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test1M40

ID: 1507881720 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 263 (261)
Sequences: 8382 (5245)
Seq/Len: 32.115
Nf(neff/√len): 324.7

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: 32.115).

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
34_S37_P3.8451.00
68_R116_T3.3761.00
38_E159_A3.3531.00
57_S126_F3.0591.00
69_R91_G2.8501.00
21_Y33_E2.6701.00
126_F129_N2.6471.00
20_G41_F2.5771.00
55_V113_L2.5341.00
58_R63_Q2.4911.00
94_V113_L2.4471.00
71_H91_G2.4271.00
165_L208_D2.4271.00
36_R39_E2.4121.00
132_D164_T2.2491.00
52_C102_I2.1721.00
162_A235_V2.1721.00
20_G158_P2.1391.00
40_R155_T2.1311.00
93_T96_E2.1271.00
206_I231_S2.1071.00
23_E234_V2.0821.00
135_T156_T2.0701.00
159_A163_T2.0511.00
22_I162_A2.0271.00
100_A106_D2.0231.00
101_A110_A1.9911.00
51_L110_A1.9811.00
65_Q68_R1.9331.00
23_E232_R1.9321.00
158_P237_Y1.9081.00
50_L127_L1.8871.00
74_Q88_L1.8831.00
76_D115_T1.8791.00
72_Y112_L1.8721.00
53_G167_K1.8591.00
46_T161_M1.8391.00
206_I223_A1.8271.00
43_M156_T1.8141.00
118_G122_E1.7991.00
73_S115_T1.7791.00
67_G95_R1.7751.00
70_I112_L1.7531.00
46_T237_Y1.7511.00
99_S103_T1.7381.00
26_L233_I1.7341.00
24_L166_R1.7261.00
25_D230_P1.7251.00
69_R93_T1.7161.00
73_S76_D1.6791.00
101_A113_L1.6761.00
58_R122_E1.6581.00
95_R99_S1.6571.00
52_C101_A1.6541.00
49_V221_I1.6471.00
66_L98_C1.6391.00
165_L221_I1.6101.00
100_A109_A1.6011.00
57_S61_A1.5971.00
161_M237_Y1.5971.00
38_E134_V1.5721.00
25_D28_S1.5701.00
37_P159_A1.5561.00
105_S209_K1.5471.00
22_I159_A1.5331.00
46_T221_I1.5071.00
70_I116_T1.4391.00
40_R134_V1.4391.00
97_L109_A1.4291.00
45_S48_K1.4151.00
54_A126_F1.4030.99
232_R256_G1.3950.99
24_L162_A1.3850.99
45_S105_S1.3680.99
122_E125_A1.3590.99
53_G126_F1.3590.99
50_L164_T1.3550.99
221_I235_V1.3540.99
225_G231_S1.3190.99
27_N231_S1.3190.99
59_V66_L1.3110.99
50_L135_T1.3100.99
162_A233_I1.3070.99
55_V98_C1.3060.99
54_A58_R1.3040.99
22_I31_I1.2880.99
55_V94_V1.2760.99
52_C98_C1.2570.99
96_E99_S1.2540.99
161_M221_I1.2450.98
130_M167_K1.2290.98
48_K107_N1.2270.98
45_S209_K1.2220.98
134_V160_A1.2130.98
216_G219_G1.2120.98
49_V165_L1.1870.98
175_T178_S1.1850.98
22_I37_P1.1770.98
54_A117_I1.1710.98
254_E257_A1.1570.97
124_T128_H1.1570.97
64_E116_T1.1550.97
54_A57_S1.1480.97
166_R233_I1.1310.97
163_T167_K1.1300.97
213_G216_G1.1140.96
126_F130_M1.1140.96
60_D175_T1.1070.96
166_R170_T1.1030.96
121_K140_W1.0990.96
132_D160_A1.0970.96
135_T160_A1.0930.96
132_D163_T1.0920.96
250_R254_E1.0880.96
18_R39_E1.0780.95
257_A261_K1.0740.95
125_A129_N1.0680.95
66_L95_R1.0610.95
200_L224_L1.0470.94
163_T166_R1.0420.94
54_A123_L1.0280.94
127_L132_D1.0170.93
194_P197_R1.0150.93
47_F154_D1.0130.93
87_H90_D1.0090.93
195_L212_A1.0080.93
223_A231_S1.0060.93
42_P150_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  
1o7eA20.99621000.292Contact Map
1hzoA20.99241000.292Contact Map
3p09A20.96961000.293Contact Map
4ua6A201000.296Contact Map
1n9bA111000.299Contact Map
3c5aA10.99241000.3Contact Map
1g6aA10.99621000.301Contact Map
3dw0A20.97721000.301Contact Map
1bsgA10.99241000.301Contact Map
1bueA10.98861000.304Contact 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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