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4rng

ID: 1500381792 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 82 (81)
Sequences: 4863 (3016.5)
Seq/Len: 60.037
Nf(neff/√len): 335.2

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: 60.037).

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
23_L27_K3.2721.00
77_F81_R2.0891.00
78_M82_Y1.8851.00
22_A74_L1.8641.00
24_K28_T1.8621.00
43_A69_L1.8061.00
25_I31_A1.7101.00
31_A79_K1.6981.00
26_Y78_M1.6961.00
8_I12_A1.6431.00
30_S33_D1.6141.00
59_I63_L1.5921.00
25_I78_M1.5821.00
53_G61_V1.5701.00
23_L26_Y1.4371.00
47_T69_L1.4221.00
54_V62_I1.3950.99
4_N8_I1.3760.99
74_L78_M1.3500.99
39_F75_I1.3410.99
19_I23_L1.3380.99
29_K82_Y1.3310.99
53_G62_I1.3110.99
50_F62_I1.3080.99
14_T18_L1.2990.99
26_Y82_Y1.2820.99
46_I68_S1.2660.99
15_T68_S1.2650.99
43_A73_F1.2440.98
14_T17_A1.2290.98
42_M46_I1.2230.98
43_A72_I1.2150.98
49_W53_G1.1790.98
15_T18_L1.1770.98
50_F66_L1.1710.98
5_L9_I1.1280.97
49_W52_Y1.1250.97
15_T67_I1.1240.97
71_L75_I1.1010.96
40_I76_I1.0960.96
66_L70_I1.0840.96
36_L40_I1.0600.95
36_L79_K1.0570.95
34_V39_F1.0540.95
20_P23_L1.0170.93
36_L76_I1.0100.93
4_N58_E1.0000.92
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  
4x5mA3199.4-0.014Contact Map
4rngA6199.4-0.008Contact Map
4qncA20.987899.4-0.007Contact Map
4qndA1199.40.003Contact Map
3pjzA20.29271.40.881Contact Map
3s8fA10.46341.40.882Contact Map
3qrxB10.24391.40.882Contact Map
4qinA10.97561.20.886Contact Map
4jkvA20.975610.89Contact Map
4p79A10.329310.892Contact 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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