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glebs
ID: 1452538211 Query Sequence

 Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 120 (108)
Sequences: 188 (97.1)
Seq/Len: 1.741
Nf(neff/√len): 9.3
Jackhmmer Results: (2015_08)
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: 1.741).

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
61_L65_K2.4791.00
47_E73_E1.9190.98
58_F61_L1.9180.98
112_E116_E1.8730.98
99_K102_E1.7700.96
49_L57_S1.6450.94
15_E20_T1.6110.93
42_V57_S1.5850.92
113_T116_E1.5570.91
22_S25_E1.4980.89
54_S58_F1.4550.87
42_V49_L1.4210.85
49_L58_F1.4180.85
51_R56_F1.3850.83
69_R74_Q1.3750.82
21_I24_S1.3650.82
21_I28_V1.3580.81
94_Q107_L1.3340.80
49_L61_L1.2730.75
17_R20_T1.2720.75
105_K110_V1.2580.74
105_K109_Q1.2570.74
112_E115_H1.2140.70
106_K115_H1.2140.70
11_E14_M1.1960.68
114_S117_D1.1900.68
103_L108_H1.1850.67
111_V115_H1.1800.67
105_K108_H1.1700.66
14_M17_R1.1520.64
106_K113_T1.1420.63
110_V114_S1.1350.62
107_L110_V1.1260.62
26_Y29_H1.1190.61
57_S61_L1.1180.61
47_E64_Q1.1180.61
96_L105_K1.1160.61
108_H116_E1.1050.59
93_E100_M1.0870.58
68_Q76_V1.0830.57
13_N16_R1.0770.56
10_K13_N1.0650.55
37_D71_K1.0570.54
14_M20_T1.0380.52
51_R54_S1.0370.52
45_C48_K1.0360.52
96_L103_L1.0290.51
78_E84_K1.0230.51
17_R25_E1.0220.51
64_Q77_N1.0210.50
104_H107_L1.0180.50
44_Y55_E1.0170.50
43_M52_G1.0130.50
97_K101_D1.0090.49
66_Y80_R1.0020.48
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  
2i3sB30.291787.10.854Contact Map
4bl0B20.3582.40.863Contact Map
2i3tB40.347.50.893Contact Map
3mmyB40.42526.10.907Contact Map
4gnkB2018.20.913Contact Map
4ll8A1014.50.917Contact Map
1lwuB40.53339.10.924Contact Map
3kdqA40.3257.40.928Contact Map
3ziaJ20.35.80.931Contact Map
3viqB20.308350.933Contact 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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