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ID: 1505351744 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 432 (389)
Sequences: 3074 (2154.1)
Seq/Len: 7.902
Nf(neff/√len): 109.2

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: 7.902).

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
68_N235_G6.2681.00
96_T106_H4.0931.00
138_E146_N3.5821.00
48_L401_M3.1201.00
251_N382_D2.8391.00
220_S223_Y2.8301.00
105_H413_D2.6031.00
234_I238_L2.4941.00
138_E143_G2.4511.00
145_E169_S2.4031.00
302_E335_L2.2811.00
253_I401_M2.2671.00
210_D214_H2.2621.00
69_L254_V2.2261.00
314_C335_L2.2191.00
70_S74_R2.1591.00
185_D236_R2.1561.00
52_S94_H2.0961.00
75_E379_Q2.0191.00
188_R240_G1.9831.00
50_L201_L1.9601.00
83_T393_D1.8981.00
85_S96_T1.8931.00
47_A200_R1.8801.00
323_R366_D1.8771.00
72_L377_L1.8701.00
316_R319_E1.8631.00
144_V149_Q1.8631.00
50_L203_T1.8411.00
242_Q247_R1.8281.00
264_A267_H1.8271.00
380_G383_L1.8261.00
90_T94_H1.8251.00
86_Y338_Q1.8211.00
69_L234_I1.8151.00
49_L250_T1.8021.00
192_A244_D1.8001.00
49_L252_I1.7981.00
213_G260_M1.7871.00
210_D363_H1.7801.00
97_L397_V1.7721.00
238_L252_I1.7601.00
68_N238_L1.7551.00
149_Q200_R1.7531.00
50_L255_V1.7411.00
102_R395_V1.7281.00
261_A371_S1.7201.00
311_H340_H1.7121.00
101_L105_H1.6941.00
239_A243_R1.6911.00
98_V203_T1.6901.00
71_Q75_E1.6881.00
102_R325_Q1.6881.00
82_M374_A1.6781.00
293_P334_S1.6641.00
214_H257_D1.6511.00
341_E371_S1.6491.00
68_N71_Q1.6461.00
214_H363_H1.6391.00
66_T70_S1.6331.00
219_E262_E1.6261.00
55_G260_M1.6051.00
210_D257_D1.5941.00
302_E306_L1.5891.00
53_I234_I1.5851.00
302_E316_R1.5421.00
384_A387_K1.5341.00
251_N383_L1.5331.00
54_D214_H1.5091.00
101_L137_G1.5021.00
218_P262_E1.4980.99
339_M345_A1.4890.99
71_Q242_Q1.4860.99
84_P93_N1.4860.99
290_G333_P1.4850.99
216_H222_Q1.4670.99
251_N381_P1.4670.99
144_V151_A1.4600.99
51_I252_I1.4580.99
97_L255_V1.4580.99
144_V405_L1.4470.99
147_T408_P1.4440.99
94_H111_N1.4400.99
114_R119_G1.4360.99
208_H212_A1.4300.99
218_P361_G1.4200.99
67_P231_D1.4140.99
48_L251_N1.4120.99
96_T394_N1.4020.99
256_S374_A1.3880.99
235_G239_A1.3810.99
313_D340_H1.3680.99
62_D78_R1.3660.99
209_V230_V1.3640.99
341_E369_L1.3570.99
53_I209_V1.3560.99
66_T227_V1.3370.99
376_F392_F1.3330.99
267_H343_W1.3320.99
393_D396_D1.3290.99
54_D257_D1.3220.98
303_A306_L1.3210.98
241_M252_I1.3180.98
90_T257_D1.3180.98
48_L405_L1.3030.98
214_H258_H1.3010.98
85_S103_P1.2930.98
221_R225_D1.2920.98
90_T111_N1.2770.98
79_A376_F1.2730.98
79_A392_F1.2690.98
98_V140_V1.2680.98
253_I378_A1.2630.98
81_W391_G1.2560.98
54_D258_H1.2520.98
72_L379_Q1.2510.98
396_D399_A1.2500.98
56_L60_M1.2500.98
93_N394_N1.2480.98
251_N404_L1.2440.97
212_A226_A1.2440.97
71_Q238_L1.2350.97
66_T69_L1.2350.97
90_T210_D1.2340.97
206_F237_L1.2290.97
149_Q405_L1.2180.97
87_P103_P1.2160.97
63_R224_A1.2130.97
49_L202_V1.2090.97
299_A316_R1.2080.97
392_F419_L1.2000.97
302_E314_C1.1990.97
48_L253_I1.1900.96
46_H382_D1.1880.96
85_S93_N1.1880.96
45_P200_R1.1780.96
152_A199_N1.1760.96
90_T258_H1.1700.96
392_F396_D1.1670.96
140_V401_M1.1640.96
186_A189_G1.1600.96
399_A412_N1.1600.96
65_I228_R1.1590.96
80_R390_P1.1560.96
204_L237_L1.1540.96
314_C337_C1.1530.96
402_S409_A1.1510.95
418_T421_P1.1510.95
167_R171_W1.1470.95
241_M250_T1.1410.95
257_D363_H1.1370.95
48_L404_L1.1350.95
111_N210_D1.1340.95
47_A198_R1.1330.95
83_T368_A1.1320.95
238_L247_R1.1320.95
150_H197_Q1.1310.95
382_D404_L1.1230.95
60_M213_G1.1080.94
144_V201_L1.1070.94
84_P88_S1.1050.94
82_M397_V1.1000.94
397_V401_M1.0970.94
225_D228_R1.0880.93
56_L227_V1.0820.93
389_L422_A1.0820.93
210_D258_H1.0790.93
187_V204_L1.0790.93
194_D198_R1.0730.93
116_P334_S1.0700.93
65_I224_A1.0620.92
73_A78_R1.0550.92
139_P142_V1.0530.92
231_D235_G1.0500.92
181_D236_R1.0460.91
142_V166_V1.0450.91
104_D327_G1.0390.91
276_P279_I1.0370.91
256_S375_V1.0330.91
241_M244_D1.0320.91
170_Q193_T1.0230.90
88_S364_G1.0220.90
258_H363_H1.0220.90
99_T106_H1.0220.90
47_A249_R1.0220.90
209_V212_A1.0220.90
419_L422_A1.0210.90
53_I230_V1.0210.90
105_H415_N1.0190.90
54_D363_H1.0170.90
77_V383_L1.0170.90
385_Q424_R1.0160.90
260_M361_G1.0130.90
153_T159_S1.0120.90
72_L76_G1.0100.89
326_Y332_I1.0040.89
72_L238_L1.0010.89
57_R60_M1.0010.89
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  
2gsoA20.88431000.377Contact Map
4lr2A10.87041000.409Contact Map
4gtwA20.93521000.438Contact Map
3nkqA10.94211000.44Contact Map
3q3qA10.88891000.484Contact Map
3szyA10.81021000.496Contact Map
1ei6A40.80561000.51Contact Map
4fdiA20.68521000.699Contact Map
3b5qA20.64811000.701Contact Map
3ed4A40.69681000.705Contact 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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