OPENSEQ.org
MSA

ID: 1518194222 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 73 (73)
Sequences: 1133 (816.6)
Seq/Len: 15.521
Nf(neff/√len): 95.6

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: 15.521).

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
28_K47_L2.9411.00
15_G18_D2.0781.00
33_K43_V2.0581.00
34_T40_V2.0571.00
64_K67_E2.0121.00
41_N60_H1.9691.00
62_W69_F1.8631.00
64_K69_F1.7991.00
9_A26_P1.7251.00
16_I59_V1.7001.00
41_N73_N1.6841.00
11_K72_F1.6581.00
4_E63_E1.6451.00
31_N45_E1.6181.00
15_G72_F1.6021.00
26_P46_V1.5711.00
32_A44_F1.5311.00
24_M57_Y1.5121.00
27_V49_G1.3970.99
30_L56_I1.3940.99
46_V59_V1.3780.99
9_A44_F1.3770.99
16_I20_N1.3540.99
38_A64_K1.3530.99
41_N62_W1.3480.99
5_Y32_A1.3150.99
48_F57_Y1.3050.99
48_F59_V1.2200.98
2_D6_M1.2010.98
63_E70_E1.1700.97
22_G50_E1.1570.97
40_V65_P1.1530.97
24_M48_F1.1440.97
9_A46_V1.1290.97
13_A48_F1.0660.95
39_G66_W1.0380.94
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  
2l4vA1199.70.04Contact Map
3ul5A4199.70.051Contact Map
3imaB20.986399.70.053Contact Map
1eqkA1199.70.064Contact Map
4n6tA1199.70.068Contact Map
4lziA1199.70.079Contact Map
5a0oB2099.60.121Contact Map
3gaxA2199.60.146Contact Map
4n6oB1199.60.146Contact Map
2ch9A1199.60.147Contact 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 0.0276 seconds.