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bbs_2_sheetp1_t2

ID: 1501724072 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 99 (92)
Sequences: 130 (95.3)
Seq/Len: 1.413
Nf(neff/√len): 9.9

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: 1.413).

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
43_I68_H1.8890.96
59_S87_L1.6860.92
19_L22_S1.6300.91
48_L84_P1.5400.87
50_F58_E1.5050.85
51_A88_H1.4980.85
12_N15_H1.4930.85
37_S40_N1.4450.82
69_L73_V1.4260.81
34_L83_I1.4050.79
36_I97_S1.4000.79
53_G63_H1.3690.77
34_L59_S1.3600.76
15_H64_P1.3490.75
44_I50_F1.3070.72
30_A81_K1.2980.71
72_S87_L1.2900.71
80_P84_P1.2690.69
45_R51_A1.2630.68
62_V81_K1.2560.68
41_D75_I1.2520.67
22_S33_E1.2370.66
24_G77_I1.2360.66
12_N91_T1.2250.65
12_N51_A1.2200.64
5_H47_V1.2160.64
50_F59_S1.2150.64
89_L98_S1.1870.61
36_I49_I1.1610.59
53_G57_G1.1410.57
12_N17_T1.1400.57
39_S89_L1.1320.56
33_E42_T1.1320.56
41_D97_S1.1260.55
52_E88_H1.1240.55
45_R79_P1.1220.55
10_P13_T1.1120.54
41_D82_D1.0910.52
17_T32_A1.0880.51
31_H94_G1.0810.51
47_V73_V1.0770.50
34_L87_L1.0630.49
46_A85_V1.0620.49
55_F58_E1.0610.49
11_A17_T1.0590.48
45_R92_F1.0570.48
44_I73_V1.0530.48
91_T96_R1.0380.46
56_A79_P1.0260.45
66_V94_G1.0170.44
63_H88_H1.0160.44
25_S31_H1.0110.44
42_T80_P1.0070.43
57_G61_V1.0030.43
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  
2pn5A10.97986.10.92Contact Map
1lnsA10.70714.90.923Contact Map
2e26A10.97984.60.924Contact Map
3prxB20.8993.40.929Contact Map
4fxkB10.96973.10.93Contact Map
4acqA40.939430.931Contact Map
2b39A20.96972.80.932Contact Map
4gioA20.34342.40.934Contact Map
2hr0B10.92932.10.937Contact Map
4ckbA20.98991.90.938Contact 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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