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T0826 1-200

ID: 1403941927 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 200 (194)
Sequences: 475 (377.6)
Seq/Len: 2.448
Nf(neff/√len): 27.1

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: 2.448).

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
62_N162_S3.2451.00
131_G135_A3.0081.00
82_L138_Y2.7101.00
52_T177_Y2.4381.00
87_A127_I2.3081.00
23_S65_F2.1521.00
79_P139_I2.1351.00
91_Q118_L2.1201.00
79_P138_Y2.0791.00
79_P135_A1.9870.99
59_F165_C1.9610.99
173_Q177_Y1.9420.99
91_Q99_F1.8680.99
15_L138_Y1.7800.98
92_E99_F1.7520.98
151_E155_R1.7180.98
49_F177_Y1.7150.98
152_L160_A1.6910.97
22_Y27_L1.6670.97
63_F159_A1.6160.96
71_P75_K1.6080.96
94_F138_Y1.5310.95
31_F185_K1.5260.94
62_N158_L1.4960.94
95_F153_L1.4610.93
68_I77_L1.4120.91
19_L78_I1.4110.91
63_F166_A1.4020.90
24_S58_F1.3980.90
63_F163_F1.3970.90
31_F192_V1.3670.89
11_G84_I1.3320.87
15_L78_I1.3310.87
188_T198_G1.3210.86
99_F118_L1.2980.85
75_K81_I1.2860.84
170_A183_N1.2580.83
175_Q183_N1.2510.82
59_F169_I1.2280.80
23_S172_L1.2080.79
161_V164_L1.2040.79
156_L160_A1.2020.78
20_S27_L1.1970.78
128_V132_V1.1790.77
24_S27_L1.1760.76
31_F35_V1.1760.76
71_P190_L1.1740.76
136_L140_A1.1640.75
129_C136_L1.1610.75
60_L199_A1.1580.75
31_F57_L1.1570.75
100_N103_M1.1380.73
68_I178_A1.1230.72
140_A144_K1.1170.71
127_I132_V1.1160.71
31_F92_E1.1140.71
165_C168_G1.1110.70
192_V198_G1.1030.70
174_Y191_I1.1010.69
104_L175_Q1.0950.69
22_Y92_E1.0940.69
179_S183_N1.0880.68
119_I124_V1.0850.68
16_I155_R1.0760.67
94_F122_G1.0710.66
80_L84_I1.0650.66
86_A131_G1.0620.65
31_F198_G1.0600.65
163_F167_L1.0580.65
7_R140_A1.0560.65
63_F155_R1.0550.65
145_Y151_E1.0530.64
169_I183_N1.0520.64
48_I173_Q1.0460.64
52_T57_L1.0440.63
185_K194_S1.0420.63
23_S81_I1.0400.63
30_A93_I1.0370.63
103_M106_N1.0370.63
190_L195_N1.0270.61
143_V159_A1.0260.61
83_V160_A1.0200.61
180_F195_N1.0180.60
168_G172_L1.0180.60
85_S196_F1.0150.60
118_L123_Y1.0140.60
32_F192_V1.0090.59
75_K79_P1.0060.59
101_K113_A1.0020.59
15_L75_K1.0000.58
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  
4humA10.834.50.966Contact Map
4httA20.274.20.966Contact Map
2ww9C10.1054.10.966Contact Map
4lz6A10.8354.10.966Contact Map
1fmeA10.11540.967Contact Map
3wajA10.7553.90.967Contact Map
2wwbC10.183.50.967Contact Map
3buaE40.083.30.968Contact Map
3mktA20.8230.969Contact Map
2a65A10.61530.969Contact 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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