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T0847

ID: 1404840924 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 176 (165)
Sequences: 4747 (3251.2)
Seq/Len: 28.770
Nf(neff/√len): 253.1

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: 28.770).

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
55_A59_R4.1601.00
37_V64_C3.6281.00
126_V156_F3.1401.00
93_S169_P3.1121.00
62_F93_S3.0221.00
30_T54_E2.8721.00
30_T51_D2.8621.00
28_C127_L2.4921.00
123_W157_D2.4531.00
36_L121_S2.4031.00
126_V153_V2.3721.00
64_C93_S2.3681.00
29_I51_D2.2551.00
26_R51_D2.1901.00
37_V62_F2.1651.00
35_V123_W2.0781.00
28_C147_K2.0771.00
37_V157_D1.9531.00
35_V157_D1.9431.00
66_L167_S1.9001.00
64_C164_Y1.8771.00
56_A92_I1.8731.00
28_C121_S1.8571.00
51_D55_A1.8531.00
120_I153_V1.8061.00
29_I36_L1.8051.00
39_L114_I1.7231.00
157_D161_R1.6791.00
127_L145_L1.6581.00
53_L58_K1.6161.00
53_L90_K1.5631.00
32_T121_S1.5551.00
67_L96_S1.5461.00
39_L118_F1.5201.00
53_L86_D1.5171.00
54_E59_R1.4721.00
25_V119_I1.4391.00
28_C125_F1.4391.00
160_F164_Y1.4381.00
43_F65_V1.4000.99
36_L52_I1.3930.99
95_R164_Y1.3460.99
137_C143_N1.3370.99
37_V161_R1.3160.99
85_S89_L1.3010.99
34_Q124_R1.3010.99
71_G77_E1.2980.99
159_E163_L1.2910.99
115_R132_S1.2800.99
148_F152_A1.2780.99
27_R31_R1.2750.99
124_R149_T1.2650.99
35_V62_F1.2620.99
32_T36_L1.2530.99
117_K132_S1.2360.98
87_S92_I1.2190.98
64_C161_R1.2170.98
41_D68_D1.2170.98
49_F53_L1.1990.98
118_F156_F1.1950.98
125_F147_K1.1930.98
36_L55_A1.1860.98
22_R45_D1.1780.98
131_Y145_L1.1760.98
37_V160_F1.1530.97
127_L147_K1.1430.97
134_T141_H1.1410.97
95_R169_P1.1370.97
51_D54_E1.1120.96
25_V127_L1.1030.96
69_Q96_S1.0770.95
21_I131_Y1.0690.95
136_L140_V1.0610.95
24_L147_K1.0510.94
155_L158_E1.0340.94
66_L163_L1.0290.94
29_I55_A1.0200.93
134_T137_C1.0080.93
24_L27_R1.0050.93
96_S170_V1.0050.93
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  
4gelA20.85899.90.355Contact Map
1byrA10.852399.90.363Contact Map
3hsiA30.926199.90.371Contact Map
4ggjA10.795599.90.399Contact Map
1v0wA10.943299.90.409Contact Map
2c1lA20.909199.90.411Contact Map
1xdpA20.903499.90.415Contact Map
2o8rA20.89299.90.438Contact Map
3qphA10.806898.20.767Contact Map
2f5tX10.715997.60.793Contact 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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