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fastrelax_13

ID: 1507196830 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 87 (87)
Sequences: 379 (168.6)
Seq/Len: 4.356
Nf(neff/√len): 18.1

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: 4.356).

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
8_P59_D3.0501.00
15_D54_K2.5401.00
36_D77_L1.7651.00
10_A18_F1.7621.00
2_L74_F1.7510.99
5_T60_T1.7210.99
22_L44_M1.6920.99
5_T85_R1.6000.99
5_T71_A1.5960.99
49_Q76_R1.5840.99
52_S55_V1.5260.98
8_P61_L1.4830.98
36_D41_I1.4630.98
28_L82_L1.4460.97
7_V49_Q1.4210.97
33_I73_T1.3920.96
20_H47_K1.3860.96
48_D52_S1.3800.96
55_V83_R1.3030.94
2_L71_A1.2520.92
9_K20_H1.2500.92
56_P63_L1.2470.92
73_T84_L1.2440.92
17_H21_L1.2410.92
17_H80_Q1.2380.92
60_T74_F1.2270.91
33_I71_A1.2140.91
59_D66_I1.2070.91
6_L48_D1.2030.90
33_I82_L1.1300.86
25_E83_R1.1090.85
4_A27_Q1.1070.85
2_L38_K1.1070.85
22_L35_L1.0510.80
73_T77_L1.0470.80
10_A80_Q1.0420.80
6_L60_T1.0310.79
29_Y58_G1.0300.78
6_L72_D1.0130.77
65_V74_F1.0080.76
25_E63_L1.0000.75
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  
3ccdA20.97798.20.774Contact Map
1kklH3198.10.778Contact Map
1ka5A1198.10.781Contact Map
1ptfA11980.783Contact Map
3ihsA20.931980.784Contact Map
1pchA10.988597.90.788Contact Map
1y51A30.988597.90.789Contact Map
1sphA20.988597.90.789Contact Map
3le1A20.988597.80.796Contact Map
3n6rA60.89668.60.938Contact 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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