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3oss_bakerMSA

ID: 1502277653 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 61 (61)
Sequences: 568 (500.8)
Seq/Len: 9.311
Nf(neff/√len): 64.1

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: 9.311).

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
41_E51_R2.8211.00
5_L16_A2.7191.00
40_I43_I2.3371.00
44_N47_H2.2111.00
43_I48_V2.1561.00
47_H58_R1.9641.00
5_L59_L1.9621.00
5_L8_I1.8601.00
7_G17_V1.8001.00
1_L57_E1.6461.00
40_I48_V1.6101.00
14_P29_Q1.5861.00
41_E56_I1.5521.00
10_F14_P1.5061.00
51_R54_G1.4401.00
27_Y33_L1.4020.99
8_I61_L1.3440.99
27_Y40_I1.2430.98
4_V59_L1.1800.97
19_E23_K1.1330.96
1_L16_A1.0680.94
39_V51_R1.0660.94
5_L48_V1.0140.92
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  
3ossC1198.80.083Contact Map
2lnvA1198.80.085Contact Map
4av2M12196.80.427Contact Map
2ivwA1193.10.545Contact Map
2lc4A1192.90.548Contact Map
2y4xA2192.60.552Contact Map
1vw4N10.950818.20.763Contact Map
4rb6V10.688510.50.787Contact Map
2zjrO10.62310.40.787Contact Map
2arzA20.901610.20.788Contact 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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