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T0833 -force run

ID: 1403811137 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 136 (128)
Sequences: 58 (44.7)
Seq/Len: 0.453
Nf(neff/√len): 4.0

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: 0.453).

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
80_D87_V1.9820.83
10_I83_N1.7670.72
75_K117_F1.6490.64
23_I27_S1.6140.62
55_L110_W1.5930.60
77_F80_D1.5880.60
14_V66_N1.5170.55
77_F117_F1.4590.50
16_T29_K1.4480.49
24_S94_Y1.4390.49
44_S60_R1.3940.45
21_L66_N1.3840.45
70_K111_D1.3830.45
2_K8_K1.3780.44
115_K121_V1.3590.43
21_L44_S1.3380.41
5_V106_N1.3040.39
78_R111_D1.2420.34
11_L19_C1.2350.34
63_F112_K1.2240.33
6_W77_F1.2170.33
76_A88_P1.2160.33
57_K91_Q1.1940.31
38_E92_I1.1940.31
46_V49_L1.1900.31
46_V63_F1.1830.31
26_A38_E1.1780.30
24_S31_Y1.1710.30
30_D60_R1.1670.30
59_V92_I1.1580.29
74_K102_E1.1560.29
60_R95_Q1.1560.29
63_F89_F1.1540.29
99_Q121_V1.1500.28
4_S113_K1.1390.28
66_N70_K1.1290.27
32_L123_N1.1250.27
36_K96_Y1.1220.27
58_Q108_G1.1210.27
77_F88_P1.1210.27
39_N62_E1.1150.26
43_I72_S1.1150.26
72_S111_D1.1150.26
49_L57_K1.1000.26
98_D112_K1.0950.25
34_D48_F1.0940.25
103_I115_K1.0820.25
36_K78_R1.0770.24
23_I51_E1.0760.24
8_K85_E1.0740.24
51_E95_Q1.0740.24
99_Q104_K1.0670.24
3_T6_W1.0660.24
18_M39_N1.0630.23
20_S40_G1.0610.23
2_K107_Y1.0610.23
52_N94_Y1.0570.23
35_T72_S1.0510.23
99_Q111_D1.0490.23
21_L87_V1.0480.23
53_G71_V1.0480.23
42_I119_L1.0390.22
37_E83_N1.0390.22
34_D78_R1.0380.22
6_W32_L1.0290.22
60_R94_Y1.0270.22
16_T93_T1.0270.22
93_T105_T1.0230.21
19_C92_I1.0210.21
36_K46_V1.0140.21
34_D96_Y1.0120.21
111_D118_S1.0110.21
38_E54_L1.0060.21
86_W124_M1.0020.20
48_F93_T1.0010.20
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: (06Aug15)
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  
4r03A10.80151000.324Contact Map
4r8oA20.72061000.355Contact Map
3mswA10.80881000.378Contact Map
4ghbA20.669141.90.934Contact Map
4u6bA40.360310.10.951Contact Map
2dckA10.72795.70.956Contact Map
4x36A104.90.958Contact Map
2m1jA10.22063.90.96Contact Map
1z65A10.22063.90.96Contact Map
1qleD10.16913.80.96Contact 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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