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T0842

ID: 1404416553 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 146 (139)
Sequences: 341 (281.8)
Seq/Len: 2.453
Nf(neff/√len): 23.9

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: 2.453).

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
95_K103_E2.3771.00
48_V87_A2.1671.00
134_E137_R1.9910.99
41_V44_W1.7780.98
99_R102_A1.6940.97
32_P41_V1.6330.97
24_I124_Q1.5870.96
44_W105_G1.5500.95
88_G102_A1.4880.93
36_A40_E1.4110.91
45_C55_L1.3850.90
120_V127_I1.3810.89
73_S117_T1.3750.89
28_M34_V1.3610.89
65_K82_S1.3240.87
54_V81_T1.3100.86
40_E92_C1.3060.86
15_T39_Q1.2990.85
121_T124_Q1.2780.84
59_M112_A1.2630.83
116_Y120_V1.2630.83
15_T113_L1.2260.80
79_N92_C1.2080.79
66_P103_E1.2070.79
127_I130_V1.2050.79
39_Q126_N1.2010.78
61_E64_Q1.1950.78
11_A142_S1.1940.78
57_E82_S1.1870.77
89_R100_R1.1770.76
84_H119_A1.1660.76
127_I131_P1.1600.75
35_Q118_S1.1600.75
49_Y109_L1.1550.75
25_A90_N1.1390.73
60_Q106_F1.1340.73
23_E127_I1.1300.72
23_E27_R1.1220.71
80_P102_A1.1180.71
4_H7_H1.1160.71
119_A122_Q1.1160.71
97_N123_A1.1080.70
13_Q49_Y1.1070.70
116_Y127_I1.1030.70
69_G120_V1.1000.69
19_L34_V1.0990.69
32_P71_D1.0970.69
23_E131_P1.0890.68
109_L116_Y1.0880.68
131_P135_A1.0880.68
20_T23_E1.0830.68
128_K139_G1.0750.67
88_G99_R1.0720.66
34_V120_V1.0690.66
28_M85_K1.0670.66
48_V102_A1.0610.65
111_Q117_T1.0590.65
31_N139_G1.0570.65
49_Y57_E1.0570.65
45_C103_E1.0550.65
41_V60_Q1.0530.64
57_E96_T1.0510.64
8_H12_M1.0510.64
66_P110_C1.0480.64
70_E116_Y1.0460.64
41_V93_G1.0420.63
47_I87_A1.0420.63
10_V142_S1.0360.63
73_S133_A1.0340.62
78_E100_R1.0250.61
73_S114_D1.0110.60
79_N96_T1.0090.60
48_V94_L1.0070.59
58_K82_S1.0060.59
85_K103_E1.0060.59
49_Y83_V1.0000.58
26_D47_I1.0000.58
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: (28Jun14)
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  
2lnmA10.41139.80.906Contact Map
2llwA10.486316.30.922Contact Map
3vejA20.27412.50.926Contact Map
2zbcA80.52749.20.931Contact Map
2ywkA10.534290.931Contact Map
3hwsA60.64388.20.932Contact Map
2cqpA10.56857.80.933Contact Map
2do4A10.57537.30.934Contact Map
2djwA100.52056.70.935Contact Map
2cq0A10.60275.80.937Contact 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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