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T0826 1-220

ID: 1403944640 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 220 (212)
Sequences: 505 (412.2)
Seq/Len: 2.382
Nf(neff/√len): 28.3

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: 2.382).

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
131_G135_A3.1291.00
82_L138_Y2.8111.00
62_N162_S2.6241.00
79_P139_I2.3761.00
52_T177_Y2.2851.00
15_L138_Y2.2101.00
79_P135_A2.1661.00
173_Q177_Y2.1181.00
91_Q118_L2.0731.00
103_M106_N2.0490.99
79_P138_Y2.0040.99
87_A127_I1.9700.99
104_L203_K1.8630.99
92_E99_F1.8320.99
49_F177_Y1.8020.98
91_Q99_F1.7800.98
22_Y27_L1.7640.98
59_F165_C1.7070.97
188_T198_G1.6810.97
23_S65_F1.6790.97
174_Y178_A1.5700.95
152_L160_A1.5540.95
63_F163_F1.5430.95
95_F153_L1.4780.93
100_N103_M1.4720.93
151_E155_R1.4620.92
19_L78_I1.4540.92
31_F185_K1.4530.92
62_N158_L1.4350.91
24_S58_F1.4220.91
31_F198_G1.4000.90
94_F138_Y1.3870.89
76_V79_P1.3690.88
49_F173_Q1.3640.88
137_A217_L1.3530.88
80_L84_I1.3380.87
108_L203_K1.3190.86
99_F214_Y1.3120.85
31_F57_L1.2990.85
140_A144_K1.2640.82
86_A161_V1.2590.82
146_R151_E1.2470.81
129_C136_L1.2330.80
63_F159_A1.2250.80
23_S184_N1.2210.79
20_S27_L1.2050.78
54_P177_Y1.2020.78
8_P140_A1.1990.78
93_I192_V1.1950.77
163_F167_L1.1910.77
71_P75_K1.1870.77
10_L18_F1.1840.76
75_K79_P1.1790.76
170_A183_N1.1730.75
31_F192_V1.1700.75
63_F166_A1.1690.75
75_K81_I1.1540.74
23_S172_L1.1520.73
91_Q123_Y1.1480.73
91_Q214_Y1.1450.73
180_F195_N1.1360.72
11_G14_A1.1250.71
136_L140_A1.1130.70
15_L78_I1.1110.70
99_F123_Y1.1070.69
86_A131_G1.1050.69
60_L166_A1.1010.69
95_F110_T1.0970.68
95_F103_M1.0970.68
31_F35_V1.0910.68
21_L58_F1.0890.67
145_Y151_E1.0870.67
89_S126_W1.0870.67
20_S64_V1.0860.67
179_S183_N1.0830.67
126_W130_L1.0750.66
212_I215_T1.0740.66
192_V198_G1.0620.64
164_L167_L1.0600.64
179_S182_R1.0590.64
129_C168_G1.0580.64
174_Y191_I1.0560.64
68_I77_L1.0530.63
19_L138_Y1.0490.63
16_I155_R1.0450.63
23_S81_I1.0450.63
156_L160_A1.0420.62
47_D51_Y1.0300.61
24_S27_L1.0240.60
78_I82_L1.0230.60
75_K143_V1.0210.60
100_N131_G1.0210.60
48_I51_Y1.0150.59
56_V169_I1.0080.58
30_A89_S1.0060.58
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: (21Jun14)
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  
1fmeA10.10452.80.97Contact Map
3ddlA20.47732.40.971Contact Map
4httA20.25452.10.972Contact Map
2yevB20.52.10.972Contact Map
3qf4A10.93181.80.973Contact Map
2a65A10.57271.70.973Contact Map
3b60A40.93181.70.973Contact Map
2r7rA10.24091.70.973Contact Map
2hi2A10.30451.60.973Contact Map
2m3eA10.22271.50.974Contact 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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