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T0824 -force run

ID: 1403115443 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 110 (110)
Sequences: 52 (44.3)
Seq/Len: 0.473
Nf(neff/√len): 4.2

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: 0.473).

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
24_D78_R3.9651.00
92_V107_F2.1730.90
28_A78_R1.6440.65
11_P68_C1.6250.64
34_C68_C1.5710.60
63_W107_F1.5330.57
98_G109_V1.4920.54
27_K76_S1.4500.51
13_S78_R1.4240.49
11_P34_C1.3790.45
24_D39_S1.3450.43
18_T26_I1.3360.42
52_I80_V1.3350.42
12_A52_I1.3350.42
24_D93_G1.3250.41
63_W96_L1.3190.41
27_K51_G1.2630.37
26_I65_M1.2610.37
91_W96_L1.2580.37
11_P79_Y1.2530.36
7_V20_A1.2490.36
10_F68_C1.2360.35
34_C65_M1.2330.35
3_R93_G1.2280.34
2_A107_F1.2260.34
20_A69_E1.2060.33
30_H104_R1.1820.31
33_V47_E1.1760.31
26_I90_S1.1710.31
68_C79_Y1.1400.29
32_D51_G1.1270.28
11_P53_P1.1250.28
2_A109_V1.1170.27
13_S31_A1.1060.27
10_F34_C1.0980.26
25_A29_G1.0960.26
43_K58_F1.0920.26
3_R99_Y1.0840.25
20_A28_A1.0800.25
10_F92_V1.0740.25
77_V97_N1.0720.25
34_C91_W1.0720.25
27_K78_R1.0710.25
12_A23_S1.0710.25
7_V98_G1.0630.24
68_C91_W1.0620.24
5_D106_L1.0530.24
18_T34_C1.0520.24
84_D87_G1.0470.23
53_P68_C1.0460.23
18_T65_M1.0440.23
24_D27_K1.0420.23
10_F91_W1.0300.22
80_V95_R1.0180.22
50_K108_I1.0160.22
16_P102_G1.0130.21
23_S40_G1.0120.21
34_C53_P1.0090.21
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  
4od6A10.727333.40.94Contact Map
2zqeA10.727321.60.946Contact Map
3qd7X10.745521.10.946Contact Map
1fwxA40.918219.80.946Contact Map
1j5pA10.93649.60.954Contact Map
2vkcA10.79.50.954Contact Map
4ry8A40.89099.10.954Contact Map
4pz0A10.90918.80.954Contact Map
2d9iA10.75458.70.954Contact Map
4jg2A10.872780.955Contact 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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