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T0849

ID: 1404964482 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 240 (199)
Sequences: 10143 (7029.7)
Seq/Len: 50.970
Nf(neff/√len): 498.3

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: 50.970).

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
25_D199_R4.1811.00
73_S94_E3.6321.00
191_A195_R3.3931.00
6_I33_L3.2231.00
77_R90_I2.9601.00
23_L30_F2.8611.00
9_Y16_A2.8331.00
6_I31_R2.8281.00
24_A30_F2.7511.00
24_A204_Q2.5771.00
135_V188_H2.5131.00
139_T188_H2.3101.00
63_V88_G2.2231.00
140_R148_A2.2081.00
149_G195_R2.2011.00
132_G186_L2.1931.00
44_K53_G2.1351.00
25_D201_A2.1041.00
86_D89_E2.0411.00
21_H202_L1.9331.00
26_A76_A1.9061.00
149_G154_E1.8761.00
190_C194_R1.7751.00
8_R59_R1.7461.00
59_R64_E1.7441.00
96_V137_R1.7401.00
6_I59_R1.6851.00
22_A72_A1.6761.00
43_H57_T1.6431.00
46_S57_T1.6161.00
77_R94_E1.6081.00
5_I58_L1.6081.00
9_Y32_D1.6001.00
164_A196_M1.5941.00
59_R62_G1.5921.00
8_R35_I1.5831.00
22_A82_Y1.5641.00
152_G157_V1.5481.00
60_W74_F1.5431.00
135_V187_P1.5371.00
156_P161_Y1.5201.00
128_P185_R1.5181.00
194_R198_Q1.5021.00
198_Q203_A1.4651.00
203_A207_S1.4601.00
41_S45_D1.4541.00
19_L72_A1.4221.00
43_H46_S1.4201.00
132_G136_A1.4050.99
156_P199_R1.4000.99
188_H191_A1.3990.99
150_W196_M1.3920.99
84_G93_L1.3870.99
28_L79_L1.3810.99
92_R95_A1.3770.99
46_S59_R1.3690.99
60_W63_V1.3670.99
5_I28_L1.3540.99
25_D156_P1.3370.99
42_Q45_D1.3170.99
122_D125_A1.3050.99
135_V139_T1.2860.99
167_I192_L1.2740.99
137_R148_A1.2640.99
151_F163_A1.2630.99
7_L23_L1.2630.99
83_E94_E1.2420.98
22_A26_A1.2260.98
65_V91_A1.2020.98
83_E93_L1.1920.98
25_D161_Y1.1790.98
184_T190_C1.1560.97
153_G160_D1.1430.97
18_A68_T1.1400.97
98_S102_T1.1340.97
164_A197_A1.1310.97
75_L79_L1.1250.97
18_A162_F1.1180.96
82_Y161_Y1.1160.96
73_S98_S1.0940.96
66_A95_A1.0870.96
182_L185_R1.0860.96
9_Y20_R1.0820.96
132_G185_R1.0750.95
7_L58_L1.0740.95
72_A158_M1.0720.95
151_F159_A1.0680.95
125_A129_L1.0640.95
54_S67_E1.0560.95
20_R24_A1.0550.95
93_L159_A1.0520.95
201_A204_Q1.0480.94
87_N91_A1.0460.94
136_A140_R1.0400.94
16_A55_L1.0390.94
124_A128_P1.0390.94
92_R137_R1.0370.94
194_R197_A1.0360.94
60_W79_L1.0340.94
88_G92_R1.0270.94
60_W78_S1.0270.94
150_W195_R1.0230.93
156_P196_M1.0050.93
97_V158_M1.0050.93
200_P204_Q1.0010.92
5_I79_L1.0000.92
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: (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  
1tw9A80.8251000.322Contact Map
2on7A40.8251000.322Contact Map
2on5A80.8251000.323Contact Map
1m0uA20.8251000.328Contact Map
3vurA10.82081000.33Contact Map
2ws2A20.81671000.332Contact Map
1yq1A20.79581000.338Contact Map
1zl9A20.82921000.338Contact Map
2a2rA20.86671000.341Contact Map
2gsqA10.8251000.342Contact 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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