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ydj1

ID: 1513695655 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 409 (354)
Sequences: 2564 (1468.1)
Seq/Len: 7.243
Nf(neff/√len): 78.0

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: 7.243).

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
18_T21_E4.1871.00
276_T281_G3.8641.00
128_Y316_M3.5971.00
266_L327_L3.5801.00
344_E351_E3.5741.00
145_E203_S3.4681.00
19_D60_S3.3541.00
125_E256_H3.1891.00
31_L37_K3.1481.00
282_E294_K3.0531.00
152_K199_D2.9331.00
132_T217_E2.7991.00
132_T219_H2.6801.00
126_E133_A2.6221.00
271_E334_K2.5951.00
161_S187_V2.5421.00
167_I182_Q2.5261.00
157_K197_P2.5071.00
5_T49_E2.4211.00
152_K202_K2.4201.00
123_S254_R2.3751.00
264_D318_I2.3361.00
214_K235_E2.3151.00
346_L350_E2.2951.00
342_S345_N2.2831.00
123_S126_E2.2571.00
267_V330_K2.2551.00
60_S63_R2.2271.00
141_I212_E2.2251.00
5_T10_I2.1521.00
269_E330_K2.1471.00
29_C32_K2.1291.00
44_A48_K2.0871.00
134_K215_I2.0651.00
284_A292_W2.0491.00
121_S254_R2.0201.00
144_K212_E2.0111.00
14_S21_E2.0081.00
273_D276_T1.9911.00
4_E71_E1.9781.00
309_K331_F1.9681.00
121_S252_S1.9301.00
136_A213_R1.9191.00
145_E152_K1.9181.00
16_T21_E1.9171.00
305_P335_F1.9141.00
266_L316_M1.9101.00
64_E68_Q1.8921.00
168_K186_D1.8861.00
38_N43_A1.8661.00
124_L266_L1.8561.00
344_E347_K1.8431.00
17_A22_I1.8311.00
160_T187_V1.8181.00
119_E252_S1.8151.00
61_E65_I1.7981.00
348_K351_E1.7791.00
7_F56_I1.7771.00
124_L316_M1.7761.00
61_E64_E1.7711.00
5_T9_D1.7351.00
226_D252_S1.7261.00
274_L278_I1.7181.00
347_K351_E1.7091.00
282_E296_G1.6881.00
271_E332_T1.6841.00
29_C50_A1.6771.00
134_K217_E1.6531.00
33_Y46_K1.6451.00
128_Y288_V1.6391.00
65_I74_L1.6061.00
156_V193_D1.6051.00
289_S324_Y1.5951.00
274_L335_F1.5941.00
4_E9_D1.5721.00
269_E332_T1.5651.00
226_D253_E1.5461.00
72_D75_S1.5441.00
224_M228_Q1.5361.00
114_K237_D1.4750.99
26_Y51_S1.4730.99
144_K203_S1.4690.99
161_S186_D1.4690.99
308_R328_I1.4680.99
117_K250_I1.4600.99
13_V22_I1.4550.99
39_P42_E1.4500.99
46_K49_E1.4370.99
278_I335_F1.4340.99
120_I251_V1.4170.99
65_I69_F1.3990.99
310_V326_N1.3980.99
7_F52_A1.3940.99
120_I220_V1.3880.99
126_E131_R1.3860.99
142_L147_E1.3760.99
136_A215_I1.3640.99
201_C204_C1.3590.99
303_I331_F1.3500.98
158_K193_D1.3400.98
30_A47_F1.3340.98
345_N352_I1.3300.98
112_R115_D1.3280.98
4_E52_A1.3220.98
169_F182_Q1.3000.98
272_I277_A1.2950.98
224_M251_V1.2910.98
144_K210_E1.2890.98
74_L77_A1.2800.98
69_F73_G1.2780.98
13_V16_T1.2780.98
228_Q319_P1.2640.97
12_G25_A1.2610.97
75_S78_G1.2600.97
349_L352_I1.2560.97
209_V240_P1.2330.97
291_D314_K1.2310.97
140_Q209_V1.2290.97
139_K214_K1.2180.96
161_S168_K1.2140.96
169_F179_Q1.2120.96
187_V203_S1.2000.96
270_A283_F1.2000.96
278_I349_L1.1930.96
140_Q211_N1.1880.96
268_Y327_L1.1770.95
232_F249_F1.1700.95
343_E350_E1.1660.95
6_K15_V1.1660.95
339_H345_N1.1600.95
127_L224_M1.1600.95
288_V327_L1.1580.95
138_N211_N1.1490.95
260_K269_E1.1420.94
317_P324_Y1.1400.94
229_R248_V1.1270.94
298_V309_K1.1260.94
344_E348_K1.1220.94
118_H135_L1.1160.93
143_C201_C1.1070.93
258_S268_Y1.1040.93
239_A243_I1.1020.93
124_L129_K1.0990.93
39_P43_A1.0970.93
5_T71_E1.0960.93
308_R330_K1.0900.92
127_L253_E1.0870.92
232_F235_E1.0840.92
284_A294_K1.0800.92
127_L225_K1.0710.91
267_V328_I1.0640.91
149_R153_K1.0610.91
276_T283_F1.0470.90
160_T194_I1.0420.90
143_C204_C1.0420.90
143_C146_C1.0360.90
73_G77_A1.0300.89
160_T163_N1.0250.89
231_V248_V1.0220.89
286_E292_W1.0120.88
343_E347_K1.0110.88
124_L128_Y1.0080.88
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  
3lz8A20.46211000.46Contact Map
4j80A40.65771000.473Contact Map
1nltA10.55751000.504Contact Map
3agxA20.42791000.663Contact Map
2q2gA20.42541000.666Contact Map
1c3gA10.41081000.684Contact Map
4j7zA60.25431000.789Contact Map
1xaoA20.28121000.793Contact Map
1bq0A10.18581000.801Contact Map
2ctqA10.234799.90.819Contact 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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