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Coevolution

ID: 1513340523 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 277 (94)
Sequences: 4845 (3394.6)
Seq/Len: 51.543
Nf(neff/√len): 350.1

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: 51.543).

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
76_I87_P3.1741.00
64_R68_E2.4191.00
79_F83_V2.3351.00
49_A53_Y2.2871.00
99_L105_P2.0531.00
57_I61_R1.9851.00
70_H74_K1.9691.00
56_F59_K1.8281.00
65_A101_P1.7501.00
62_V65_A1.7291.00
71_G75_D1.7071.00
55_D58_E1.6371.00
53_Y56_F1.5601.00
70_H73_A1.4871.00
80_A86_Y1.4661.00
65_A68_E1.4391.00
48_L51_P1.3540.99
63_A67_S1.3490.99
57_I60_A1.3390.99
18_R21_R1.3290.99
78_G82_A1.3120.99
53_Y57_I1.3110.99
22_S25_R1.3010.99
76_I80_A1.2950.99
46_A50_V1.2550.99
31_S34_E1.2480.99
47_A51_P1.2410.98
77_K86_Y1.2310.98
76_I86_Y1.2270.98
49_A52_N1.2090.98
19_R22_S1.2030.98
20_S24_L1.1550.97
77_K96_S1.1230.97
79_F85_A1.1060.96
58_E61_R1.1060.96
18_R22_S1.0970.96
21_R25_R1.0870.96
50_V54_M1.0670.95
68_E72_L1.0650.95
22_S26_H1.0570.95
63_A66_I1.0460.94
18_R23_C1.0440.94
51_P55_D1.0420.94
74_K78_G1.0290.94
20_S23_C1.0240.93
89_S110_R1.0220.93
73_A77_K1.0220.93
90_L93_V1.0190.93
40_S43_G1.0050.93
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  
3sokA20.433299.50.822Contact Map
2hi2A10.50999.30.833Contact Map
2m7gA10.220299.30.835Contact Map
1oqwA20.469399.20.847Contact Map
3g20A20.353898.90.862Contact Map
1t92A20.3105980.896Contact Map
3gn9A30.328597.90.899Contact Map
2kepA10.321397.70.901Contact Map
2opeA40.404397.60.904Contact Map
4kblA20.137275.50.949Contact 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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