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bv1 30-245 20-216 -force run

ID: 1513452196 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 197 (197)
Sequences: 153 (45.5)
Seq/Len: 0.777
Nf(neff/√len): 3.2

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: 0.777).

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
5_Q38_Y2.1700.96
21_F61_M2.0720.94
84_V192_Y2.0630.94
4_N50_L1.9570.92
56_Q108_S1.7680.85
3_E15_N1.6820.81
181_W187_S1.5450.73
50_L160_R1.5370.72
171_T195_F1.5290.72
28_V144_L1.5250.71
65_I147_K1.4980.69
76_I127_V1.4960.69
3_E38_Y1.4820.68
23_T26_R1.4580.66
97_F116_R1.4440.65
49_T105_G1.4150.63
148_R177_V1.3550.58
82_P98_G1.3480.57
1_V177_V1.3360.56
12_L24_Y1.3280.56
15_N38_Y1.3270.56
76_I197_L1.3160.55
164_N168_G1.3080.54
44_L197_L1.3010.53
70_G97_F1.2960.53
70_G116_R1.2960.53
71_V132_D1.2920.53
3_E107_L1.2800.52
14_Q112_A1.2770.51
38_Y76_I1.2680.51
92_T149_Y1.2630.50
65_I149_Y1.2620.50
6_F168_G1.2480.49
11_V23_T1.2430.48
22_V195_F1.2370.48
113_L138_L1.2290.47
90_L176_L1.2230.47
78_V125_R1.2220.47
23_T45_R1.2150.46
49_T187_S1.2120.46
22_V136_I1.1990.45
53_E119_I1.1980.45
8_P106_N1.1940.44
21_F125_R1.1870.44
145_S172_K1.1770.43
175_L185_A1.1710.42
26_R160_R1.1490.40
98_G116_R1.1370.39
178_Y184_D1.1330.39
80_R119_I1.1280.39
154_S159_E1.1280.39
5_Q163_C1.1260.38
19_S102_H1.1230.38
24_Y85_G1.1220.38
82_P97_F1.1200.38
82_P116_R1.1200.38
79_G98_G1.1170.38
79_G97_F1.1140.38
79_G116_R1.1140.38
156_S171_T1.1060.37
79_G82_P1.1010.36
26_R159_E1.1000.36
22_V31_V1.0990.36
66_S119_I1.0980.36
35_T80_R1.0970.36
86_Q195_F1.0960.36
20_T29_R1.0900.36
1_V56_Q1.0830.35
154_S177_V1.0820.35
18_L134_L1.0790.35
76_I96_L1.0780.35
52_I95_A1.0770.35
152_W155_F1.0770.35
152_W157_D1.0770.35
76_I87_S1.0740.34
57_G64_P1.0650.34
9_E21_F1.0610.33
45_R119_I1.0600.33
12_L69_Q1.0520.33
12_L156_S1.0520.33
41_L90_L1.0490.32
66_S127_V1.0490.32
15_N107_L1.0440.32
155_F165_G1.0440.32
155_F167_Y1.0440.32
157_D165_G1.0440.32
157_D167_Y1.0440.32
45_R86_Q1.0430.32
84_V159_E1.0420.32
119_I195_F1.0390.32
87_S115_D1.0360.31
73_S76_I1.0330.31
119_I176_L1.0300.31
159_E176_L1.0280.31
32_P114_K1.0260.31
59_T112_A1.0250.31
26_R45_R1.0230.30
2_Q71_V1.0180.30
193_V196_E1.0170.30
165_G173_N1.0140.30
167_Y173_N1.0140.30
108_S114_K1.0130.30
181_W184_D1.0130.30
67_T106_N1.0120.30
37_T117_Y1.0090.29
79_G95_A1.0020.29
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  
4bz7A40.31984.10.977Contact Map
2ixkA20.63964.10.977Contact Map
3i6uA20.482240.978Contact Map
4hdqC10.02543.30.978Contact Map
3ilcA10.47213.20.979Contact Map
3k44A40.24872.70.979Contact Map
2xk0A10.34522.30.98Contact Map
5a3gA102.30.98Contact Map
1dzrA20.62941.80.981Contact Map
1ep0A10.64971.70.981Contact 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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