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4rng

ID: 1501760835 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 82 (80)
Sequences: 583 (577.3)
Seq/Len: 7.287
Nf(neff/√len): 64.5

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: 7.287).

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
25_I78_M2.0911.00
23_L27_K2.0161.00
49_W52_Y1.8111.00
14_T18_L1.5671.00
8_I12_A1.5601.00
17_A42_M1.5230.99
19_I63_L1.4870.99
36_L40_I1.4830.99
42_M46_I1.4030.99
49_W53_G1.3790.99
24_K28_T1.3760.99
47_T69_L1.3370.98
9_I19_I1.2740.98
5_L9_I1.2460.97
64_A72_I1.2270.97
24_K70_I1.2040.96
62_I65_N1.1950.96
52_Y65_N1.1690.95
14_T49_W1.1600.95
21_Q35_S1.1560.95
43_A69_L1.1480.95
64_A75_I1.1390.94
46_I68_S1.1370.94
49_W61_V1.1300.94
34_V75_I1.1240.94
73_F80_I1.1210.94
21_Q45_G1.1190.94
54_V62_I1.1080.93
72_I78_M1.1070.93
26_Y29_K1.1070.93
66_L70_I1.0930.93
66_L71_L1.0930.93
20_P26_Y1.0920.93
40_I76_I1.0900.92
25_I31_A1.0840.92
6_I12_A1.0720.92
20_P75_I1.0410.90
34_V79_K1.0330.90
40_I55_L1.0260.89
38_M52_Y1.0150.88
30_S33_D1.0120.88
32_R36_L1.0100.88
45_G72_I1.0090.88
55_L73_F1.0050.88
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  
4x5mA3199.50.021Contact Map
4rngA6199.50.027Contact Map
4qncA20.987899.50.036Contact Map
4qndA1199.50.044Contact Map
2k9pA10.84152.60.877Contact Map
2y69M20.35372.30.88Contact Map
1v54M20.35372.30.88Contact Map
3qrxB10.24391.90.886Contact Map
4ogqC10.47561.30.896Contact Map
4cofA50.65851.20.898Contact 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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