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T0856

ID: 1405450263 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 159 (152)
Sequences: 3301 (2131.7)
Seq/Len: 21.717
Nf(neff/√len): 172.9

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: 21.717).

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
40_Q105_T4.1761.00
33_G137_Y2.8671.00
10_C19_T2.8591.00
30_A138_P2.7891.00
42_K105_T2.5771.00
38_C109_D2.2611.00
41_W108_L2.2081.00
63_P134_A2.1181.00
3_D6_K2.0141.00
70_R75_M1.8971.00
85_L88_N1.8811.00
33_G135_E1.8811.00
12_V16_Q1.8391.00
34_V39_Y1.7601.00
40_Q107_V1.7341.00
109_D112_A1.5721.00
86_Y89_G1.5661.00
71_T74_D1.5561.00
2_F28_G1.5441.00
107_V116_S1.5441.00
62_W137_Y1.5231.00
62_W135_E1.5171.00
19_T28_G1.4961.00
122_E125_K1.4841.00
147_P150_K1.4721.00
9_C21_G1.4631.00
102_D120_N1.4591.00
2_F7_A1.4531.00
105_T118_G1.4431.00
41_W106_C1.4351.00
149_E153_I1.4281.00
58_G69_H1.4201.00
87_H90_E1.4141.00
44_Y103_F1.3560.99
123_E127_A1.3390.99
72_T75_M1.3300.99
37_G41_W1.3260.99
60_S137_Y1.3110.99
116_S123_E1.3090.99
27_Y139_C1.2990.99
4_P12_V1.2940.99
41_W59_V1.2690.99
5_E16_Q1.2440.98
1_G24_G1.2300.98
45_I55_T1.2190.98
33_G138_P1.2070.98
11_L22_S1.1960.98
34_V108_L1.1920.98
40_Q118_G1.1890.98
60_S135_E1.1780.98
59_V115_I1.1590.97
64_V75_M1.1560.97
42_K103_F1.1530.97
132_D136_L1.1450.97
60_S64_V1.1420.97
15_G18_L1.1390.97
151_V155_D1.1240.97
124_P127_A1.1210.97
110_M132_D1.1160.96
61_R134_A1.1100.96
106_C115_I1.1100.96
149_E154_C1.0810.95
30_A106_C1.0700.95
149_E152_K1.0620.95
147_P151_V1.0440.94
113_R132_D1.0420.94
107_V118_G1.0340.94
48_E147_P1.0340.94
43_F138_P1.0320.94
16_Q31_S1.0290.94
34_V110_M1.0280.94
13_E19_T1.0210.93
99_T119_K1.0200.93
46_V102_D1.0030.93
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: (12Jul14)
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  
4b8eA20.92451000.16Contact Map
2vokA20.94971000.168Contact Map
4b3nA20.93081000.172Contact Map
2wl1A10.9561000.174Contact Map
4n7iA10.94341000.18Contact Map
2fbeA40.96861000.181Contact Map
3emwA10.97481000.188Contact Map
2afjA10.98111000.189Contact Map
3uv9A10.92451000.194Contact Map
3tojA20.97481000.199Contact 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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