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2TRX

ID: 1515789910 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 108 (105)
Sequences: 19813 (13161.7)
Seq/Len: 188.695
Nf(neff/√len): 1284.5

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: 188.695).

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
86_V89_T2.2691.00
60_I67_A2.2071.00
79_L89_T2.1331.00
48_E100_K2.0651.00
44_E96_K1.9911.00
13_D69_K1.9721.00
88_A102_F1.9711.00
100_K104_D1.9451.00
9_D65_G1.8751.00
70_Y81_F1.8661.00
21_G54_T1.8521.00
38_I78_L1.8261.00
7_L56_A1.7991.00
79_L86_V1.7621.00
60_I75_I1.7221.00
32_C35_C1.7121.00
95_S98_Q1.6841.00
23_I54_T1.6651.00
9_D66_T1.6471.00
49_Y104_D1.6451.00
26_D57_K1.6191.00
41_I44_E1.5681.00
11_S15_D1.5231.00
22_A82_K1.4871.00
49_Y100_K1.4851.00
27_F72_I1.4241.00
48_E96_K1.4211.00
59_N62_Q1.4020.99
102_F106_N1.3960.99
80_L106_N1.3910.99
8_T11_S1.3570.99
98_Q101_E1.3090.99
41_I96_K1.2830.99
25_V81_F1.2830.99
9_D63_N1.2800.99
39_A57_K1.2790.99
15_D54_T1.2470.99
24_L78_L1.2410.98
22_A80_L1.2320.98
23_I56_A1.2120.98
27_F70_Y1.2070.98
90_K94_L1.2010.98
24_L42_L1.2010.98
80_L102_F1.1710.98
26_D39_A1.1530.97
96_K100_K1.1510.97
42_L55_V1.1390.97
30_E59_N1.1380.97
94_L98_Q1.1350.97
45_I100_K1.1110.96
28_W57_K1.1070.96
45_I96_K1.1040.96
88_A106_N1.1030.96
81_F86_V1.1030.96
31_W61_D1.0950.96
37_M93_A1.0890.96
27_F60_I1.0870.96
26_D38_I1.0680.95
3_K47_D1.0640.95
39_A43_D1.0450.94
13_D18_K1.0200.93
7_L15_D1.0140.93
102_F105_A1.0120.93
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  
3f8uA20.981599.8-0.014Contact Map
2r2jA10.953799.80.002Contact Map
3apoA10.916799.80.005Contact Map
2b5eA10.990799.80.011Contact Map
4kcaA20.972299.80.038Contact Map
4ekzA10.990799.80.043Contact Map
3ed3A2199.80.045Contact Map
1sjiA20.981599.70.061Contact Map
3us3A10.981599.70.067Contact Map
3t58A4199.70.076Contact 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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