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4ku0

ID: 1500382089 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 96 (90)
Sequences: 1204 (732)
Seq/Len: 13.378
Nf(neff/√len): 77.2

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: 13.378).

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
75_Q78_D3.1051.00
5_Y8_C2.9881.00
6_D24_T2.9381.00
37_V40_D2.3701.00
9_V89_A2.3011.00
59_T74_V2.2251.00
4_S21_V2.0421.00
31_G90_S1.9921.00
29_F67_Y1.8981.00
58_V81_S1.8941.00
68_V73_A1.8791.00
7_K33_I1.8581.00
50_K55_H1.8261.00
61_P78_D1.7331.00
32_G70_G1.7061.00
9_V20_V1.6861.00
25_Q37_V1.6751.00
25_Q69_T1.6241.00
36_L59_T1.5801.00
39_G71_K1.5051.00
80_I84_D1.4721.00
79_P85_T1.4501.00
23_A40_D1.4231.00
23_A41_P1.4050.99
31_G92_K1.3960.99
35_V73_A1.3830.99
21_V36_L1.3610.99
16_W19_T1.2850.99
13_H84_D1.2550.99
38_A72_K1.2530.99
28_V35_V1.2430.98
61_P79_P1.2400.98
38_A62_R1.2390.98
41_P58_V1.2330.98
28_V66_V1.2020.98
37_V71_K1.1980.98
74_V86_V1.1640.97
30_T35_V1.1460.97
5_Y90_S1.1410.97
4_S86_V1.1210.97
42_I84_D1.0990.96
3_L35_V1.0710.95
63_T75_Q1.0660.95
42_I80_I1.0660.95
15_A47_E1.0600.95
22_N43_T1.0560.95
59_T86_V1.0510.94
10_T84_D1.0340.94
37_V74_V1.0280.94
77_A85_T1.0120.93
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  
4ku0D1199.90.062Contact Map
4jivD10.968899.90.13Contact Map
4jiwD40.968899.90.13Contact Map
4cqmB80.44792.70.926Contact Map
3zqjA60.88542.60.926Contact Map
4zjmA102.20.929Contact Map
1tonA10.39582.20.929Contact Map
2pkaA20.41672.20.929Contact Map
2r6fA20.78122.20.93Contact Map
4nsvA20.520.931Contact 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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