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T0842

ID: 1404411904 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 146 (128)
Sequences: 169 (150.8)
Seq/Len: 1.320
Nf(neff/√len): 13.3

HHblits Results: (2013_03)
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: 1.320).

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_E2.6711.00
48_V87_A2.2350.99
45_C55_L1.8580.95
99_R102_A1.7330.93
49_Y57_E1.7040.92
24_I124_Q1.6350.90
57_E96_T1.6120.89
17_P137_R1.4900.83
40_E92_C1.4880.83
60_Q72_L1.4580.81
44_W105_G1.4310.79
120_V127_I1.4250.79
62_V113_L1.4220.79
35_Q105_G1.4170.78
73_S120_V1.3860.76
17_P46_K1.3630.75
28_M54_V1.3450.73
32_P41_V1.3230.71
38_Q49_Y1.3050.70
134_E137_R1.2720.67
34_V73_S1.2680.67
23_E131_P1.2670.67
23_E127_I1.2660.67
39_Q126_N1.2650.66
111_Q117_T1.2590.66
48_V94_L1.2460.65
131_P135_A1.2370.64
88_G102_A1.2330.64
34_V122_Q1.2200.62
49_Y76_V1.2060.61
79_N83_V1.1860.59
104_E122_Q1.1740.58
61_E64_Q1.1670.57
25_A62_V1.1640.57
36_A40_E1.1350.54
87_A102_A1.1260.53
59_M112_A1.1250.53
72_L82_S1.1140.52
66_P117_T1.1050.51
35_Q108_H1.0970.50
24_I96_T1.0870.49
52_S64_Q1.0810.49
41_V44_W1.0690.47
20_T74_R1.0680.47
48_V93_G1.0630.47
25_A85_K1.0610.47
112_A141_E1.0570.46
25_A34_V1.0560.46
56_K130_V1.0510.46
94_L106_F1.0470.45
130_V141_E1.0460.45
22_E76_V1.0400.45
31_N139_G1.0380.44
34_V38_Q1.0330.44
88_G99_R1.0300.44
23_E104_E1.0240.43
86_L102_A1.0210.43
72_L114_D1.0170.42
38_Q41_V1.0100.42
49_Y53_D1.0050.41
31_N131_P1.0050.41
65_K82_S1.0020.41
19_L23_E1.0020.41
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  
2lnmA10.404137.20.931Contact Map
2llwA10.486325.80.936Contact Map
2zbcA80.5274220.938Contact Map
2llvA10.4863220.938Contact Map
3hwsA60.643818.50.94Contact Map
2djwA100.520513.10.944Contact Map
3v3kB80.43157.90.95Contact Map
4o4fA10.94527.40.95Contact Map
1um8A10.63017.20.95Contact Map
2oeqA40.47266.20.952Contact 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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