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T0798

ID: 1401386785 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 198 (167)
Sequences: 18491 (11088.3)
Seq/Len: 110.725
Nf(neff/√len): 858.0

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: 110.725).

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
23_R151_S3.2151.00
12_D94_N3.1371.00
115_V157_A2.8451.00
20_L83_V2.7111.00
144_I160_N2.6461.00
83_V117_N2.5051.00
160_N163_T2.4381.00
81_L115_V2.4031.00
86_I116_G2.3701.00
142_S160_N2.3001.00
89_H131_E2.2751.00
117_N148_A2.1711.00
133_R137_E2.1641.00
84_Y143_F2.1361.00
129_T133_R2.0291.00
153_N156_E1.9721.00
79_G161_I1.9441.00
20_L154_V1.9261.00
9_L21_L1.9241.00
86_I119_S1.9111.00
132_A136_A1.8011.00
8_V77_A1.7861.00
55_A162_L1.7761.00
116_G145_E1.7731.00
146_T157_A1.7401.00
119_S145_E1.7211.00
119_S152_T1.7041.00
160_N164_E1.6721.00
99_L112_I1.6491.00
113_M144_I1.6191.00
88_K91_T1.6111.00
96_E138_K1.6111.00
20_L157_A1.5531.00
19_N148_A1.5241.00
81_L161_I1.5191.00
9_L81_L1.4801.00
135_F139_N1.4781.00
134_A138_K1.4641.00
85_D118_K1.4641.00
85_D88_K1.3920.99
113_M160_N1.3670.99
115_V146_T1.3410.99
7_V79_G1.3090.99
132_A143_F1.3080.99
5_F165_I1.3040.99
82_L95_V1.2920.99
100_K103_R1.2870.99
164_E167_R1.2780.99
156_E159_K1.2550.99
82_L99_L1.2400.98
115_V144_I1.2360.98
87_A121_L1.2330.98
81_L157_A1.2070.98
47_Q52_T1.2030.98
125_R145_E1.1960.98
36_T62_G1.1930.98
118_K121_L1.1880.98
155_E159_K1.1790.98
22_S30_N1.1770.98
133_R136_A1.1590.97
20_L24_F1.1490.97
128_P131_E1.1320.97
131_E134_A1.1250.97
99_L103_R1.1210.97
47_Q50_G1.1160.96
53_I162_L1.0980.96
114_L141_L1.0920.96
100_K104_D1.0830.96
130_D134_A1.0810.95
156_E160_N1.0800.95
23_R27_N1.0760.95
84_Y132_A1.0730.95
116_G132_A1.0720.95
20_L148_A1.0630.95
12_D15_V1.0590.95
79_G165_I1.0520.95
23_R154_V1.0430.94
34_K37_I1.0420.94
96_E135_F1.0320.94
116_G143_F1.0290.94
22_S26_R1.0070.93
61_A64_E1.0050.93
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: (24May14)
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  
3cpjB10.82831000.332Contact Map
4lhwA50.86871000.335Contact Map
3dz8A10.85351000.336Contact Map
2a5jA10.85351000.341Contact Map
2f7sA20.87881000.348Contact Map
2yc2C20.7021000.348Contact Map
1zbdA10.87881000.35Contact Map
2ew1A10.85861000.351Contact Map
2gf9A10.86361000.351Contact Map
4dkxA20.78791000.352Contact 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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