OPENSEQ.org
Precursor RRE

ID: 1515795750 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 130 (125)
Sequences: 308 (267)
Seq/Len: 2.464
Nf(neff/√len): 23.9

HHblits Results: (2016_02)
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: 2.464).

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
6_Y9_P2.9671.00
6_Y21_T2.0621.00
106_V111_A1.9560.99
26_A29_G1.8380.99
13_K72_E1.8380.99
11_L127_M1.7230.98
63_M81_A1.5680.95
25_T29_G1.5100.94
108_R112_E1.4320.92
91_H96_V1.4240.91
74_W111_A1.3770.89
6_Y15_G1.3760.89
29_G32_L1.3760.89
25_T32_L1.3420.88
32_L35_V1.3370.87
37_P40_I1.3200.87
6_Y114_D1.3100.86
14_V20_A1.3000.85
15_G21_T1.2990.85
27_E35_V1.2810.84
111_A115_I1.2750.84
112_E116_A1.2360.81
87_L111_A1.2240.80
96_V119_V1.2190.80
9_P21_T1.1880.77
59_T62_G1.1840.77
81_A85_Q1.1620.75
28_W37_P1.1560.75
74_W125_N1.1520.74
120_T129_L1.1470.74
6_Y17_F1.1450.74
28_W35_V1.1370.73
54_I65_L1.1360.73
122_L127_M1.1360.73
58_Q63_M1.1320.73
98_Q102_S1.1290.72
56_V63_M1.1270.72
82_L128_A1.1100.70
61_Y104_Y1.1030.70
67_D70_S1.1000.69
28_W31_E1.1000.69
92_S95_D1.0960.69
4_K103_E1.0820.68
74_W84_V1.0820.68
122_L128_A1.0820.68
15_G20_A1.0780.67
28_W32_L1.0760.67
116_A120_T1.0730.67
6_Y16_E1.0660.66
64_V71_G1.0630.66
100_L115_I1.0600.65
50_L84_V1.0590.65
66_L122_L1.0580.65
93_P119_V1.0510.64
18_K30_L1.0500.64
64_V73_Y1.0500.64
30_L40_I1.0480.64
22_G31_E1.0460.64
6_Y19_E1.0450.64
82_L103_E1.0430.63
49_R94_A1.0390.63
87_L90_G1.0390.63
85_Q119_V1.0370.63
22_G34_F1.0310.62
70_S81_A1.0240.61
67_D126_G1.0230.61
17_F21_T1.0200.61
31_E35_V1.0160.60
31_E34_F1.0110.60
27_E31_E1.0080.60
94_A112_E1.0080.60
16_E21_T1.0080.60
114_D122_L1.0020.59
30_L36_F1.0020.59
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  
3g2bA10.676999.20.525Contact Map
4v1tA20.607781.40.832Contact Map
3h5nA40.576979.60.835Contact Map
4a0zA20.435.60.876Contact Map
2gqqA40.407729.30.882Contact Map
4un1A20.4270.884Contact Map
2cfxA80.3923260.884Contact Map
1i1gA20.376922.50.888Contact Map
4pcqA40210.89Contact Map
3i4pA10.376920.90.89Contact 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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