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3qfl

ID: 1505135865 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 115 (84)
Sequences: 5162 (3596)
Seq/Len: 61.452
Nf(neff/√len): 392.4

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: 61.452).

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 > 50% 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
40_A59_L3.3291.00
43_I55_S3.3031.00
33_K63_E2.8561.00
59_L63_E2.5081.00
5_N8_P2.2121.00
36_E59_L2.0671.00
81_Q84_G1.9981.00
69_Y73_D1.7961.00
37_S56_Q1.7771.00
44_K54_D1.7701.00
80_V83_D1.6851.00
36_E62_D1.6221.00
32_G36_E1.6101.00
36_E63_E1.5411.00
31_L71_I1.3590.99
19_K22_K1.3470.99
37_S59_L1.3060.99
45_I61_A1.2890.99
27_N30_D1.2130.98
12_E16_E1.1880.98
17_E21_H1.1270.97
49_P52_Q1.1190.96
30_D34_E1.1170.96
77_K81_Q1.1070.96
69_Y72_E1.1060.96
16_E19_K1.0790.95
44_K55_S1.0730.95
57_D60_W1.0640.95
34_E38_M1.0570.95
72_E76_D1.0560.95
24_V78_F1.0480.94
18_F21_H1.0410.94
9_K12_E1.0360.94
14_L17_E1.0280.94
44_K56_Q1.0260.94
34_E37_S1.0220.93
60_W64_V1.0200.93
38_M41_A1.0050.93
13_L17_E1.0010.92
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  
3qflA10.956599.5-0.079Contact Map
4btfA10.730413.30.811Contact Map
4m70A50.78266.30.836Contact Map
2msvA10.85225.10.844Contact Map
3a7pA20.73913.80.853Contact Map
4n78F10.878320.873Contact Map
1vcsA10.80871.90.875Contact Map
1a31A10.18261.80.877Contact Map
3pp5A10.38261.80.877Contact Map
3vviA80.18261.60.878Contact 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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