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OPENSEQ.org

rdlB

ID: 1510658046 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 133 (131)
Sequences: 344 (142.8)
Seq/Len: 2.626
Nf(neff/√len): 12.5

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: 2.626).

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
91_N95_D2.5971.00
2_I6_V2.5241.00
96_D112_G1.9860.99
7_A14_S1.9730.99
82_I85_V1.9610.99
83_G86_P1.9410.99
45_Q103_E1.8750.99
29_I126_S1.8220.99
2_I5_V1.8190.99
95_D113_A1.5860.96
1_M5_V1.5320.95
122_S125_S1.5200.95
55_N61_A1.4710.94
16_M31_D1.4680.94
66_S103_E1.4130.92
70_P102_A1.4040.91
80_S87_I1.3970.91
51_M55_N1.3960.91
92_V95_D1.3850.91
59_Q64_Q1.3830.91
102_A118_L1.3820.91
11_I17_G1.3440.89
61_A70_P1.3380.89
76_D96_D1.3290.88
95_D112_G1.3150.87
109_K112_G1.3120.87
7_A10_A1.2980.87
6_V21_A1.2930.86
50_S120_D1.2680.85
60_M63_I1.2560.84
8_Y12_A1.2470.83
60_M70_P1.2190.81
29_I37_S1.2170.81
60_M67_F1.2140.81
61_A66_S1.2130.81
35_P50_S1.1890.79
45_Q69_K1.1880.79
51_M74_V1.1850.79
63_I67_F1.1820.79
19_S27_M1.1800.78
70_P118_L1.1770.78
67_F73_A1.1660.77
110_R115_A1.1600.77
4_K14_S1.1600.77
75_S78_P1.1440.75
35_P121_V1.1430.75
50_S53_T1.1210.73
53_T61_A1.1030.72
4_K13_A1.1020.71
117_L121_V1.0980.71
19_S22_A1.0970.71
39_N47_F1.0970.71
55_N60_M1.0930.71
65_G70_P1.0770.69
30_G33_S1.0760.69
80_S86_P1.0690.68
91_N94_G1.0590.67
5_V11_I1.0420.65
115_A121_V1.0410.65
64_Q100_Q1.0340.64
9_A18_A1.0320.64
79_V83_G1.0270.64
8_Y22_A1.0190.63
37_S47_F1.0180.63
75_S97_M1.0100.62
81_V85_V1.0090.62
5_V9_A1.0030.61
82_I86_P1.0000.61
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  
4oc8A40.36095.20.963Contact Map
2vdaB10.16543.10.967Contact Map
4ujti102.60.968Contact Map
4ui9T102.30.969Contact Map
2pq4B10.21052.10.97Contact Map
3j3bq10.13531.80.971Contact Map
4kt0F10.48121.70.971Contact Map
4by8A10.06771.60.972Contact Map
1jb0F10.48121.50.972Contact Map
3ucpA10.54891.40.972Contact 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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