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OPENSEQ.org

T0790-D1

ID: 1491920377 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 135 (130)
Sequences: 507 (404.6)
Seq/Len: 3.900
Nf(neff/√len): 35.5

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: 3.900).

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
74_T99_A2.2951.00
75_V108_A2.1551.00
12_Q51_E2.1551.00
14_W33_P1.8070.99
28_V110_R1.7280.99
13_A25_Y1.6690.99
14_W41_R1.6690.99
17_A76_C1.6250.99
66_P69_A1.6140.99
99_A106_V1.5660.98
75_V117_F1.5520.98
63_A129_V1.5400.98
13_A17_A1.5310.98
9_T12_Q1.5250.98
16_L64_V1.5120.98
12_Q55_M1.5090.98
79_T101_R1.5060.98
37_D40_Q1.4610.97
40_Q47_A1.4230.96
28_V85_R1.4100.96
78_A95_R1.4060.96
84_L96_G1.4010.96
79_T100_R1.3790.95
59_N63_A1.3670.95
43_A47_A1.3550.95
82_L86_F1.3440.94
37_D55_M1.3280.94
26_P75_V1.3220.94
26_P83_D1.2760.92
12_Q57_V1.2620.91
43_A99_A1.2350.90
23_G26_P1.2020.89
51_E124_H1.1980.88
20_L127_A1.1970.88
4_N43_A1.1850.88
47_A51_E1.1620.86
20_L52_L1.1530.86
100_R125_Q1.1520.86
16_L68_V1.1480.85
35_Y41_R1.1330.84
98_V105_T1.1250.84
60_S105_T1.1130.83
123_G128_L1.1030.82
17_A22_A1.1000.82
19_V49_S1.0970.81
78_A81_W1.0920.81
32_T35_Y1.0820.80
39_S90_P1.0720.79
23_G83_D1.0700.79
98_V125_Q1.0660.79
13_A68_V1.0640.79
96_G131_V1.0550.78
44_F48_Q1.0460.77
28_V86_F1.0310.76
47_A70_Q1.0300.75
30_A93_L1.0110.74
82_L128_L1.0100.73
46_A132_L1.0040.73
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  
4l4wA2199.90.116Contact Map
4w4iA10.977899.90.159Contact Map
4w4lC10.985299.90.163Contact Map
3r9zA10.25934.20.919Contact Map
4koqA10.31853.70.921Contact Map
2l4dA10.27412.80.926Contact Map
3hhtB10.89632.40.929Contact Map
1o98A10.88892.20.93Contact Map
3h8dA40.34812.20.93Contact Map
3iuuA10.97042.10.931Contact 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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