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bbs_2_sheetp1

ID: 1501723156 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 86 (75)
Sequences: 126 (97.4)
Seq/Len: 1.680
Nf(neff/√len): 11.2

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: 1.680).

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
30_I55_H1.7870.96
46_S74_L1.6600.94
35_L71_P1.5750.91
24_S27_N1.5500.90
59_S74_L1.5350.90
37_F45_E1.5300.90
38_A75_H1.4870.88
21_L70_I1.4770.87
31_I37_F1.4230.84
76_L85_S1.4080.84
28_D62_I1.3800.82
56_L60_V1.3670.81
40_G50_H1.3260.78
23_I84_S1.3230.78
17_A68_K1.3190.78
9_S20_E1.2970.76
32_R38_A1.2710.74
67_P71_P1.2380.71
49_V68_K1.2360.71
26_S76_L1.2340.71
78_T83_R1.1920.67
34_V60_V1.1860.66
31_I60_V1.1820.66
21_L46_S1.1810.66
33_A72_V1.1670.65
23_I36_I1.1560.64
28_D64_I1.1420.62
37_F46_S1.1300.61
33_A50_H1.1290.61
39_E75_H1.1250.60
28_D69_D1.1180.60
7_S10_L1.1150.59
21_L74_L1.1130.59
40_G44_G1.0660.54
42_F45_E1.0510.53
67_P80_V1.0490.52
18_H81_G1.0410.52
49_V80_V1.0290.50
32_R66_P1.0140.49
19_A50_H1.0030.48
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  
1lnsA10.67443.30.922Contact Map
2mniA10.41862.50.926Contact Map
3zrhA10.89532.40.927Contact Map
4acqA40.90720.93Contact Map
3efoB10.941920.931Contact Map
3zjeA20.88371.90.931Contact Map
3eh2A30.94191.90.931Contact Map
3hs8A10.44191.80.932Contact Map
4ckbA20.98841.70.933Contact Map
2pn5A10.93021.60.934Contact 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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