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6_1ifcpdb

ID: 1516869620 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 131 (131)
Sequences: 1233 (706.5)
Seq/Len: 9.412
Nf(neff/√len): 61.7

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: 9.412).

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
63_E66_V3.4941.00
67_D79_T2.8531.00
6_W108_I2.5291.00
72_L76_T2.4901.00
80_G91_G2.3231.00
16_K19_E2.2501.00
88_K107_E2.1971.00
69_A77_E2.0761.00
46_K63_E1.9891.00
111_N130_K1.9801.00
116_T125_K1.9761.00
46_K61_V1.9611.00
50_K59_D1.9471.00
2_F108_I1.7721.00
70_Y91_G1.7711.00
5_T39_T1.7671.00
26_V30_L1.7431.00
69_A79_T1.7091.00
107_E116_T1.7011.00
71_S77_E1.6951.00
40_I49_V1.6461.00
88_K105_V1.5751.00
48_T61_V1.5481.00
4_G130_K1.5451.00
105_V116_T1.5361.00
52_S57_N1.5181.00
29_K32_A1.5171.00
84_M89_L1.5171.00
70_Y80_G1.4871.00
18_M31_G1.4491.00
14_Y18_M1.4260.99
17_F102_L1.3630.99
105_V118_T1.3420.99
118_T123_E1.3250.99
39_T52_S1.3190.99
92_K96_V1.3020.99
12_E125_K1.2790.99
13_N17_F1.2740.99
45_N63_E1.2590.98
125_K129_K1.1870.97
104_A115_Q1.1870.97
15_E19_E1.1620.97
83_T92_K1.1380.96
69_A96_V1.1330.96
13_N18_M1.1320.96
115_Q120_E1.1240.96
8_V11_N1.1040.96
42_Q47_F1.0960.95
109_S114_I1.0900.95
13_N16_K1.0890.95
43_E46_K1.0840.95
15_E18_M1.0810.95
30_L34_D1.0800.95
108_I111_N1.0730.95
116_T127_I1.0680.94
41_T48_T1.0590.94
44_G65_G1.0580.94
91_G95_R1.0520.94
109_S112_E1.0430.94
13_N122_V1.0360.93
119_Y122_V1.0330.93
67_D96_V1.0330.93
3_D42_Q1.0320.93
7_K131_E1.0280.93
23_I28_R1.0230.93
46_K66_V1.0170.92
8_V126_R1.0160.92
6_W13_N1.0110.92
123_E126_R1.0030.92
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  
3q6lA10.9847100-0.04Contact Map
4aznA20.9847100-0.04Contact Map
3wbgA40.9847100-0.04Contact Map
4a60A10.9771100-0.038Contact Map
3p6dA10.9847100-0.03Contact Map
4bvmA10.9847100-0.03Contact Map
4tkbA10.9847100-0.028Contact Map
1ifcA11100-0.028Contact Map
1fdqA20.9847100-0.028Contact Map
1vyfA10.9847100-0.026Contact 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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