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TargetPilE 1-70

ID: 1513816953 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 70 (65)
Sequences: 11071 (8176.4)
Seq/Len: 170.323
Nf(neff/√len): 1014.2

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: 170.323).

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
47_A51_Q2.8981.00
62_A66_D2.4841.00
40_K44_A2.1931.00
32_A36_Y2.1191.00
45_A48_A1.9301.00
53_A57_S1.7841.00
57_S61_A1.7401.00
59_L63_Y1.7311.00
48_A51_Q1.6701.00
53_A56_M1.6561.00
38_K41_R1.6511.00
36_Y40_K1.5941.00
54_S58_E1.5711.00
56_M60_A1.4191.00
45_A49_T1.4081.00
39_Y42_K1.3150.99
31_V34_P1.2920.99
46_S49_T1.2690.99
34_P37_T1.2500.99
61_A65_D1.2380.98
33_I37_T1.2190.98
7_E11_K1.1780.98
8_N11_K1.1710.98
54_S57_S1.1680.97
60_A63_Y1.1160.96
51_Q55_C1.1110.96
50_G54_S1.1010.96
42_K46_S1.0710.95
41_R45_A1.0620.95
63_Y68_T1.0540.95
48_A59_L1.0530.95
40_K43_A1.0530.95
44_A48_A1.0350.94
35_Q38_K1.0340.94
30_A34_P1.0220.93
49_T53_A1.0180.93
63_Y67_S1.0090.93
48_A52_I1.0010.92
20_I36_Y1.0010.92
41_R44_A1.0000.92
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  
2hi2A10.8143990.133Contact Map
3sokA20.8286990.144Contact Map
1oqwA20.828698.80.179Contact Map
2m7gA10.828698.80.201Contact Map
3g20A20.585797.40.441Contact Map
3gn9A30.471487.80.642Contact Map
1t92A20.471486.70.648Contact Map
2kepA10.485785.90.653Contact Map
4noaA10.4571830.665Contact Map
2m3kA10.485780.80.672Contact 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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