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SWISSPROTP20724

ID: 1516225168 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 84 (72)
Sequences: 139 (118.3)
Seq/Len: 1.931
Nf(neff/√len): 13.9

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: 1.931).

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_K78_D4.7421.00
12_G74_Y2.1420.99
9_Y58_L2.0380.99
42_I59_D1.5680.93
7_E64_D1.5650.93
48_F71_A1.4270.87
42_I62_D1.3910.86
10_L53_V1.3850.85
21_Q24_D1.3830.85
34_S42_I1.3580.84
59_D62_D1.3160.81
7_E67_E1.2810.78
58_L70_P1.2660.77
44_L82_T1.2590.77
45_L82_T1.2480.76
76_E81_V1.1920.71
55_S78_D1.1860.71
7_E77_E1.1420.66
35_S80_E1.1410.66
7_E61_E1.1330.65
10_L81_V1.1280.65
24_D75_I1.1210.64
46_H79_A1.1150.64
10_L57_E1.1020.62
23_V31_Y1.0900.61
12_G52_P1.0900.61
13_F62_D1.0720.59
56_V78_D1.0690.59
11_I55_S1.0610.58
16_Q45_L1.0420.56
53_V74_Y1.0150.53
13_F40_V1.0070.52
18_V21_Q1.0010.51
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  
2z30B10.773898.90.443Contact Map
3cnqP10.821498.70.467Contact Map
3whiA20.857198.60.495Contact Map
1v5iB10.857198.40.519Contact Map
3wiuA30.785798.40.522Contact Map
3afgA20.86998.20.543Contact Map
2w2nP10.940598.20.549Contact Map
4nmxA10.952498.10.555Contact Map
3t41A20.797697.60.606Contact Map
2p4eP20.952497.60.608Contact 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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