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T0808 150-330 -force run

ID: 1405035249 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 181 (178)
Sequences: 155 (124.7)
Seq/Len: 0.871
Nf(neff/√len): 9.3

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: 0.871).

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_E2.6370.99
71_S106_S2.2410.97
66_L109_Q2.1090.96
24_E127_Q2.0280.95
90_L156_F1.9140.92
126_M140_A1.8470.90
120_N144_A1.7760.88
70_W104_E1.7350.86
42_Y171_F1.5760.78
40_H43_Y1.5700.78
70_W101_F1.5660.77
52_Y173_E1.5370.75
31_T121_T1.4640.70
5_W87_I1.4400.68
101_F104_E1.4330.68
31_T119_G1.4180.67
25_W141_Y1.3590.62
79_K85_Q1.3450.61
83_D86_K1.3370.60
128_I165_Y1.3290.59
84_D88_K1.3190.58
122_Y142_F1.3010.57
82_P85_Q1.3010.57
3_D179_Q1.2990.57
44_M47_G1.2910.56
112_L153_I1.2780.55
144_A151_K1.2590.53
80_E83_D1.2550.53
99_G103_N1.2530.53
71_S101_F1.2520.53
3_D43_Y1.2460.52
71_S103_N1.2450.52
21_G115_P1.2410.52
115_P129_R1.2380.51
70_W102_G1.2360.51
103_N106_S1.2200.50
46_A66_L1.2180.50
62_E174_N1.2150.49
44_M156_F1.2120.49
79_K84_D1.2060.48
112_L172_L1.1920.47
4_Y134_G1.1880.47
23_T83_D1.1830.46
70_W103_N1.1820.46
104_E171_F1.1600.44
84_D87_I1.1590.44
82_P103_N1.1570.44
79_K83_D1.1540.44
68_S93_G1.1510.44
25_W167_R1.1440.43
94_K120_N1.1370.42
45_A65_I1.1370.42
51_G107_G1.1360.42
3_D85_Q1.1270.41
101_F116_W1.1210.41
63_R116_W1.1140.40
66_L111_Y1.1110.40
20_E146_D1.1060.40
41_S96_V1.0970.39
32_V43_Y1.0960.39
135_N157_L1.0910.38
18_L149_E1.0900.38
47_G150_W1.0840.38
137_T160_K1.0830.38
87_I90_L1.0780.37
36_G154_A1.0720.37
16_Y28_N1.0710.37
55_M63_R1.0710.37
131_D134_G1.0570.36
24_E179_Q1.0550.35
88_K133_N1.0520.35
15_G18_L1.0520.35
68_S119_G1.0500.35
26_F168_P1.0490.35
3_D6_G1.0460.35
4_Y126_M1.0370.34
50_E163_T1.0310.33
6_G10_P1.0270.33
37_E40_H1.0260.33
4_Y161_T1.0240.33
52_Y70_W1.0240.33
20_E30_I1.0230.33
120_N133_N1.0200.33
26_F145_T1.0190.33
61_T86_K1.0190.33
52_Y56_Q1.0180.32
32_V48_F1.0170.32
93_G96_V1.0170.32
102_G110_S1.0150.32
15_G178_E1.0140.32
83_D132_G1.0130.32
60_P80_E1.0070.32
108_G170_S1.0060.32
144_A176_S1.0060.32
75_T159_P1.0050.31
73_F177_P1.0000.31
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  
2bhuA10.64645.90.962Contact Map
1yo8A10.77355.50.963Contact Map
3vgfA10.58563.70.966Contact Map
2zwsA10.3263.20.967Contact Map
3uzeC20.06082.90.968Contact Map
2eqjA10.36462.80.968Contact Map
2e5qA10.30392.80.968Contact Map
2czvC20.62432.70.968Contact Map
1as4B10.18232.60.968Contact Map
1m93C10.171320.97Contact 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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