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T0814 240-360

ID: 1404852198 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 121 (120)
Sequences: 223 (205.7)
Seq/Len: 1.858
Nf(neff/√len): 18.8

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: 1.858).

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
109_N116_E6.4891.00
106_M117_K2.5041.00
88_S105_K2.4141.00
5_E53_D2.0000.99
32_N76_H1.9310.98
90_Y104_S1.9020.98
37_T78_T1.8780.98
58_I87_G1.8160.97
14_N73_Y1.7620.97
5_E51_D1.7340.96
21_V35_L1.6660.95
101_D104_S1.6510.95
96_F104_S1.5660.92
90_Y105_K1.5240.91
7_R38_D1.4150.86
60_C63_C1.4130.86
2_A111_E1.3420.82
11_F73_Y1.3100.80
53_D97_N1.2970.79
104_S119_V1.2770.77
6_Y98_N1.2740.77
95_L104_S1.2610.76
6_Y31_Y1.2580.76
58_I75_V1.2560.76
55_R94_E1.2520.75
13_S71_D1.2430.74
6_Y105_K1.2380.74
91_L119_V1.2370.74
6_Y59_R1.2100.72
112_T116_E1.2090.72
44_G78_T1.2060.71
10_E49_D1.2020.71
83_P110_F1.1810.69
18_G64_N1.1790.69
33_V73_Y1.1720.68
12_L52_Q1.1480.66
108_Y114_Q1.1420.65
17_N21_V1.1420.65
81_C84_L1.1410.65
74_I118_A1.1370.65
63_C70_A1.1370.65
83_P91_L1.1280.64
75_V110_F1.0960.60
2_A120_L1.0770.58
6_Y49_D1.0600.57
88_S119_V1.0580.56
37_T114_Q1.0470.55
5_E79_L1.0200.52
49_D52_Q1.0170.52
106_M119_V1.0090.51
12_L95_L1.0070.51
38_D106_M1.0040.51
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  
4aefA20.487690.50.881Contact Map
2qlvB20.388486.50.889Contact Map
2z0bA60.471185.30.891Contact Map
4aeeA20.495985.30.891Contact Map
1ac0A10.4545820.895Contact Map
2lu3A10.487668.80.906Contact Map
1z0nA30.347158.50.912Contact Map
1ea9C20.570238.90.922Contact Map
1vemA10.917437.30.923Contact Map
1m7xA40.537233.70.924Contact 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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