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bbs_2_sheetp1_t2

ID: 1505417043 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 99 (96)
Sequences: 302 (214.7)
Seq/Len: 3.146
Nf(neff/√len): 21.9

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: 3.146).

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
54_V81_K1.7800.99
80_P84_P1.6640.98
53_G58_E1.6280.98
37_S72_S1.6230.98
17_T21_V1.6170.98
14_K19_L1.5790.97
14_K39_S1.5670.97
9_I40_N1.5540.97
50_F59_S1.5160.96
36_I44_I1.4580.95
38_T42_T1.4580.95
13_T38_T1.4550.95
50_F81_K1.3400.92
62_V81_K1.3340.91
57_G88_H1.3230.91
51_A88_H1.3080.90
67_H73_V1.3030.90
48_L78_T1.2850.89
48_L84_P1.2790.89
50_F58_E1.2760.89
47_V73_V1.2660.88
45_R92_F1.2620.88
81_K89_L1.2560.88
28_Q36_I1.2510.87
12_N94_G1.2350.86
50_F88_H1.2230.86
27_A65_S1.1930.84
9_I13_T1.1880.83
22_S33_E1.1750.82
35_C74_R1.1680.82
34_L44_I1.1640.82
51_A58_E1.1640.82
44_I73_V1.1430.80
54_V70_S1.1160.78
32_A54_V1.1120.77
62_V93_V1.0890.75
61_V64_P1.0750.74
56_A74_R1.0750.74
36_I96_R1.0740.74
33_E85_V1.0710.74
53_G63_H1.0700.73
30_A59_S1.0550.72
65_S83_I1.0510.72
4_G23_L1.0490.71
50_F86_D1.0450.71
51_A82_D1.0430.71
10_P40_N1.0190.68
52_E88_H1.0000.66
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  
2pn5A10.95967.50.917Contact Map
1lnsA10.71726.10.92Contact Map
4ckbA20.979850.923Contact Map
4fxkB10.94953.60.928Contact Map
2b39A20.95962.70.933Contact Map
3prxB20.92932.60.934Contact Map
4acqA40.93942.40.934Contact Map
2e26A10.97982.30.935Contact Map
4epiA10.61621.90.939Contact Map
4pf1A40.78791.80.939Contact 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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