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NTER

ID: 1505648334 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 154 (153)
Sequences: 207 (134.2)
Seq/Len: 1.353
Nf(neff/√len): 10.8

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: 1.353).

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_L112_E2.5451.00
3_Q116_L1.7390.93
1_M37_W1.7350.93
35_A117_Q1.6710.91
124_Q127_G1.6380.90
29_E68_Y1.6190.89
8_Q15_L1.6050.89
34_L64_I1.5240.85
105_V112_E1.4820.83
13_R116_L1.4810.83
132_P135_A1.4670.82
10_L15_L1.4550.81
98_P109_L1.4300.80
61_L67_Q1.4080.78
15_L26_F1.3640.75
65_D71_F1.3510.74
105_V109_L1.3310.73
61_L65_D1.3280.72
19_H102_A1.3190.72
55_L81_H1.3100.71
41_Q56_V1.3000.70
1_M10_L1.2920.70
16_E19_H1.2890.69
47_A103_R1.2860.69
23_S83_L1.2800.68
16_E76_N1.2790.68
124_Q129_A1.2730.68
53_A57_F1.2600.67
118_T144_L1.2450.65
67_Q87_K1.2280.64
101_I112_E1.2210.63
139_E148_L1.2130.62
93_R104_I1.1980.61
60_L90_L1.1970.61
31_R39_E1.1770.59
124_Q128_Q1.1740.59
28_M32_Q1.1660.58
111_E114_R1.1520.56
62_G113_S1.1510.56
3_Q10_L1.1450.56
105_V115_L1.1410.55
98_P112_E1.1310.54
28_M87_K1.1270.54
102_A113_S1.1220.53
32_Q101_I1.1210.53
29_E36_P1.1170.53
80_Q84_R1.1170.53
102_A112_E1.1170.53
31_R112_E1.1140.53
39_E43_W1.1140.53
48_S114_R1.1130.53
102_A115_L1.1100.52
133_T141_Q1.1080.52
55_L91_Q1.1080.52
6_Q120_A1.1070.52
47_A102_A1.1060.52
41_Q93_R1.1020.51
71_F74_E1.1010.51
109_L115_L1.0970.51
17_Q81_H1.0930.51
23_S101_I1.0900.50
8_Q79_Y1.0870.50
92_S100_E1.0810.49
56_V89_F1.0720.48
109_L119_A1.0680.48
7_L15_L1.0580.47
11_D57_F1.0560.47
126_G129_A1.0560.47
63_E66_Q1.0560.47
67_Q78_L1.0480.46
21_L49_K1.0480.46
57_F65_D1.0430.46
83_L125_Q1.0390.45
6_Q90_L1.0350.45
48_S120_A1.0300.44
115_L119_A1.0290.44
101_I109_L1.0270.44
107_R116_L1.0230.44
113_S150_D1.0190.43
125_Q131_H1.0160.43
23_S32_Q1.0020.42
28_M81_H1.0010.41
14_Y71_F1.0010.41
27_P31_R1.0010.41
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  
1yvlA20.94161000.027Contact Map
4ziaA501000.12Contact Map
3wwtA101000.13Contact Map
1bgfA10.79871000.144Contact Map
3r6nA20.61046.60.948Contact Map
3zkvA10.5265.10.951Contact Map
3o2tA10.69483.50.954Contact Map
4imiA20.70133.10.956Contact Map
1yviA20.68182.90.956Contact Map
3j94A60.38962.60.957Contact 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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