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T0808 150-329 -force run

ID: 1405035023 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 180 (178)
Sequences: 156 (126.1)
Seq/Len: 0.876
Nf(neff/√len): 9.5

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: 0.876).

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
77_N80_E2.6460.99
71_S106_S2.1610.97
66_L109_Q2.0880.96
24_E127_Q2.0490.95
90_L156_F1.9790.94
126_M140_A1.7660.88
120_N144_A1.7470.87
42_Y171_F1.7270.86
70_W104_E1.6840.84
52_Y173_E1.6320.81
70_W101_F1.5630.77
3_D179_Q1.5300.75
25_W141_Y1.5040.73
5_W87_I1.4620.70
83_D86_K1.4340.68
40_H43_Y1.4180.67
101_F104_E1.3760.64
112_L172_L1.3590.62
144_A151_K1.3410.61
31_T121_T1.3370.60
31_T119_G1.3310.60
128_I165_Y1.3300.60
79_K85_Q1.3220.59
79_K84_D1.3110.58
99_G103_N1.3010.57
71_S103_N1.2990.57
71_S101_F1.2900.56
44_M47_G1.2810.55
82_P85_Q1.2710.54
122_Y142_F1.2470.52
4_Y134_G1.2260.50
44_M156_F1.2240.50
3_D43_Y1.2070.49
115_P129_R1.2040.48
55_M63_R1.2030.48
103_N106_S1.2010.48
101_F116_W1.2000.48
25_W167_R1.1950.48
84_D88_K1.1890.47
61_T86_K1.1810.46
3_D6_G1.1800.46
80_E83_D1.1660.45
21_G115_P1.1630.45
68_S93_G1.1590.44
51_G107_G1.1440.43
43_Y76_Q1.1430.43
81_I84_D1.1430.43
3_D85_Q1.1410.43
41_S96_V1.1410.43
40_H51_G1.1360.42
79_K83_D1.1340.42
82_P103_N1.1330.42
70_W102_G1.1330.42
23_T83_D1.1280.42
6_G81_I1.1270.42
70_W103_N1.1160.41
37_E40_H1.1100.40
112_L153_I1.1100.40
131_D134_G1.1060.40
24_E179_Q1.1050.40
68_S119_G1.0950.39
16_Y28_N1.0830.38
26_F168_P1.0810.38
63_R116_W1.0780.37
137_T160_K1.0720.37
18_L149_E1.0710.37
94_K120_N1.0680.37
87_I90_L1.0640.36
85_Q179_Q1.0560.36
36_G154_A1.0520.35
46_A66_L1.0480.35
15_G167_R1.0460.35
62_E174_N1.0430.35
49_G131_D1.0370.34
135_N157_L1.0340.34
66_L111_Y1.0330.34
21_G179_Q1.0300.34
91_R98_I1.0300.34
3_D36_G1.0270.33
70_W116_W1.0260.33
52_Y56_Q1.0200.33
49_G132_G1.0200.33
4_Y161_T1.0190.33
52_Y70_W1.0190.33
84_D87_I1.0170.32
47_G50_E1.0150.32
35_E57_Y1.0140.32
50_E163_T1.0120.32
47_G150_W1.0120.32
24_E136_T1.0100.32
75_T159_P1.0080.32
93_G96_V1.0060.32
104_E171_F1.0040.31
26_F145_T1.0000.31
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  
1yo8A10.77788.60.959Contact Map
3vgfA10.58898.10.96Contact Map
2bhuA10.66114.70.964Contact Map
2zwsA10.327830.967Contact Map
2eqjA10.36672.50.968Contact Map
1as4B10.18332.50.968Contact Map
2e5qA10.30562.50.968Contact Map
3uzeC20.06112.50.969Contact Map
2czvC20.62782.30.969Contact Map
1m93C10.172220.97Contact 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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