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fastRelax_offset_1

ID: 1507196349 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 87 (87)
Sequences: 614 (277)
Seq/Len: 7.057
Nf(neff/√len): 29.7

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: 7.057).

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
79_E83_F2.2591.00
4_Y78_L2.1961.00
48_E63_I2.1961.00
38_R60_E2.0981.00
36_L41_I2.0901.00
22_L25_L1.7381.00
72_D75_R1.7021.00
3_F48_E1.6581.00
5_W62_L1.5370.99
37_Y58_D1.5310.99
35_L42_I1.5240.99
27_D32_P1.5100.99
56_D86_L1.5040.99
68_E74_L1.4120.99
55_V71_R1.3990.99
10_E51_R1.3930.99
15_D54_D1.3500.98
34_W43_L1.3240.98
65_V74_L1.2650.97
10_E56_D1.2470.97
17_R35_L1.2400.97
33_L54_D1.2300.97
46_V61_Y1.2300.97
21_A79_E1.2170.96
19_A74_L1.2140.96
32_P39_G1.2030.96
37_Y59_I1.1950.96
33_L77_T1.1730.95
8_V15_D1.1440.94
10_E58_D1.1300.94
27_D30_V1.1170.93
24_R64_V1.1130.93
29_F63_I1.1000.92
42_I75_R1.0900.92
9_I77_T1.0600.91
17_R45_L1.0590.90
20_I24_R1.0460.90
3_F78_L1.0440.90
21_A53_L1.0400.89
50_L53_L1.0330.89
2_L84_E1.0200.88
19_A55_V1.0150.88
81_L85_R1.0090.87
1_D66_T1.0070.87
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  
1ka5A11980.759Contact Map
1kklH31980.761Contact Map
1ptfA11980.762Contact Map
1sphA20.988597.90.766Contact Map
1y51A30.988597.90.767Contact Map
1pchA10.988597.90.768Contact Map
3ccdA20.97797.80.771Contact Map
3ihsA20.896697.80.773Contact Map
3le1A20.988597.60.781Contact Map
1vhfA10.32185.80.937Contact 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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