OPENSEQ.org
TssF_454-585

ID: 1516103804 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 142 (139)
Sequences: 993 (645.4)
Seq/Len: 7.144
Nf(neff/√len): 54.7

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: 7.144).

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_H44_Y4.1481.00
104_N135_N3.7851.00
58_A89_G3.3501.00
80_D120_T3.0821.00
65_H80_D2.7601.00
100_G121_L2.7541.00
58_A90_F2.5231.00
87_G123_V2.2001.00
78_G116_F2.1941.00
103_L107_L2.1911.00
81_V107_L2.1701.00
82_E122_I2.0801.00
106_F110_Y1.8941.00
83_V103_L1.8801.00
81_V117_N1.8621.00
128_K131_R1.6421.00
80_D118_Q1.6341.00
59_I83_V1.5721.00
120_T131_R1.5561.00
36_V62_V1.5180.99
69_R118_Q1.5120.99
59_I85_L1.5030.99
18_R39_G1.4700.99
55_R95_D1.3810.99
57_D125_P1.3720.99
62_V83_V1.3630.98
87_G125_P1.3400.98
63_Q82_E1.3080.98
26_G114_N1.2990.98
63_Q84_T1.2540.97
60_L86_D1.2530.97
22_H43_L1.2450.97
120_T128_K1.2380.97
77_R137_N1.2340.97
41_L56_L1.2220.96
97_H130_I1.1920.96
85_L99_F1.1810.95
26_G30_M1.1700.95
83_V119_L1.1690.95
98_L113_M1.1580.95
101_E132_W1.1490.94
47_R52_N1.1460.94
60_L84_T1.1270.94
23_L27_F1.1230.94
79_L119_L1.0990.93
70_F89_G1.0980.93
45_N53_H1.0970.92
43_L56_L1.0930.92
92_G95_D1.0920.92
80_D131_R1.0910.92
105_R139_R1.0550.90
88_N108_A1.0330.89
85_L121_L1.0320.89
62_V81_V1.0280.89
118_Q134_E1.0210.88
34_A72_K1.0170.88
25_T39_G1.0130.88
37_L103_L1.0110.88
104_N117_N1.0080.88
59_I79_L1.0070.88
45_N52_N1.0020.87
96_I121_L1.0010.87
26_G29_N1.0010.87
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  
1qvrA30.66230.946Contact Map
2d96A10.61272.80.947Contact Map
2ee7A10.60562.60.947Contact Map
2xgaA20.6692.50.948Contact Map
2izvA10.3382.20.95Contact Map
1ry9A40.6692.10.95Contact Map
4icsA20.83820.951Contact Map
1z21A10.4931.80.952Contact Map
3g5bA10.5071.80.952Contact Map
3u85B10.06341.60.953Contact 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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