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3oss

ID: 1501759049 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 65 (61)
Sequences: 477 (470)
Seq/Len: 7.820
Nf(neff/√len): 60.2

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: 7.820).

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 > 50% 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
43_I46_I2.7521.00
8_L19_A2.4981.00
43_I51_V2.1761.00
44_E54_R2.1401.00
10_G20_V1.8941.00
4_L60_E1.8671.00
50_H61_R1.8211.00
7_V22_E1.7291.00
8_L11_I1.6841.00
41_A51_V1.5511.00
46_I51_V1.4520.99
40_N55_Y1.4390.99
47_N50_H1.3270.98
11_I19_A1.2170.97
55_Y60_E1.2150.97
29_V41_A1.1890.96
12_A64_L1.1720.96
10_G13_F1.1500.95
42_V57_G1.1260.95
37_D40_N1.0940.93
35_R42_V1.0850.93
28_Q31_L1.0630.92
5_N47_N1.0500.92
35_R61_R1.0420.91
43_I53_L1.0390.91
5_N45_E1.0340.91
45_E52_M1.0170.90
54_R59_I1.0010.89
48_R64_L1.0010.89
6_V57_G1.0010.89
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  
3ossC1198.90.089Contact Map
2lnvA1198.80.116Contact Map
4av2M121970.429Contact Map
2lc4A1195.10.52Contact Map
2ivwA1195.10.521Contact Map
2y4xA20.984694.90.527Contact Map
1vw4N10.876922.10.762Contact Map
2zjrO10.630814.40.782Contact Map
4rb6V10.661513.70.785Contact Map
3j3wR10.676913.30.786Contact 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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