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OPENSEQ.org
SRF-Lum trimmed
ID: 1424978338 Query Sequence

 Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 107 (105)
Sequences: 220 (160.4)
Seq/Len: 2.095
Nf(neff/√len): 15.7
Jackhmmer Results: (2015_01_07)
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: 2.095).

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
49_I75_F2.6971.00
49_I100_L1.9970.99
23_S28_P1.7550.97
69_L73_Y1.7010.97
7_L53_N1.6210.95
32_L49_I1.5880.94
19_R57_D1.5660.94
17_Y45_T1.5630.94
53_N61_V1.4860.91
84_G90_D1.4690.91
8_R56_W1.4680.91
57_D62_Q1.4670.91
32_L100_L1.4490.90
75_F100_L1.4330.89
33_K101_E1.4290.89
23_S26_L1.4120.88
29_I99_G1.4110.88
40_G106_Y1.3960.87
4_R86_E1.3870.87
98_C102_Y1.3680.86
67_T91_Q1.3510.85
36_G73_Y1.3430.85
44_Y67_T1.3360.84
36_G44_Y1.3310.84
25_R96_G1.3310.84
36_G40_G1.3050.82
3_D95_R1.2960.82
54_K64_E1.2940.81
21_T25_R1.2930.81
11_K61_V1.2830.81
8_R12_A1.2830.81
78_T100_L1.2730.80
47_K74_K1.2430.78
16_H77_K1.2060.75
38_T64_E1.1900.73
97_S102_Y1.1860.73
50_Q62_Q1.1840.73
17_Y47_K1.1790.72
15_L99_G1.1560.70
41_C106_Y1.1330.68
3_D74_K1.1240.67
44_Y69_L1.1020.65
16_H72_A1.0980.64
100_L104_L1.0740.62
27_D54_K1.0620.61
49_I78_T1.0570.60
93_V105_D1.0450.59
46_P87_S1.0350.58
30_P33_K1.0320.57
21_T90_D1.0260.57
41_C45_T1.0220.56
12_A45_T1.0200.56
22_T96_G1.0010.54
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: (31Jan15)
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  
3rgaA10.34585.70.95Contact Map
3wmdA20.33644.90.951Contact Map
3bjsA20.28044.90.952Contact Map
2l5qA10.33644.50.952Contact Map
3b9oA20.32714.50.952Contact Map
1ewsA10.25234.40.952Contact Map
1ohpA40.33643.30.956Contact Map
1kqhA10.224330.956Contact Map
2xrbA10.81312.70.957Contact Map
1kmtA20.37382.20.959Contact 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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