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Ter

ID: 1501797639 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 95 (87)
Sequences: 228 (204.9)
Seq/Len: 2.621
Nf(neff/√len): 22.0

Jackhmmer Results: (2016_04)
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: 2.621).

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
84_T89_S2.9291.00
32_S35_H2.8041.00
58_V61_N2.4741.00
82_Y89_S2.1801.00
21_I44_A2.0100.99
24_D57_K1.6740.97
83_Y88_V1.6600.97
72_D90_H1.5840.96
73_L82_Y1.5160.95
23_F56_K1.4400.93
82_Y90_H1.4400.93
72_D82_Y1.4200.92
26_G35_H1.4110.92
37_F47_I1.3810.91
35_H50_G1.3460.89
31_C37_F1.3040.87
37_F89_S1.2810.86
48_K57_K1.2710.85
42_I50_G1.2550.84
29_I37_F1.2400.83
20_H28_E1.2390.83
70_L82_Y1.1920.79
18_Y49_V1.1780.78
25_D56_K1.1730.78
20_H30_K1.1560.76
37_F42_I1.1560.76
70_L91_N1.1300.74
34_N41_K1.1170.73
36_S92_C1.1160.73
14_Y40_D1.1150.73
82_Y91_N1.1140.73
72_D92_C1.1060.72
81_L89_S1.1010.71
37_F74_L1.0850.70
50_G58_V1.0790.69
23_F35_H1.0320.64
77_G86_G1.0290.64
73_L89_S1.0230.63
56_K68_I1.0190.63
72_D91_N1.0120.62
13_V92_C1.0100.62
16_P33_D1.0060.61
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  
4e2uA10.968499.80.355Contact Map
1mi8A10.957999.80.369Contact Map
3nzmA10.926399.80.376Contact Map
2imzA20.926399.80.383Contact Map
1am2A10.936899.80.384Contact Map
4o1rA10.936899.80.395Contact Map
2lcjA10.947499.80.395Contact Map
4o1sA20.957999.80.398Contact Map
2in0A10.936899.70.409Contact Map
2jmzA10.989599.70.417Contact 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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