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T0814 120-240

ID: 1404852157 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 121 (120)
Sequences: 227 (201.7)
Seq/Len: 1.892
Nf(neff/√len): 18.4

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: 1.892).

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
15_S41_E3.0031.00
22_V33_F2.2161.00
76_I83_L2.1280.99
100_L118_L1.9690.99
92_R95_N1.9240.98
44_V74_F1.9200.98
88_Y93_R1.6880.95
64_Q119_I1.6640.95
57_D62_H1.6100.94
32_I46_I1.5870.93
15_S65_V1.5720.93
83_L110_I1.5640.92
3_L20_I1.5590.92
52_G59_N1.5490.92
76_I82_D1.5490.92
79_P84_K1.4880.90
5_L12_F1.4480.88
87_V118_L1.3880.85
67_F85_I1.3610.83
97_V100_L1.3270.81
38_S93_R1.3080.80
48_A67_F1.3050.80
21_Q31_I1.2840.78
36_C115_N1.2770.78
37_F110_I1.2370.74
49_S66_S1.2330.74
65_V87_V1.2270.74
61_S68_N1.2180.73
105_I111_S1.2080.72
78_Y81_T1.2010.71
47_S67_F1.1880.70
37_F65_V1.1770.69
8_D69_I1.1750.69
59_N114_Y1.1670.68
30_Q44_V1.1200.64
69_I79_P1.1070.62
109_Q112_Y1.1050.62
13_K60_Q1.0940.61
35_A40_V1.0750.59
72_K82_D1.0590.57
55_D101_Q1.0560.57
54_T64_Q1.0550.57
39_V60_Q1.0530.56
77_T82_D1.0530.56
39_V108_N1.0460.56
46_I51_S1.0450.56
89_Q95_N1.0430.55
71_N76_I1.0410.55
47_S70_N1.0380.55
96_A99_D1.0360.55
19_A87_V1.0350.54
34_T101_Q1.0340.54
54_T114_Y1.0330.54
64_Q114_Y1.0310.54
9_D32_I1.0170.53
56_I61_S1.0170.53
65_V96_A1.0120.52
24_N30_Q1.0070.51
86_F111_S1.0060.51
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  
2p9rA20.31422.30.931Contact Map
3cu7A20.900818.50.934Contact Map
3prxB20.884318.10.934Contact Map
4acqA40.867817.40.935Contact Map
4k0mC10.710715.90.936Contact Map
4geiA10.355414.40.937Contact Map
2pn5A10.818290.943Contact Map
2xwxA20.33888.10.944Contact Map
2hr0A10.884380.944Contact Map
1avyA30.49596.40.946Contact 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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