GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
test3

ID: 1516304078 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 79 (65)
Sequences: 773 (573)
Seq/Len: 11.892
Nf(neff/√len): 71.1

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: 11.892).

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
39_K48_N4.7841.00
28_R35_E3.8841.00
27_R65_F3.1131.00
51_E55_N2.5961.00
20_V41_K2.2541.00
27_R66_M2.2371.00
30_V35_E2.0351.00
36_Y66_M2.0201.00
27_R34_V1.9711.00
22_E39_K1.9581.00
52_P55_N1.8941.00
37_L48_N1.6561.00
61_L65_F1.5641.00
58_C61_L1.5421.00
56_L61_L1.5001.00
45_E48_N1.4601.00
19_Y43_F1.3840.99
67_K70_K1.3340.99
39_K45_E1.2600.99
20_V38_L1.2190.98
25_L45_E1.1640.97
37_L50_W1.1320.97
63_S67_K1.1120.96
34_V38_L1.0080.93
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  
1ap0A10.924199.70.242Contact Map
4qucA10.696299.70.245Contact Map
2rsoA10.96299.70.245Contact Map
2kvmA10.898799.70.249Contact Map
3lweA20.759599.70.255Contact Map
4x3kA20.810199.70.261Contact Map
2d9uA10.898799.70.264Contact Map
1g6zA10.848199.70.27Contact Map
1pdqA10.645699.70.272Contact Map
2dntA10.936799.70.272Contact 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.

Page generated in 0.0134 seconds.