y1.0560.38
170_F292_Y1.0540.38
111_Q173_K1.0540.38
448_P576_P1.0530.38
170_F354_Y1.0520.38
372_G387_P1.0520.38
296_E419_S1.0510.38
195_V203_S1.0490.37
91_C118_C1.0470.37
339_P362_Y1.0460.37
275_P278_P1.0460.37
498_L512_Y1.0460.37
242_H554_F1.0450.37
551_Y614_F1.0440.37
85_P325_P1.0410.37
140_W321_W1.0400.37
179_E210_K1.0380.36
112_E610_E1.0370.36
176_V612_I1.0350.36
294_H319_G1.0330.36
358_D610_E1.0330.36
153_C208_C1.0310.36
249_G283_S1.0310.36
327_C515_C1.0300.36
323_E376_I1.0300.36
77_T83_P1.0300.36
283_S308_I1.0290.36
409_D482_I1.0290.36
283_S342_I1.0270.36
235_D358_D1.0270.36
30_V33_G1.0270.36
616_C619_D1.0270.36
176_V226_P1.0260.35
241_C267_C1.0250.35
178_Y484_F1.0240.35
559_L611_Y1.0210.35
81_W260_W1.0190.35
57_F85_P1.0180.35
132_V283_S1.0160.35
419_S610_E1.0150.35
431_L448_P1.0130.34
146_C450_C1.0130.34
611_Y635_Q1.0120.34
118_C140_W1.0120.34
222_G283_S1.0110.34
146_C515_C1.0110.34
287_T298_V1.0070.34
300_I484_F1.0060.34
482_I537_S1.0050.34
308_I325_P1.0050.34
81_W87_C1.0040.34
396_C425_C1.0040.34
221_N245_Y1.0040.34
342_I345_G1.0030.34
158_L161_G1.0030.34
215_S338_E1.0000.33
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  
1haqA10.92741000.256Contact Map
2gsxA10.88961000.348Contact Map
2q7zA10.92441000.35Contact Map
1qubA10.45841000.646Contact Map
1ntlA20.64751000.657Contact Map
1ntjA10.43871000.66Contact Map
2c8iE10.34951000.668Contact Map
3iypF10.34951000.695Contact Map
2wiiC10.3481000.705Contact Map
1ridA20.34641000.713Contact 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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