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beps_core_with 2 iterations -force run

ID: 1507626336 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 123 (123)
Sequences: 110 (67.8)
Seq/Len: 0.894
Nf(neff/√len): 6.1

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: 0.894).

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
91_G95_R1.9840.94
92_R95_R1.9210.93
29_M123_S1.9020.92
100_N103_K1.7810.89
70_N117_E1.7330.87
81_N119_M1.7140.86
81_N91_G1.6750.84
81_N94_Q1.5070.74
66_R107_H1.5000.74
63_G103_K1.4350.69
100_N110_N1.4310.69
46_E93_T1.4290.68
63_G106_G1.4280.68
3_N60_N1.4250.68
42_D96_L1.4150.67
38_F84_H1.3440.61
44_I49_Q1.3340.61
62_Q70_N1.3230.60
58_K72_E1.2950.57
8_A12_R1.2950.57
50_R53_Q1.2880.57
38_F92_R1.2860.56
65_T77_F1.2780.56
7_W18_F1.2620.54
84_H92_R1.2520.53
14_I79_S1.2410.52
84_H87_R1.2400.52
76_L98_F1.2400.52
52_D109_L1.2350.52
58_K68_E1.2200.51
32_T51_L1.2090.50
10_Y22_T1.2050.49
57_E119_M1.2050.49
51_L71_S1.1950.48
20_D44_I1.1780.47
39_A47_G1.1750.46
23_T122_A1.1630.45
60_N104_A1.1570.45
11_L87_R1.1560.45
35_K53_Q1.1300.42
52_D94_Q1.1230.42
31_R34_W1.1220.42
7_W12_R1.1200.42
5_F99_E1.1180.41
6_E66_R1.1110.41
43_E103_K1.0940.39
91_G119_M1.0890.39
74_I117_E1.0880.39
87_R95_R1.0810.38
64_L105_A1.0770.38
41_G58_K1.0720.37
72_E107_H1.0720.37
109_L113_L1.0720.37
61_L64_L1.0630.37
81_N92_R1.0540.36
51_L76_L1.0530.36
16_F66_R1.0500.36
1_F12_R1.0430.35
17_T108_Q1.0370.35
24_A84_H1.0320.34
80_L101_L1.0310.34
73_A107_H1.0290.34
88_E109_L1.0150.33
32_T37_A1.0140.33
15_P73_A1.0120.33
3_N96_L1.0100.32
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  
4npsA10.918799.90.597Contact Map
4n67A1199.90.598Contact Map
2jk8A2199.90.6Contact Map
4py3A10099.90.603Contact Map
4m16A1199.90.606Contact Map
3zc7A10.87899.80.658Contact Map
3shgA10.87899.80.678Contact Map
3se5A40.788699.50.749Contact Map
2f6sA20.788699.50.753Contact Map
3zlmA10.788699.40.764Contact 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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