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T0808 1-150 -force run

ID: 1405031116 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 150 (145)
Sequences: 77 (68.2)
Seq/Len: 0.531
Nf(neff/√len): 5.7

Jackhmmer Results: (2014_04_16)
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: 0.531).

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
61_F117_I2.7130.98
25_V57_V2.6040.98
34_T58_S1.9640.86
90_F107_I1.8500.81
62_Y132_I1.7790.77
121_G129_F1.7010.72
58_S118_D1.6640.70
69_A146_Y1.5830.64
69_A139_N1.5130.59
25_V102_V1.5000.58
58_S116_R1.4790.56
58_S120_Q1.4440.54
58_S61_F1.4300.53
20_P117_I1.4260.52
61_F137_A1.4090.51
75_A94_L1.3980.50
33_V99_F1.3940.50
109_I112_A1.3910.50
34_T47_V1.3850.49
79_S121_G1.3680.48
82_K89_G1.3640.48
34_T120_Q1.3140.44
63_L117_I1.3060.43
66_P146_Y1.2990.42
18_A71_L1.2860.41
32_Y139_N1.2520.39
51_T64_H1.2470.39
52_N60_Y1.2450.38
145_N149_D1.2410.38
25_V82_K1.2310.37
125_S130_G1.2300.37
67_T139_N1.2250.37
32_Y58_S1.2220.37
56_I120_Q1.2160.36
90_F149_D1.2060.36
25_V66_P1.2000.35
125_S149_D1.1990.35
26_G149_D1.1890.34
94_L146_Y1.1750.33
25_V119_L1.1700.33
110_R132_I1.1650.33
34_T118_D1.1560.32
53_P130_G1.1490.32
77_G130_G1.1460.31
63_L94_L1.1350.31
30_N121_G1.1270.30
10_L15_T1.1260.30
45_R128_G1.1220.30
92_V132_I1.1100.29
9_A13_C1.1040.29
22_Q25_V1.0990.28
63_L66_P1.0980.28
26_G69_A1.0820.27
83_V117_I1.0800.27
58_S115_V1.0750.27
83_V118_D1.0750.27
106_S148_K1.0710.27
68_T146_Y1.0700.26
30_N59_I1.0660.26
33_V147_V1.0650.26
60_Y111_Q1.0620.26
31_G135_L1.0590.26
54_K57_V1.0510.25
25_V63_L1.0500.25
61_F118_D1.0380.25
42_I121_G1.0360.24
71_L136_I1.0340.24
29_G132_I1.0300.24
43_T81_I1.0250.24
76_K136_I1.0200.24
73_L94_L1.0190.23
102_V135_L1.0180.23
47_V120_Q1.0140.23
71_L118_D1.0080.23
26_G90_F1.0070.23
119_L130_G1.0010.22
35_R112_A1.0000.22
52_N147_V1.0000.22
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: (05Jul14)
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  
2bgoA10.7296.50.854Contact Map
3zm8A10.8694.20.875Contact Map
4kmqA10.84910.888Contact Map
2vzpA20.773389.90.89Contact Map
2w87A20.8489.80.89Contact Map
2vzsA20.173388.40.893Contact Map
2w47A10.826788.20.894Contact Map
2w3jA10.846783.30.901Contact Map
2wz8A10.7533790.905Contact Map
2cdpA40.826770.90.911Contact 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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