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1_1ayipdb

ID: 1516869498 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 86 (82)
Sequences: 311 (249.8)
Seq/Len: 3.793
Nf(neff/√len): 27.6

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: 3.793).

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
19_L69_V3.1791.00
70_K74_E3.0571.00
46_E81_K2.6301.00
40_H44_I2.3051.00
74_E78_A2.2731.00
64_S67_G2.1491.00
78_A83_G1.8561.00
12_E73_K1.8110.99
61_R71_E1.7430.99
78_A86_Q1.7220.99
79_N83_G1.6750.99
40_H43_K1.6620.99
42_V51_T1.6130.98
70_K78_A1.6070.98
20_K65_P1.5840.98
17_Q20_K1.5550.98
20_K66_E1.5540.98
49_D58_S1.5420.98
63_D67_G1.5080.97
60_N64_S1.3600.94
21_E33_V1.3130.93
52_D56_Y1.2580.91
41_F50_G1.2570.91
41_F47_H1.2530.91
23_E62_D1.2390.90
57_P63_D1.1630.86
68_I71_E1.1540.85
28_A86_Q1.1520.85
15_F41_F1.1390.84
21_E37_L1.1010.81
37_L40_H1.0870.80
17_Q68_I1.0830.80
50_G53_L1.0760.79
77_A83_G1.0680.78
15_F44_I1.0600.78
35_D39_E1.0490.77
35_D38_L1.0400.76
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  
1fr2A10.96511000.023Contact Map
1unkA40.98841000.026Contact Map
1gxgA10.97671000.03Contact Map
4f37A211000.035Contact Map
3u43A10.96511000.037Contact Map
4uhpB401000.04Contact Map
4qkoA401000.065Contact Map
2k0dX10.98841000.065Contact Map
4h3kB20.627931.70.9Contact Map
3p9yA40.627922.30.907Contact 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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