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T0815

ID: 1402517900 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 106 (104)
Sequences: 250 (211.2)
Seq/Len: 2.404
Nf(neff/√len): 20.7

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: 2.404).

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
32_V48_W3.1141.00
11_F74_V2.1221.00
27_A101_A1.9500.99
35_E61_E1.9270.99
51_A55_A1.8450.99
35_E48_W1.8410.99
32_V35_E1.4900.93
77_K88_T1.4790.93
62_P85_S1.4380.91
49_W53_K1.4210.91
28_P69_G1.4050.90
19_T74_V1.3830.89
94_T102_R1.3790.89
3_L95_I1.3690.89
7_V72_A1.3200.86
47_R91_Y1.3130.86
10_Y74_V1.2880.84
30_A69_G1.2860.84
11_F86_P1.2510.82
11_F104_E1.2320.80
6_I95_I1.2220.80
20_D31_V1.2080.78
49_W52_A1.2070.78
87_V99_R1.2060.78
32_V39_H1.1930.77
29_D40_Q1.1860.77
79_S85_S1.1790.76
78_V86_P1.1610.75
3_L6_I1.1370.72
74_V97_D1.1240.71
57_S81_R1.1230.71
20_D46_L1.1200.71
63_L77_K1.1170.70
25_T81_R1.1000.69
38_R59_V1.0930.68
10_Y26_F1.0880.67
2_D47_R1.0860.67
11_F76_A1.0830.67
54_K60_A1.0790.67
62_P86_P1.0780.66
7_V100_I1.0710.66
5_D46_L1.0680.65
40_Q50_V1.0640.65
52_A62_P1.0600.65
26_F70_D1.0480.63
31_V101_A1.0200.60
35_E100_I1.0200.60
4_P44_A1.0190.60
61_E75_R1.0110.59
54_K79_S1.0100.59
30_A35_E1.0090.59
13_A18_D1.0040.58
78_V85_S1.0010.58
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: (07Jun14)
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  
3mg1A2199.30.672Contact Map
4h3uA2199.30.675Contact Map
3dm8A1199.20.691Contact Map
4mjdA20.981199.20.694Contact Map
2a15A10.981199.10.7Contact Map
3g16A2199.10.7Contact Map
3ff2A1199.10.701Contact Map
1ohpA40.990699.10.702Contact Map
3dmcA2199.10.703Contact Map
2k54A1199.10.706Contact 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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