GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
bc1

ID: 1513230186 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 116 (116)
Sequences: 167 (66.9)
Seq/Len: 1.440
Nf(neff/√len): 6.2

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: 1.440).

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
80_F85_M1.9690.98
62_E71_M1.7780.95
89_I93_M1.6950.93
5_N8_G1.6300.91
77_I116_V1.6210.91
43_M106_D1.6190.90
57_F61_E1.5990.90
32_T35_P1.5430.87
84_D91_M1.4840.85
76_R104_I1.4230.81
19_E116_V1.4100.80
3_Y45_P1.3460.76
22_S29_L1.3210.74
56_D59_I1.3210.74
101_D113_N1.2970.72
46_Y56_D1.2940.71
50_G96_E1.2860.71
99_V102_I1.2840.71
81_R105_A1.2830.71
23_I34_S1.2660.69
100_I115_C1.2560.68
16_K59_I1.2550.68
55_F58_N1.2530.68
3_Y13_I1.2440.67
49_D74_D1.1950.63
95_H100_I1.1950.63
40_K100_I1.1810.61
68_L85_M1.1770.61
4_N77_I1.1440.58
24_L114_V1.1400.57
1_I45_P1.1380.57
26_L93_M1.1370.57
10_E38_A1.1300.56
2_K10_E1.1120.54
34_S60_L1.1120.54
4_N74_D1.1090.54
33_R40_K1.1090.54
95_H113_N1.1040.54
26_L82_Q1.1020.53
49_D75_S1.0990.53
80_F102_I1.0980.53
43_M82_Q1.0960.53
91_M116_V1.0910.52
50_G97_A1.0850.52
68_L71_M1.0840.51
17_I99_V1.0810.51
28_E69_K1.0780.51
12_R81_R1.0670.50
19_E24_L1.0600.49
112_T115_C1.0550.49
77_I86_V1.0540.48
110_V114_V1.0500.48
73_K115_C1.0480.48
4_N33_R1.0460.48
66_N69_K1.0410.47
27_V51_I1.0410.47
8_G11_F1.0400.47
46_Y55_F1.0320.46
74_D81_R1.0210.45
48_H96_E1.0080.44
9_M75_S1.0060.44
97_A108_Y1.0060.44
56_D67_I1.0040.43
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  
3hqiA20.92246.40.954Contact Map
1vb3A10.77595.10.956Contact Map
2z8hA10.87074.60.957Contact Map
2ihcA40.85344.50.957Contact Map
2if5A10.83624.10.958Contact Map
1dj7B10.53.90.958Contact Map
3bgyA20.56033.60.959Contact Map
4ajyC10.66383.50.959Contact Map
3fkcA10.77593.30.96Contact Map
3ohuA60.86212.90.961Contact 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 0.0329 seconds.