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Tm13

ID: 1506715902 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 253 (235)
Sequences: 7681 (4914.7)
Seq/Len: 32.685
Nf(neff/√len): 320.6

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: 32.685).

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_E154_P3.9771.00
157_K215_D3.6741.00
95_K118_V3.2291.00
126_K134_E3.1471.00
10_N13_H3.1271.00
73_Y84_I3.0561.00
40_E69_R2.6691.00
140_A150_V2.6441.00
126_K136_E2.6321.00
210_S231_K2.5651.00
44_L74_T2.5191.00
70_H97_Y2.3871.00
128_K134_E2.3861.00
153_D156_A2.2671.00
60_A90_I2.1591.00
33_Y160_F2.1121.00
207_D234_L2.0861.00
70_H95_K1.9501.00
100_S121_S1.9491.00
133_N156_A1.9031.00
44_L160_F1.8951.00
135_L151_L1.8891.00
158_I216_M1.8601.00
158_I218_A1.8281.00
152_Y157_K1.8251.00
72_F151_L1.7971.00
97_Y118_V1.7891.00
74_T151_L1.7601.00
134_E155_V1.7371.00
36_L41_G1.6911.00
10_N16_M1.6841.00
231_K235_E1.6771.00
123_K208_M1.6291.00
16_M36_L1.6081.00
137_I151_L1.5911.00
58_N61_E1.5901.00
71_I84_I1.5691.00
34_L41_G1.5621.00
210_S234_L1.5621.00
42_I129_L1.5501.00
157_K213_K1.5351.00
120_I149_F1.5211.00
71_I94_A1.5211.00
15_F153_D1.4981.00
36_L66_S1.4941.00
235_E239_N1.4941.00
34_L59_V1.4841.00
98_I102_W1.4791.00
99_S139_P1.4741.00
148_N162_G1.4601.00
118_V125_T1.4551.00
207_D238_R1.4541.00
46_P71_I1.4351.00
134_E154_P1.4311.00
38_G132_G1.4221.00
101_L104_R1.4091.00
42_I72_F1.4010.99
53_P57_S1.3980.99
14_K133_N1.3920.99
80_V163_D1.3780.99
42_I70_H1.3730.99
91_C94_A1.3680.99
15_F35_I1.3660.99
33_Y218_A1.3650.99
14_K156_A1.3640.99
42_I135_L1.3620.99
133_N153_D1.3490.99
52_F86_L1.3490.99
44_L151_L1.3210.99
37_D132_G1.3190.99
75_H163_D1.3180.99
137_I149_F1.3170.99
152_Y214_I1.3050.99
10_N14_K1.3030.99
56_M90_I1.2820.99
15_F158_I1.2770.99
41_G69_R1.2760.99
56_M60_A1.2740.99
238_R242_C1.2700.99
121_S125_T1.2680.99
86_L89_S1.2570.99
150_V164_I1.2540.99
32_Q47_G1.2510.99
57_S61_E1.2430.98
128_K132_G1.2420.98
100_S119_P1.2400.98
34_L43_L1.2350.98
12_Q156_A1.2250.98
201_A204_K1.2170.98
139_P149_F1.2050.98
208_M211_K1.2010.98
160_F218_A1.1970.98
138_L208_M1.1930.98
39_N130_L1.1900.98
203_K238_R1.1650.97
71_I96_I1.1490.97
74_T162_G1.1490.97
135_L153_D1.1460.97
207_D211_K1.1430.97
103_V107_P1.1410.97
133_N155_V1.1400.97
179_D226_R1.1380.97
219_P222_G1.1350.97
152_Y159_L1.1310.97
99_S149_F1.1270.97
79_D221_H1.1220.97
52_F83_G1.1210.97
203_K241_K1.1210.97
136_E152_Y1.1110.96
80_V221_H1.1090.96
15_F160_F1.0990.96
12_Q216_M1.0990.96
98_I103_V1.0910.96
35_I44_L1.0790.95
16_M62_V1.0770.95
41_G68_I1.0680.95
43_L87_W1.0590.95
144_H163_D1.0500.94
103_V119_P1.0460.94
216_M226_R1.0390.94
12_Q215_D1.0350.94
45_D75_H1.0340.94
126_K154_P1.0330.94
77_D80_V1.0250.93
75_H80_V1.0250.93
235_E238_R1.0240.93
204_K207_D1.0230.93
104_R107_P1.0110.93
198_S201_A1.0040.93
136_E212_K1.0020.92
67_S93_N1.0020.92
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  
2q9uA20.97631000.323Contact Map
2yheA60.90511000.347Contact Map
4nurA20.90911000.353Contact Map
2cfuA10.90121000.354Contact Map
1ycgA40.95261000.355Contact Map
2ohhA40.96051000.355Contact Map
4fekA20.95261000.357Contact Map
4pdxA201000.357Contact Map
2vw8A10.89721000.358Contact Map
4dikA20.95651000.358Contact 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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