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4ryr

ID: 1500382201 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 151 (135)
Sequences: 1997 (1539.9)
Seq/Len: 14.793
Nf(neff/√len): 132.5

HHblits Results: (2016_02)
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: 14.793).

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
109_A138_A4.0711.00
91_F104_D3.7461.00
43_M47_M3.0291.00
38_W142_Y2.9931.00
112_T137_S2.9821.00
62_I123_S2.7941.00
99_F148_Y2.4331.00
84_F111_T2.2371.00
115_L130_L2.1751.00
102_T145_W2.0651.00
102_T144_S1.9941.00
120_S127_A1.8081.00
145_W149_S1.7911.00
116_I127_A1.7761.00
128_W131_I1.7551.00
60_V78_F1.7311.00
146_T149_S1.7171.00
29_W98_L1.7121.00
115_L119_S1.7101.00
146_T150_I1.6981.00
77_L118_F1.6931.00
109_A141_T1.6441.00
59_S130_L1.6431.00
109_A137_S1.5611.00
77_L114_L1.4931.00
105_C141_T1.4761.00
35_K39_T1.4541.00
60_V75_W1.4351.00
142_Y146_T1.3650.99
34_E150_I1.3360.99
38_W146_T1.2850.99
35_K147_I1.2620.99
120_S128_W1.2620.99
91_F101_A1.2450.98
53_F85_N1.2380.98
120_S124_K1.2330.98
56_I60_V1.2180.98
116_I130_L1.2110.98
97_N100_L1.2110.98
105_C144_S1.2000.98
83_I87_A1.1880.98
109_A112_T1.1770.98
63_I119_S1.1690.97
74_F119_S1.1620.97
62_I65_N1.1390.97
29_W96_K1.1280.97
84_F107_L1.1270.97
63_I74_F1.1240.97
60_V64_Y1.1090.96
37_S146_T1.1040.96
114_L118_F1.0850.96
79_L83_I1.0750.95
57_A61_A1.0680.95
108_V133_Y1.0670.95
88_F144_S1.0590.95
101_A104_D1.0550.95
59_S115_L1.0520.95
116_I134_F1.0390.94
63_I122_L1.0360.94
76_F80_L1.0270.94
29_W39_T1.0180.93
66_N122_L1.0150.93
88_F92_Q1.0130.93
81_N115_L1.0090.93
59_S126_S1.0080.93
95_Q98_L1.0010.92
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: (06Aug15)
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  
4ryoA101000.119Contact Map
4uc1A30.98011000.152Contact Map
2mgyA111000.213Contact Map
4phzK30.75524.40.927Contact Map
1yewC30.576217.20.932Contact Map
4ev6A50.4043.30.951Contact Map
4i0uA100.39072.70.953Contact Map
4g09A10.337720.956Contact Map
4p79A10.410610.964Contact Map
3dh4A40.43050.80.965Contact 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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