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OPENSEQ.org
84-1
ID: 1477484602 Query Sequence

 Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 114 (98)
Sequences: 329 (205)
Seq/Len: 3.357
Nf(neff/√len): 20.7
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: 3.357).

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
59_L76_N1.8650.99
65_Y79_M1.6490.98
46_L86_R1.6240.98
85_V91_D1.5970.98
21_F89_I1.5530.97
68_I74_D1.5390.97
60_N63_K1.5380.97
40_D61_I1.5350.97
75_L89_I1.4880.96
68_I75_L1.4710.96
65_Y76_N1.4660.96
57_V82_L1.3850.94
83_K87_A1.3800.94
44_S55_E1.3220.92
53_V99_C1.3100.91
51_I97_D1.3020.91
85_V96_L1.2630.89
14_K20_H1.2570.89
65_Y75_L1.2510.89
40_D44_S1.2370.88
25_D44_S1.2210.87
49_L69_M1.2200.87
46_L50_S1.2180.87
16_L81_E1.2090.86
71_V92_L1.2020.86
86_R92_L1.1960.85
58_K71_V1.1740.84
26_F70_T1.1640.83
22_N25_D1.1450.82
77_V96_L1.1440.82
62_N94_E1.1430.82
24_K30_K1.1260.80
21_F99_C1.1200.80
23_A52_Q1.1130.79
65_Y89_I1.1070.79
68_I78_A1.0960.78
17_A47_T1.0870.77
51_I54_Q1.0850.77
64_S68_I1.0800.76
38_T81_E1.0690.75
26_F68_I1.0610.74
61_I89_I1.0540.74
18_N22_N1.0530.74
39_I43_T1.0520.74
57_V64_S1.0490.73
103_A106_R1.0470.73
23_A41_K1.0400.72
27_V80_L1.0360.72
43_T58_K1.0320.71
81_E92_L1.0250.71
47_T81_E1.0250.71
67_E81_E1.0210.70
41_K45_N1.0210.70
39_I76_N1.0110.69
37_I43_T1.0060.69
36_A90_N1.0030.68
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  
2jqqA10.245645.50.89Contact Map
3qneA10.8509350.897Contact Map
3ghgA40.894725.80.904Contact Map
2yy0A40.447423.40.906Contact Map
4linA120.964919.80.909Contact Map
4u6uA20.587716.10.913Contact Map
2dq0A20.824614.70.914Contact Map
4cr2L10.412312.60.917Contact Map
1lwuC40.552611.90.917Contact Map
3oa7A10.666711.40.918Contact 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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