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T0812 -force run

ID: 1402423018 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 204 (201)
Sequences: 110 (70.2)
Seq/Len: 0.547
Nf(neff/√len): 5.0

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: 0.547).

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
179_I182_I2.2450.94
199_A203_E1.8890.83
80_Y98_Q1.8840.83
66_F161_I1.7670.77
4_K50_R1.7620.77
155_L160_D1.7300.75
73_A130_E1.7040.73
145_V159_Y1.5410.62
1_S50_R1.5290.61
80_Y84_F1.5200.61
38_Q122_G1.5030.59
80_Y170_Y1.4690.57
167_K181_E1.4620.56
101_I129_I1.4450.55
199_A202_I1.4270.53
1_S4_K1.4220.53
155_L176_Q1.4220.53
45_H160_D1.4100.52
62_L76_G1.4090.52
69_K131_M1.4010.51
4_K51_E1.4000.51
62_L66_F1.3990.51
37_F47_D1.3860.50
31_T97_P1.3590.48
113_V157_I1.3490.47
33_K69_K1.3460.47
44_A97_P1.3280.46
46_M97_P1.3090.44
62_L136_W1.3080.44
127_H148_T1.3020.44
70_K189_Q1.2870.42
48_L187_A1.2860.42
179_I184_M1.2660.41
151_R168_A1.2570.40
145_V160_D1.2560.40
131_M150_T1.2490.39
137_K167_K1.2480.39
138_Y149_V1.2340.38
84_F174_M1.2210.37
150_T187_A1.2130.37
146_H160_D1.2110.37
69_K189_Q1.2100.37
192_G196_T1.2000.36
44_A82_I1.1980.36
168_A187_A1.1920.35
57_P80_Y1.1900.35
154_F167_K1.1700.34
151_R158_L1.1580.33
101_I131_M1.1490.32
1_S79_K1.1400.32
84_F176_Q1.1380.31
29_H69_K1.1360.31
66_F76_G1.1340.31
74_Y158_L1.1320.31
50_R107_T1.1230.30
187_A199_A1.1170.30
136_W169_T1.1170.30
20_L23_V1.1160.30
88_E137_K1.1130.30
138_Y153_D1.1120.30
64_E183_S1.1090.30
71_L184_M1.1060.29
66_F136_W1.1050.29
42_I159_Y1.0990.29
96_N102_R1.0930.28
6_L69_K1.0920.28
30_T111_I1.0840.28
60_W168_A1.0840.28
6_L106_P1.0810.28
43_V73_A1.0800.28
35_I96_N1.0770.27
59_Y84_F1.0760.27
174_M179_I1.0720.27
117_A120_L1.0690.27
29_H161_I1.0690.27
2_E142_D1.0650.27
83_Y169_T1.0640.27
124_L185_E1.0530.26
107_T194_T1.0520.26
49_M73_A1.0520.26
58_F130_E1.0510.26
117_A162_H1.0490.26
50_R194_T1.0450.25
130_E185_E1.0430.25
72_M146_H1.0390.25
165_L183_S1.0320.25
50_R193_T1.0300.25
2_E51_E1.0260.24
56_E165_L1.0260.24
74_Y133_E1.0260.24
99_V152_E1.0240.24
101_I202_I1.0230.24
158_L168_A1.0220.24
20_L154_F1.0220.24
37_F184_M1.0220.24
75_G154_F1.0200.24
21_P37_F1.0170.24
46_M155_L1.0160.24
1_S51_E1.0110.23
1_S107_T1.0100.23
148_T186_V1.0050.23
129_I158_L1.0040.23
4_K106_P1.0010.23
160_D164_I1.0000.23
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  
4yeqU101000.293Contact Map
4yepA201000.341Contact Map
2fokA20.88734.80.967Contact Map
2di9A10.362740.969Contact Map
4mkqC20.044140.969Contact Map
4tr8A20.3483.40.97Contact Map
3if8B10.31863.20.97Contact Map
1vpkA10.2992.90.971Contact Map
3t0pA20.2992.70.971Contact Map
4k3lA20.29412.60.972Contact 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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