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T0846

ID: 1404841774 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 146 (143)
Sequences: 205 (186)
Seq/Len: 1.434
Nf(neff/√len): 15.6

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: 1.434).

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
94_K102_E2.8501.00
47_V86_A2.0760.98
31_H40_I2.0700.98
43_L104_N1.9510.97
39_E91_F1.8930.97
40_I43_L1.8220.96
58_L111_A1.6650.92
48_F56_N1.6210.90
6_H44_S1.5800.89
22_E126_I1.5750.89
98_R101_A1.5600.88
44_S54_L1.5190.86
22_E130_H1.4570.83
133_E136_R1.4490.82
23_F123_M1.4090.80
56_N95_N1.3630.77
46_I86_A1.3400.75
10_I141_V1.3280.74
56_N135_K1.3190.73
3_H6_H1.3010.72
59_S105_I1.2990.72
126_I130_H1.2870.71
61_I112_I1.2870.71
22_E51_Q1.2730.70
68_T119_V1.2570.68
78_S95_N1.2390.67
30_D138_A1.2360.66
96_S119_V1.2020.63
83_A118_A1.1980.63
27_V84_K1.1940.62
35_E39_E1.1920.62
13_Q45_Q1.1880.62
47_V93_I1.1860.62
59_S71_I1.1850.61
87_G101_A1.1810.61
34_Q107_K1.1780.61
20_Y123_M1.1780.61
27_V53_Q1.1770.61
9_F141_V1.1700.60
60_Q63_E1.1620.59
23_F95_N1.1540.58
119_V126_I1.1430.57
46_I100_Q1.1320.56
18_L126_I1.1230.55
41_R52_N1.1010.53
17_P24_I1.0810.51
26_K136_R1.0810.51
9_F13_Q1.0810.51
5_H74_T1.0800.51
38_K125_N1.0800.51
65_P116_A1.0680.50
127_I138_A1.0600.49
74_T131_N1.0590.49
68_T116_A1.0530.48
84_K127_I1.0480.48
51_Q63_E1.0390.47
43_L141_V1.0370.47
23_F71_I1.0360.46
54_L60_Q1.0340.46
3_H14_K1.0290.46
15_I62_H1.0280.46
96_S114_K1.0250.45
89_K99_K1.0250.45
56_N81_S1.0240.45
37_E40_I1.0210.45
9_F15_I1.0120.44
13_Q77_N1.0080.44
10_I144_P1.0050.43
43_L67_F1.0020.43
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  
2lnmA10.404136.90.929Contact Map
2llwA10.486314.30.942Contact Map
2zbcA80.527411.60.944Contact Map
2llvA10.486311.30.944Contact Map
2a2fX10.801410.80.945Contact Map
2f4mB10.41180.948Contact Map
2djwA100.52057.50.949Contact Map
3hwsA60.6377.50.949Contact Map
2oeqA40.46585.30.952Contact Map
3k8pC10.46584.90.953Contact 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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