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fastrelax bb

ID: 1505158896 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 87 (87)
Sequences: 487 (166.5)
Seq/Len: 5.598
Nf(neff/√len): 17.9

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: 5.598).

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
22_L80_L2.0921.00
14_L62_L1.8921.00
42_I72_D1.8111.00
4_Y82_E1.7681.00
4_Y78_V1.5700.99
60_D77_T1.5290.99
14_L55_V1.5120.99
8_V86_F1.4570.99
15_R49_Q1.4510.98
28_I81_L1.4330.98
30_A55_V1.4310.98
30_A64_V1.4160.98
32_I71_I1.3790.98
6_L62_L1.3710.98
5_W23_V1.3320.97
14_L74_L1.3300.97
23_V52_G1.3250.97
35_L42_I1.3200.97
32_I51_L1.3120.97
12_H41_L1.2950.96
40_I51_L1.2680.96
51_L81_L1.2550.95
25_R76_F1.2540.95
6_L54_D1.2400.95
49_Q79_R1.2370.95
49_Q68_E1.1710.92
23_V59_S1.1670.92
32_I63_L1.1580.92
1_H76_F1.1520.92
43_L56_D1.1170.90
32_I70_A1.0960.89
36_H45_L1.0890.88
9_F22_L1.0680.87
4_Y28_I1.0650.87
36_H51_L1.0650.87
41_L51_L1.0650.87
41_L49_Q1.0630.87
3_S57_R1.0620.87
10_D18_S1.0570.86
35_L64_V1.0540.86
19_A72_D1.0460.86
37_F85_R1.0380.85
16_S63_L1.0350.85
35_L79_R1.0330.85
5_W8_V1.0270.84
70_A75_L1.0180.83
37_F59_S1.0150.83
6_L52_G1.0080.83
4_Y74_L1.0040.82
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  
1kklH3197.80.787Contact Map
1ka5A1197.80.789Contact Map
1ptfA1197.80.789Contact Map
1sphA20.988597.70.793Contact Map
1pchA10.988597.70.793Contact Map
1y51A30.988597.70.794Contact Map
3ccdA20.97797.50.801Contact Map
3ihsA20.942597.50.802Contact Map
3le1A20.988597.40.807Contact Map
1vhfA10.321810.40.935Contact 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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