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4ku0

ID: 1501760672 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 96 (88)
Sequences: 630 (598.8)
Seq/Len: 7.159
Nf(neff/√len): 63.8

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: 7.159).

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 > 50% 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
75_Q78_D3.3661.00
37_V40_D3.2631.00
5_Y8_C3.1121.00
59_T74_V2.9361.00
6_D24_T2.5211.00
4_S21_V2.1871.00
68_V73_A2.1771.00
39_G71_K2.0781.00
32_G70_G1.9491.00
36_L59_T1.9481.00
28_V66_V1.7581.00
25_Q69_T1.7571.00
27_K69_T1.7471.00
58_V81_S1.7141.00
31_G90_S1.7091.00
59_T86_V1.6381.00
31_G92_K1.6031.00
23_A40_D1.5911.00
12_G15_A1.5411.00
63_T75_Q1.5070.99
35_V73_A1.4270.99
23_A41_P1.3960.99
61_P78_D1.3870.99
74_V86_V1.3500.98
42_I80_I1.3460.98
93_V96_K1.3350.98
73_A95_I1.3260.98
10_T14_E1.2950.98
21_V36_L1.2840.98
57_G80_I1.2340.97
37_V71_K1.2070.96
9_V20_V1.1880.96
29_F67_Y1.1870.96
80_I84_D1.1320.94
38_A72_K1.1220.94
30_T35_V1.0830.92
57_G84_D1.0200.88
42_I57_G1.0160.88
25_Q37_V1.0050.87
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  
4ku0D1199.9-0.03Contact Map
4jiwD40.968899.90.048Contact Map
4jivD10.968899.90.049Contact Map
4zjmA101.70.921Contact Map
4xinA20.60421.20.928Contact Map
3zqjA60.885410.932Contact Map
2kddA20.11460.90.933Contact Map
3sk3A20.39580.90.934Contact Map
2r6fA20.78120.80.936Contact Map
4om9A10.89580.70.937Contact 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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