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T0821

ID: 1402944438 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 275 (246)
Sequences: 27788 (23125.3)
Seq/Len: 112.959
Nf(neff/√len): 1474.4

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: 112.959).

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
176_N179_E3.1771.00
142_N145_W3.1651.00
244_E247_R3.1391.00
108_E111_K3.1381.00
210_K213_R3.1041.00
74_K77_E3.1001.00
37_D40_S2.9481.00
62_L81_S2.2941.00
201_R217_D2.1691.00
133_R149_D2.1511.00
100_A116_Y2.1321.00
99_R115_D2.1221.00
66_G82_Y2.1171.00
134_G150_F2.1171.00
198_Y217_D2.1031.00
232_Y251_D2.0781.00
202_A218_I2.0451.00
235_R251_D2.0361.00
65_L81_S2.0331.00
130_L149_D2.0091.00
167_H183_I1.9851.00
45_L64_N1.9691.00
96_L115_D1.9611.00
164_R183_I1.9501.00
219_E235_R1.9271.00
117_N133_R1.9231.00
151_D167_H1.9131.00
46_K65_L1.8961.00
185_N201_R1.8811.00
168_A184_F1.8641.00
83_T99_R1.8441.00
236_G252_F1.7631.00
29_S45_L1.6991.00
28_K44_S1.6451.00
82_Y98_N1.6301.00
116_Y132_C1.6001.00
218_I234_L1.5271.00
150_F166_G1.4371.00
215_M219_E1.4291.00
184_F200_G1.4251.00
42_E46_K1.4161.00
79_L83_T1.3880.99
25_L44_S1.3870.99
69_Q81_S1.3840.99
103_Y111_K1.3800.99
137_Y145_W1.3740.99
69_Q77_E1.3740.99
113_L117_N1.3570.99
147_E151_D1.3530.99
181_E185_N1.3420.99
199_E234_L1.3240.99
103_Y115_D1.3210.99
215_M238_I1.2820.99
42_E69_Q1.2800.99
99_R103_Y1.2770.99
239_K247_R1.2750.99
171_E179_E1.2680.99
39_V72_Q1.2670.99
254_K257_S1.2520.99
76_Q106_L1.2390.98
239_K244_E1.2340.98
133_R137_Y1.2310.98
32_F40_S1.2260.98
152_K155_E1.2200.98
42_E68_I1.2160.98
201_R205_Y1.2150.98
187_L197_L1.2130.98
86_L95_I1.2060.98
249_A253_K1.2040.98
42_E72_Q1.2000.98
220_K223_T1.2000.98
181_E204_L1.1940.98
84_S87_S1.1870.98
110_E140_L1.1850.98
79_L102_L1.1850.98
92_N95_I1.1830.98
205_Y213_R1.1800.98
221_V231_L1.1800.98
63_T98_N1.1620.97
65_L69_Q1.1570.97
147_E170_L1.1560.97
32_F37_D1.1520.97
205_Y210_K1.1520.97
153_I163_A1.1510.97
194_D197_L1.1440.97
137_Y149_D1.1360.97
171_E183_I1.1360.97
212_A242_Q1.1350.97
167_H171_E1.1280.97
118_T121_I1.1270.97
171_E176_N1.1230.97
144_M174_R1.1220.97
235_R239_K1.1200.96
113_L136_L1.1150.96
181_E205_Y1.1130.96
49_M61_L1.1120.96
178_D208_M1.1060.96
206_F218_I1.1060.96
69_Q74_K1.1040.96
188_I197_L1.1040.96
32_F44_S1.1030.96
28_K32_F1.1010.96
239_K251_D1.0980.96
97_E132_C1.0980.96
181_E208_M1.0890.96
147_E174_R1.0850.96
152_K156_V1.0820.96
113_L133_R1.0790.95
127_Q153_I1.0750.95
131_Y166_G1.0750.95
77_E80_I1.0710.95
165_L200_G1.0710.95
203_D234_L1.0700.95
42_E65_L1.0640.95
186_Y189_S1.0630.95
79_L106_L1.0630.95
31_D35_K1.0620.95
48_A61_L1.0600.95
228_T231_L1.0570.95
29_S48_A1.0500.94
236_G255_A1.0490.94
191_M194_D1.0480.94
205_Y217_D1.0470.94
179_E182_R1.0430.94
225_S228_T1.0430.94
213_R216_A1.0390.94
111_K114_N1.0330.94
120_L129_A1.0330.94
79_L99_R1.0300.94
126_H129_A1.0270.94
130_L152_K1.0160.93
247_R250_L1.0140.93
137_Y142_N1.0130.93
215_M239_K1.0080.93
215_M242_Q1.0060.93
169_I200_G1.0050.93
100_A119_L1.0030.93
198_Y220_K1.0010.92
172_K184_F1.0000.92
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: (14Jun14)
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  
3iegA20.921000.219Contact Map
2y4tA30.98911000.237Contact Map
4eqfA10.92361000.251Contact Map
4kvmA40.94551000.259Contact Map
2xpiA20.98551000.26Contact Map
3hymB60.98911000.261Contact Map
1w3bA20.98911000.261Contact Map
4l9pA10.98551000.262Contact Map
3uq3A10.89091000.263Contact Map
1fchA20.961000.264Contact 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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