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dbpa2

ID: 1502217694 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 457 (454)
Sequences: 1628 (984.3)
Seq/Len: 3.586
Nf(neff/√len): 46.2

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: 3.586).

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
136_H141_T3.8871.00
58_G91_L3.8861.00
128_A142_V3.6301.00
11_P63_Q3.5301.00
128_A133_L2.9831.00
134_L138_Q2.9291.00
20_E97_F2.8941.00
29_V45_V2.8071.00
41_K203_L2.7051.00
150_L171_I2.5331.00
75_L147_L2.5221.00
61_L74_A2.4551.00
104_L123_P2.3731.00
134_L169_D2.3641.00
309_S337_N2.2901.00
14_Q63_Q2.2901.00
251_K274_D2.2801.00
36_A205_I2.1791.00
138_Q169_D2.0581.00
10_L59_L1.9761.00
217_E340_L1.9671.00
37_I181_L1.9661.00
254_C272_H1.9661.00
134_L137_L1.9611.00
126_I142_V1.9481.00
67_A124_H1.9361.00
257_V296_V1.9211.00
12_P16_T1.9161.00
169_D173_F1.9081.00
318_L343_S1.9021.00
386_C390_G1.8941.00
40_G179_Q1.8621.00
399_D447_K1.8470.99
390_G395_M1.8030.99
390_G397_P1.7830.99
71_Q146_A1.7770.99
77_L133_L1.7740.99
387_I390_G1.7190.99
446_I451_C1.7180.99
285_V289_N1.6980.99
385_L389_G1.6870.99
217_E365_N1.6860.99
315_N329_I1.6810.99
23_Y94_L1.6740.99
112_F141_T1.6740.99
218_Q329_I1.6690.99
2_T6_T1.6520.99
16_T97_F1.6390.98
215_P338_S1.6250.98
381_E390_G1.6170.98
42_D178_R1.6020.98
254_C270_S1.5840.98
231_L344_F1.5800.98
381_E386_C1.5790.98
233_Q264_V1.5770.98
386_C389_G1.5670.98
258_C270_S1.5650.98
66_D124_H1.5590.98
192_A204_A1.5540.98
73_Q124_H1.5500.98
390_G394_K1.5460.98
315_N343_S1.5390.97
137_L147_L1.5350.97
20_E96_R1.5320.97
381_E384_T1.5230.97
242_S311_E1.5130.97
61_L149_T1.4870.97
228_K317_E1.4710.96
91_L125_I1.4620.96
390_G393_A1.4590.96
221_Y367_Q1.4590.96
382_M390_G1.4570.96
427_V446_I1.4410.96
42_D180_T1.4280.96
248_C254_C1.4240.96
251_K272_H1.4210.95
189_E193_A1.4160.95
236_L294_V1.4140.95
357_S363_K1.4020.95
219_Q340_L1.3910.95
116_R141_T1.3890.95
36_A203_L1.3870.95
384_T390_G1.3820.94
168_D197_R1.3790.94
237_S266_Q1.3760.94
402_G406_G1.3750.94
235_L342_I1.3640.94
315_N341_A1.3630.94
137_L173_F1.3630.94
5_S19_N1.3600.94
391_K397_P1.3580.94
401_L415_I1.3570.94
133_L142_V1.3560.94
72_T142_V1.3410.93
88_A105_T1.3390.93
381_E389_G1.3340.93
382_M385_L1.3240.93
370_P400_V1.3070.92
74_A149_T1.3050.92
389_G395_M1.3020.92
229_I257_V1.2970.92
78_C87_V1.2930.91
23_Y55_A1.2920.91
116_R139_K1.2780.91
147_L174_A1.2710.91
396_R399_D1.2710.91
361_Q370_P1.2680.90
76_V91_L1.2660.90
36_A39_A1.2580.90
381_E387_I1.2540.90
323_E326_V1.2530.90
137_L144_L1.2450.89
213_L216_I1.2400.89
381_E395_M1.2380.89
112_F116_R1.2380.89
220_F366_W1.2270.88
44_R195_S1.2260.88
382_M386_C1.2240.88
32_A203_L1.2230.88
383_A390_G1.2230.88
4_F26_M1.2190.88
110_Q136_H1.2060.87
383_A386_C1.2010.87
235_L314_V1.1990.87
73_Q148_N1.1920.86
219_Q367_Q1.1920.86
269_L286_R1.1900.86
42_D202_P1.1850.86
218_Q315_N1.1840.86
66_D73_Q1.1830.86
400_V425_V1.1830.86
389_G397_P1.1790.86
157_R160_D1.1780.86
23_Y58_G1.1730.85
123_P126_I1.1730.85
384_T387_I1.1690.85
249_N312_L1.1640.85
244_C294_V1.1630.85
269_L292_A1.1600.84
106_L141_T1.1570.84
399_D402_G1.1530.84
32_A205_I1.1510.84
290_G337_N1.1510.84
243_S310_L1.1470.83
18_L424_H1.1370.83
286_R291_S1.1360.83
239_H311_E1.1350.83
244_C314_V1.1340.82
382_M395_M1.1330.82
51_S106_L1.1330.82
386_C392_K1.1330.82
383_A388_D1.1310.82
403_A407_D1.1300.82
135_D139_K1.1300.82
296_V317_E1.1300.82
91_L103_I1.1260.82
382_M387_I1.1250.82
77_L170_V1.1140.81
243_S287_F1.1130.81
387_I395_M1.1020.80
281_D284_L1.0980.80
383_A455_L1.0960.79
387_I400_V1.0930.79
266_Q294_V1.0910.79
69_L124_H1.0880.79
231_L369_P1.0870.79
255_Q272_H1.0860.79
107_C281_D1.0850.78
357_S360_L1.0850.78
65_I124_H1.0820.78
114_M117_D1.0810.78
416_G428_A1.0760.78
395_M400_V1.0760.78
261_L294_V1.0740.77
419_A448_G1.0730.77
223_T231_L1.0710.77
382_M388_D1.0710.77
134_L173_F1.0620.76
412_G415_I1.0620.76
90_E93_R1.0600.76
418_I427_V1.0580.76
402_G407_D1.0580.76
434_A438_W1.0570.76
146_A439_K1.0570.76
414_D433_V1.0550.76
394_K397_P1.0530.75
193_A196_G1.0530.75
235_L239_H1.0490.75
143_S146_A1.0490.75
393_A449_K1.0470.75
169_D172_R1.0440.75
276_E279_D1.0440.75
222_E350_A1.0350.74
351_Q354_N1.0350.74
445_K450_T1.0320.73
387_I394_K1.0280.73
39_A205_I1.0280.73
312_L342_I1.0280.73
176_A200_R1.0280.73
311_E342_I1.0270.73
41_K201_D1.0240.73
27_T253_D1.0240.73
159_L191_I1.0240.73
3_A6_T1.0180.72
391_K395_M1.0170.72
439_K442_Q1.0150.72
287_F295_L1.0140.71
411_D414_D1.0120.71
24_L105_T1.0080.71
253_D317_E1.0060.71
16_T20_E1.0050.71
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  
3sqwA10.96061000.476Contact Map
3i5xA10.97161000.482Contact Map
4pxaA10.81841000.495Contact Map
2db3A40.80741000.501Contact Map
3fmpB20.44641000.514Contact Map
4ljyA10.84461000.515Contact Map
4nhoA10.80311000.519Contact Map
4w7sA20.85121000.52Contact Map
4d25A10.80961000.521Contact Map
4c9bA10.81181000.534Contact 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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