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Precursor RRE

ID: 1500592901 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 131 (130)
Sequences: 304 (261.4)
Seq/Len: 2.338
Nf(neff/√len): 22.9

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: 2.338).

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
13_Y16_P2.8611.00
13_Y28_T2.0370.99
107_I112_A1.9460.99
35_G38_N1.8290.98
20_E73_V1.8040.98
18_V128_V1.7850.98
64_I82_A1.6040.96
92_G97_A1.4760.92
75_W112_A1.4490.91
34_W38_N1.4430.91
109_E113_R1.4020.90
41_S44_R1.3490.87
22_G28_T1.3330.86
34_W41_S1.3320.86
13_Y115_D1.3260.86
38_N41_S1.3260.86
13_Y22_G1.3160.85
36_F44_R1.3080.85
112_A116_V1.2730.83
21_M27_V1.2610.82
97_A120_I1.2540.81
113_R117_E1.2340.80
37_E46_C1.2070.78
93_D96_V1.2060.78
83_E129_L1.2000.77
75_W126_V1.1990.77
60_T63_G1.1710.75
37_E44_R1.1690.74
55_I66_L1.1540.73
29_L38_N1.1500.73
123_L128_V1.1390.72
37_E40_W1.1350.71
88_L112_A1.1310.71
82_A86_R1.1290.71
123_L129_L1.1280.71
13_Y24_F1.1270.71
65_V72_G1.1260.70
83_E104_R1.1080.69
50_I95_D1.1050.68
75_W85_L1.1030.68
94_R120_I1.0990.68
37_E41_S1.0930.67
99_A103_D1.0920.67
65_V74_Y1.0920.67
57_S64_I1.0910.67
86_R90_E1.0860.66
22_G27_V1.0850.66
16_P28_T1.0850.66
51_D85_L1.0800.66
121_R130_R1.0790.66
101_I116_V1.0740.65
115_D123_L1.0720.65
25_S39_D1.0700.65
71_K82_A1.0690.65
67_L123_L1.0610.64
62_D105_Y1.0510.63
39_D46_C1.0460.62
24_F28_T1.0420.62
39_D45_V1.0390.61
31_R40_W1.0390.61
76_H85_L1.0370.61
78_N115_D1.0250.60
59_E64_I1.0230.60
117_E121_R1.0220.60
68_D71_K1.0200.59
40_W44_R1.0190.59
86_R120_I1.0190.59
2_D5_K1.0180.59
3_E7_G1.0160.59
30_G40_W1.0080.58
30_G39_D1.0080.58
68_D78_N1.0020.57
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  
3g2bA10.671899.20.533Contact Map
3h5nA40.5725850.829Contact Map
4v1tA20.603183.40.832Contact Map
4a0zA20.396933.30.881Contact Map
4un1A20.396924.90.889Contact Map
2gqqA40.4046240.889Contact Map
2cfxA80.389322.40.891Contact Map
1i1gA20.37419.10.894Contact Map
2dk5A10.511519.10.894Contact Map
1p6rA10.435118.80.895Contact 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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