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NPP

ID: 1505317066 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 432 (401)
Sequences: 3651 (2361.9)
Seq/Len: 9.105
Nf(neff/√len): 117.9

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: 9.105).

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_G5.9511.00
96_T106_H3.4971.00
105_H413_D3.3261.00
138_E146_N3.2881.00
48_L401_M3.2701.00
185_D236_R2.8211.00
251_N382_D2.7321.00
220_S223_Y2.6541.00
145_E169_S2.5901.00
75_E379_Q2.3951.00
188_R240_G2.3541.00
234_I238_L2.3171.00
138_E143_G2.2721.00
210_D214_H2.2511.00
192_A244_D2.2101.00
72_L377_L2.2091.00
314_C335_L2.2071.00
49_L252_I2.1811.00
71_Q242_Q2.1351.00
49_L250_T2.1181.00
242_Q247_R2.1141.00
323_R366_D2.0771.00
52_S94_H2.0771.00
50_L203_T2.0331.00
70_S74_R1.9881.00
69_L254_V1.9391.00
83_T393_D1.9001.00
144_V149_Q1.8941.00
97_L397_V1.8841.00
253_I401_M1.8481.00
213_G260_M1.8321.00
47_A200_R1.8071.00
90_T94_H1.7991.00
238_L252_I1.7951.00
261_A371_S1.7801.00
82_M374_A1.7791.00
239_A243_R1.7651.00
66_T70_S1.7621.00
316_R319_E1.7591.00
50_L255_V1.7511.00
86_Y338_Q1.7491.00
68_N71_Q1.7191.00
210_D363_H1.7161.00
50_L201_L1.7141.00
102_R395_V1.7061.00
380_G383_L1.7001.00
68_N238_L1.6871.00
85_S96_T1.6681.00
290_G333_P1.6661.00
98_V203_T1.6611.00
311_H340_H1.6521.00
302_E335_L1.6331.00
214_H257_D1.6291.00
69_L234_I1.6181.00
341_E371_S1.6121.00
293_P334_S1.6071.00
264_A267_H1.5971.00
313_D340_H1.5901.00
384_A387_K1.5841.00
149_Q200_R1.5841.00
147_T408_P1.5831.00
55_G260_M1.5801.00
256_S374_A1.5541.00
214_H363_H1.5531.00
93_N394_N1.5471.00
101_L105_H1.5381.00
66_T227_V1.5281.00
208_H212_A1.5261.00
84_P93_N1.5261.00
81_W391_G1.5101.00
65_I228_R1.5071.00
96_T394_N1.5051.00
71_Q75_E1.4981.00
393_D396_D1.4931.00
210_D257_D1.4931.00
219_E262_E1.4781.00
53_I56_L1.4721.00
251_N383_L1.4691.00
101_L137_G1.4651.00
399_A412_N1.4641.00
339_M345_A1.4591.00
67_P231_D1.4521.00
94_H111_N1.4410.99
85_S103_P1.4380.99
102_R325_Q1.4340.99
341_E369_L1.4270.99
218_P361_G1.4270.99
56_L227_V1.4170.99
398_Y412_N1.4040.99
79_A376_F1.4040.99
212_A226_A1.3990.99
184_V237_L1.3990.99
241_M252_I1.3950.99
144_V405_L1.3940.99
251_N381_P1.3870.99
251_N404_L1.3770.99
80_R390_P1.3750.99
209_V230_V1.3640.99
218_P262_E1.3600.99
98_V140_V1.3570.99
181_D236_R1.3510.99
53_I209_V1.3480.99
187_V204_L1.3460.99
267_H343_W1.3450.99
53_I234_I1.3420.99
392_F396_D1.3340.99
144_V151_A1.3240.99
136_G329_H1.3070.99
71_Q238_L1.3030.99
51_I252_I1.2940.99
56_L60_M1.2860.99
62_D78_R1.2760.98
66_T69_L1.2730.98
216_H222_Q1.2710.98
292_E333_P1.2670.98
302_E316_R1.2650.98
214_H258_H1.2640.98
73_A78_R1.2630.98
72_L379_Q1.2620.98
253_I378_A1.2600.98
396_D414_G1.2450.98
79_A392_F1.2390.98
402_S412_N1.2380.98
90_T210_D1.2320.98
51_I237_L1.2310.98
90_T257_D1.2280.98
402_S409_A1.2280.98
152_A199_N1.2250.98
419_L422_A1.2190.98
97_L255_V1.2180.98
114_R119_G1.2130.98
87_P103_P1.2120.98
54_D214_H1.2090.98
90_T111_N1.2080.98
235_G239_A1.2080.98
48_L251_N1.1970.97
231_D235_G1.1860.97
49_L202_V1.1820.97
90_T258_H1.1760.97
276_P279_I1.1660.97
46_H382_D1.1650.97
396_D418_T1.1620.97
397_V401_M1.1620.97
48_L404_L1.1560.97
54_D257_D1.1500.97
82_M397_V1.1480.96
241_M250_T1.1430.96
15_L20_S1.1390.96
150_H197_Q1.1380.96
376_F392_F1.1380.96
111_N210_D1.1380.96
221_R225_D1.1310.96
144_V201_L1.1280.96
137_G410_A1.1120.96
314_C337_C1.1040.95
142_V163_I1.0980.95
181_D206_F1.0930.95
149_Q405_L1.0890.95
186_A190_W1.0890.95
392_F419_L1.0840.95
81_W373_R1.0820.95
300_A304_S1.0800.95
210_D258_H1.0780.95
77_V383_L1.0770.94
398_Y402_S1.0720.94
256_S375_V1.0710.94
83_T368_A1.0710.94
15_L18_A1.0700.94
238_L247_R1.0690.94
187_V202_V1.0680.94
153_T159_S1.0640.94
63_R224_A1.0610.94
418_T421_P1.0580.94
54_D258_H1.0530.94
409_A412_N1.0520.94
45_P200_R1.0500.93
383_L400_L1.0490.93
257_D363_H1.0480.93
382_D404_L1.0440.93
206_F237_L1.0380.93
60_M213_G1.0370.93
116_P334_S1.0350.93
396_D399_A1.0340.93
17_A20_S1.0330.93
240_G243_R1.0320.93
191_L202_V1.0310.93
181_D233_A1.0310.93
53_I254_V1.0300.93
238_L242_Q1.0290.93
16_L20_S1.0210.92
88_S364_G1.0210.92
139_P142_V1.0150.92
72_L254_V1.0090.92
51_I204_L1.0090.92
65_I224_A1.0070.91
53_I230_V1.0040.91
153_T203_T1.0040.91
184_V206_F1.0030.91
204_L237_L1.0030.91
82_M394_N1.0000.91
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  
2gsoA20.88431000.337Contact Map
4lr2A10.87041000.364Contact Map
4gtwA20.93981000.386Contact Map
3nkqA10.9121000.386Contact Map
3q3qA10.88431000.456Contact Map
3szyA10.81481000.472Contact Map
1ei6A40.80561000.482Contact Map
4fdiA20.68291000.669Contact Map
3b5qA20.64581000.68Contact Map
1fsuA10.65741000.682Contact 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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