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scEMC5

ID: 1504851149 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 141 (135)
Sequences: 152 (108.1)
Seq/Len: 1.126
Nf(neff/√len): 9.3

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: 1.126).

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
11_V15_V2.1040.98
1_M5_S1.8480.94
6_K68_F1.6750.89
51_Y56_G1.6720.88
21_F116_T1.6620.88
76_I83_I1.6120.86
19_S49_I1.6090.86
106_G111_G1.5530.83
47_K59_L1.5270.81
12_S19_S1.5270.81
43_S58_I1.5250.81
57_L127_K1.4500.77
24_Y57_L1.4500.77
108_N114_I1.3560.69
22_S25_E1.3520.69
8_L47_K1.3240.67
25_E121_D1.3160.66
59_L98_A1.3140.66
11_V14_L1.2920.64
15_V55_A1.2910.64
76_I84_I1.2910.64
29_L53_T1.2730.62
28_H31_K1.2680.62
29_L66_T1.2370.59
2_S14_L1.2350.59
1_M109_P1.2320.59
87_G125_K1.2040.56
34_S110_N1.1970.55
83_I86_Q1.1900.55
2_S11_V1.1810.54
36_N39_Q1.1740.53
12_S16_L1.1680.52
62_L118_S1.1540.51
59_L115_F1.1410.50
26_F32_L1.1330.49
89_Y95_L1.1290.49
127_K131_E1.1290.49
6_K97_K1.1100.47
83_I90_L1.1030.46
74_L91_K1.1020.46
7_L40_G1.0980.46
71_L82_K1.0980.46
116_T129_C1.0970.46
77_E122_V1.0910.45
13_A135_N1.0860.45
83_I91_K1.0850.45
17_F124_M1.0830.44
126_R132_W1.0820.44
93_I120_V1.0810.44
4_V100_N1.0810.44
43_S135_N1.0800.44
70_K111_G1.0740.44
8_L11_V1.0700.43
38_A42_I1.0690.43
30_L33_N1.0570.42
60_F68_F1.0570.42
128_I131_E1.0570.42
67_S111_G1.0550.42
22_S52_E1.0530.42
73_Y76_I1.0450.41
77_E80_D1.0430.41
51_Y59_L1.0420.41
8_L67_S1.0420.41
44_K58_I1.0410.40
91_K94_A1.0390.40
38_A41_A1.0370.40
71_L118_S1.0360.40
108_N132_W1.0290.39
131_E134_S1.0270.39
86_Q89_Y1.0270.39
51_Y55_A1.0220.39
61_V102_D1.0190.38
27_H125_K1.0180.38
5_S66_T1.0150.38
117_P120_V1.0140.38
18_H25_E1.0110.38
8_L32_L1.0100.38
20_G122_V1.0090.38
19_S26_F1.0000.37
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  
4ezcA30.148910.50.951Contact Map
4hvtA10.19868.40.953Contact Map
1yr2A10.32627.30.954Contact Map
1rijA10.12775.70.956Contact Map
1ciiA10.47525.70.956Contact Map
2xdwA10.34044.50.958Contact Map
3g21A10.18443.90.96Contact Map
2pk2A40.28373.20.961Contact Map
3sjaC50.262430.962Contact Map
3g9wC20.18442.80.962Contact 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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