GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
leafs_1ptf_fastRelax_10

ID: 1507536266 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 87 (87)
Sequences: 501 (372.4)
Seq/Len: 5.759
Nf(neff/√len): 39.9

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: 5.759).

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
11_E17_H3.0141.00
35_L42_I2.5281.00
4_E74_F2.3641.00
30_D68_S2.1701.00
20_I47_W2.1531.00
49_M52_A1.8531.00
5_I62_K1.7381.00
74_F78_L1.7191.00
21_I84_A1.6020.99
8_V81_L1.5890.99
7_I60_E1.5790.99
10_A33_F1.5140.99
3_A74_F1.5080.99
45_R80_L1.5010.99
26_A42_I1.4710.99
14_L50_I1.4580.99
4_E78_L1.3650.98
9_R85_N1.3080.97
2_I63_I1.2950.96
27_T72_S1.2920.96
26_A33_F1.2710.96
4_E50_I1.2590.96
11_E63_I1.2570.96
18_I50_I1.2380.95
2_I74_F1.2190.95
35_L50_I1.1630.93
32_Q81_L1.1600.92
10_A29_F1.1530.92
37_G45_R1.1480.92
18_I68_S1.1420.92
46_K49_M1.1290.91
18_I30_D1.1200.91
24_E72_S1.1190.91
30_D34_I1.1080.90
7_I50_I1.1060.90
12_V17_H1.0960.89
1_P86_I1.0920.89
34_I82_L1.0850.89
80_L86_I1.0430.86
10_A18_I1.0350.85
23_H27_T1.0350.85
18_I62_K1.0210.84
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  
3ccdA20.97789.10.857Contact Map
1kklH3187.20.861Contact Map
1ka5A1186.70.862Contact Map
1ptfA11860.864Contact Map
3ihsA20.942584.40.867Contact Map
1pchA10.988582.30.87Contact Map
1sphA20.988581.40.871Contact Map
1y51A30.9885810.871Contact Map
3le1A20.988574.80.878Contact Map
2k2wA10.33332.20.947Contact 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 0.0163 seconds.