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PHD cluster submitted Dec 27 minus LcCMI

ID: 1514412466 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 185 (185)
Sequences: 410 (278.2)
Seq/Len: 2.216
Nf(neff/√len): 20.5

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: 2.216).

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
160_D176_Y3.1451.00
123_C126_C2.5081.00
159_C178_C2.4301.00
156_H159_C2.4181.00
5_C8_C2.4131.00
102_C105_C2.3481.00
132_C135_C2.1881.00
178_C181_C2.1641.00
156_H178_C2.0140.99
156_H181_C1.9370.99
78_H81_C1.8460.98
159_C181_C1.6640.96
151_C178_C1.6480.96
116_W120_Y1.6160.95
71_D90_P1.5740.95
139_Y145_I1.5590.94
53_T76_S1.4940.92
73_C81_C1.4910.92
106_G116_W1.4880.92
96_C99_C1.4740.92
70_C73_C1.4720.92
49_C52_C1.4480.91
124_G127_A1.4460.91
22_C30_H1.4390.90
126_C135_C1.4150.89
102_C126_C1.4140.89
160_D179_V1.3950.88
148_C151_C1.3900.88
53_T72_D1.3880.88
102_C123_C1.3760.87
5_C30_H1.3320.85
148_C156_H1.3080.84
151_C159_C1.3010.83
116_W126_C1.2970.83
162_I171_C1.2970.83
34_T50_L1.2960.83
148_C159_C1.2950.83
63_D80_Y1.2840.82
4_I10_A1.2790.82
30_H52_C1.2750.81
77_Y82_M1.2610.80
105_C126_C1.2480.79
176_Y179_V1.2420.79
64_E72_D1.2320.78
70_C78_H1.2290.78
151_C156_H1.2220.77
73_C78_H1.2220.77
148_C178_C1.1910.75
19_L31_P1.1870.75
132_C148_C1.1790.74
67_L76_S1.1790.74
135_C156_H1.1740.73
70_C81_C1.1710.73
9_G32_Y1.1710.73
99_C102_C1.1690.73
54_I65_G1.1650.73
132_C151_C1.1580.72
111_G116_W1.1480.71
135_C148_C1.1470.71
116_W123_C1.1460.71
67_L90_P1.1360.70
116_W121_S1.1290.69
74_D90_P1.1280.69
123_C135_C1.1270.69
55_C58_C1.1240.69
55_C70_C1.1210.68
58_C70_C1.1150.68
126_C132_C1.1150.68
67_L86_L1.1070.67
5_C22_C1.1060.67
99_C105_C1.1060.67
105_C123_C1.0960.66
132_C181_C1.0960.66
49_C70_C1.0950.66
45_K53_T1.0840.65
5_C52_C1.0800.64
155_L176_Y1.0770.64
21_A50_L1.0640.62
63_D74_D1.0630.62
157_C163_K1.0600.62
151_C181_C1.0550.62
1_T185_D1.0470.61
63_D66_R1.0460.61
4_I7_M1.0440.60
8_C30_H1.0380.60
108_S113_N1.0350.59
154_W165_E1.0310.59
58_C78_H1.0260.58
100_A108_S1.0250.58
107_S111_G1.0170.57
48_R59_G1.0120.57
59_G67_L1.0080.56
79_I82_M1.0040.56
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  
2ysmA10.57399.90.57Contact Map
3v43A10.551499.80.602Contact Map
2kwjA10.578499.80.603Contact Map
4lk9A10.562299.80.607Contact Map
4gneA10.491999.60.682Contact Map
3ql9A10.545999.60.687Contact Map
2lbmA10.637899.60.688Contact Map
4tvrA1099.50.711Contact Map
3shbA10.356899.40.727Contact Map
3aslA10.362299.40.73Contact 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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