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glebs
ID: 1452521265 Query Sequence

 Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 120 (110)
Sequences: 166 (85.2)
Seq/Len: 1.509
Nf(neff/√len): 8.1
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: 1.509).

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_K2.5521.00
112_E116_E1.9140.97
49_L58_F1.8330.96
99_K102_E1.7660.95
42_V57_S1.6890.93
15_E20_T1.6430.92
49_L57_S1.6300.92
113_T116_E1.5830.90
22_S25_E1.5630.89
47_E73_E1.5270.88
21_I28_V1.5150.87
21_I24_S1.4820.85
68_Q76_V1.4810.85
57_S61_L1.4450.83
58_F61_L1.4250.82
94_Q107_L1.3960.80
43_M52_G1.3270.75
54_S58_F1.3130.74
17_R20_T1.2940.73
105_K109_Q1.2840.72
51_R56_F1.2450.69
9_D12_S1.2200.66
106_K115_H1.2090.65
11_E14_M1.2070.65
41_V66_Y1.2050.65
103_L108_H1.2050.65
66_Y80_R1.1960.64
105_K110_V1.1910.64
14_M17_R1.1870.63
64_Q77_N1.1830.63
112_E115_H1.1730.62
114_S117_D1.1730.62
39_E78_E1.1680.61
111_V115_H1.1670.61
108_H116_E1.1410.59
105_K108_H1.1390.59
23_K40_Q1.1210.57
96_L105_K1.1120.56
93_E100_M1.1050.55
21_I43_M1.0990.54
53_E61_L1.0910.54
110_V114_S1.0900.54
10_K13_N1.0870.53
13_N16_R1.0860.53
69_R74_Q1.0860.53
94_Q102_E1.0770.52
14_M20_T1.0670.51
41_V96_L1.0600.50
106_K113_T1.0550.50
31_S34_S1.0440.49
107_L110_V1.0420.49
80_R107_L1.0360.48
13_N17_R1.0330.48
96_L103_L1.0230.47
71_K99_K1.0190.46
78_E84_K1.0170.46
109_Q115_H1.0170.46
53_E93_E1.0060.45
26_Y29_H1.0000.44
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  
2i3sB30.291788.70.864Contact Map
4bl0B20.3585.90.87Contact Map
2i3tB40.346.60.903Contact Map
3mmyB40.42519.70.92Contact Map
4gnkB2018.50.921Contact Map
4ll8A1014.80.924Contact Map
1lwuB40.53339.50.931Contact Map
3ziaJ20.38.20.933Contact Map
3kdqA40.3257.10.935Contact Map
3m0dC10.50836.20.936Contact 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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