GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
ont3

ID: 1500030776 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 130 (125)
Sequences: 333 (218.7)
Seq/Len: 2.664
Nf(neff/√len): 19.6

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: 2.664).

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
45_F79_A2.7641.00
86_W92_N2.5481.00
41_A82_V2.4041.00
33_H97_A2.0020.99
83_M99_V1.8900.99
84_S100_K1.8560.99
37_D100_K1.8230.99
32_T97_A1.8200.99
70_F74_I1.8160.99
48_P74_I1.7100.98
63_Y95_A1.6300.97
119_P122_V1.6070.97
22_C25_W1.5160.95
16_Y71_A1.5150.95
32_T101_V1.5130.95
17_A30_I1.5030.95
17_A21_Y1.4620.94
55_M67_I1.4230.92
116_P123_A1.3940.91
71_A75_L1.3910.91
38_A85_I1.3520.90
97_A101_V1.3410.89
69_L106_A1.3150.88
74_I103_T1.3060.87
20_G25_W1.2740.85
40_I104_A1.2740.85
17_A23_L1.2540.84
30_I88_L1.2480.84
70_F107_S1.2290.83
23_L94_G1.2160.82
49_L106_A1.1940.80
74_I77_C1.1840.79
66_M106_A1.1710.78
17_A88_L1.1610.77
59_E118_I1.1480.76
126_S130_L1.1320.75
73_F81_H1.1310.75
81_H107_S1.1210.74
55_M64_G1.1170.73
20_G23_L1.0860.70
38_A61_I1.0830.70
12_F15_S1.0800.70
76_A108_V1.0800.70
19_H25_W1.0710.69
74_I80_T1.0670.68
29_L88_L1.0670.68
28_A98_V1.0530.67
89_W93_Y1.0530.67
48_P77_C1.0430.66
58_R125_P1.0420.66
44_Y107_S1.0410.66
43_A67_I1.0400.65
64_G76_A1.0280.64
63_Y120_K1.0220.63
23_L96_E1.0200.63
26_E68_A1.0160.63
121_A124_L1.0090.62
103_T107_S1.0080.62
8_L12_F1.0080.62
87_T91_G1.0080.62
22_C107_S1.0030.61
51_L67_I1.0020.61
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  
2kdrX10.21541.40.954Contact Map
2l34A20.253810.958Contact Map
2jwaA20.33080.90.959Contact Map
2xq2A10.67690.90.959Contact Map
2ks1B10.33080.80.961Contact Map
2mc7A10.23080.80.961Contact Map
2lq0A10.19230.70.962Contact Map
2hi7B10.26920.70.962Contact Map
4xnjA100.70.963Contact Map
4z0nA10.36150.60.964Contact 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.

Page generated in 0.0426 seconds.