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OPENSEQ.org

Phil Arnold

ID: 1495530848 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 128 (116)
Sequences: 29416 (18159.2)
Seq/Len: 253.586
Nf(neff/√len): 1686.0

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: 253.586).

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
22_P37_S2.4381.00
21_R24_D2.1671.00
20_V28_Q2.1391.00
15_L28_Q2.1101.00
67_V109_I2.0811.00
22_P40_L2.0361.00
82_A107_N2.0191.00
16_A40_L1.9971.00
26_S36_V1.9841.00
86_R90_L1.8921.00
20_V24_D1.8811.00
15_L20_V1.8211.00
102_S105_S1.8161.00
15_L29_L1.8121.00
67_V113_K1.7361.00
103_V107_N1.7211.00
33_H37_S1.6991.00
16_A25_I1.6871.00
80_M84_E1.6491.00
69_K73_Y1.6361.00
6_E10_Q1.6301.00
5_P8_V1.6261.00
104_S107_N1.6021.00
88_R92_E1.5451.00
12_I36_V1.5401.00
81_F84_E1.4981.00
86_R106_I1.4971.00
73_Y88_R1.4901.00
34_G37_S1.4751.00
69_K92_E1.4641.00
32_S35_C1.4611.00
104_S108_R1.4581.00
71_G113_K1.4281.00
10_Q14_D1.4261.00
23_C33_H1.4141.00
11_R15_L1.3970.99
86_R103_V1.3960.99
11_R14_D1.3120.99
82_A103_V1.2960.99
90_L100_V1.2780.99
63_T66_V1.2720.99
4_L8_V1.2640.99
67_V112_T1.2520.99
69_K72_D1.2420.98
62_A66_V1.2400.98
107_N111_R1.2350.98
40_L44_Y1.2220.98
15_L25_I1.2060.98
22_P33_H1.1730.98
105_S108_R1.1660.97
70_I85_I1.1660.97
16_A22_P1.1540.97
25_I29_L1.1420.97
23_C27_R1.1400.97
34_G38_K1.1200.96
82_A110_I1.1140.96
35_C38_K1.0940.96
109_I113_K1.0930.96
31_V36_V1.0700.95
63_T105_S1.0690.95
8_V31_V1.0630.95
7_V10_Q1.0610.95
67_V71_G1.0580.95
80_M88_R1.0570.95
13_V43_Y1.0520.95
71_G75_R1.0430.94
109_I112_T1.0370.94
8_V11_R1.0270.94
24_D28_Q1.0230.93
15_L18_Q1.0200.93
93_G98_D1.0000.92
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  
1k78A30.882899.40.111Contact Map
1pdnC10.859499.30.153Contact Map
2k27A10.960999.30.159Contact Map
1u78A10.789199.20.168Contact Map
4u7bA30.8906990.256Contact Map
4fcyA20.921998.30.413Contact Map
1hlvA10.87597.50.508Contact Map
2lvsA10.812597.50.512Contact Map
2elhA10.531297.20.53Contact Map
2m8eA10.406296.90.555Contact 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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