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v1 -force run

ID: 1514663401 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 177 (177)
Sequences: 176 (61)
Seq/Len: 0.994
Nf(neff/√len): 4.6

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: 0.994).

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
77_D84_E1.8010.91
115_T124_K1.7250.88
68_F110_R1.5620.80
83_G88_M1.5520.80
110_R115_T1.5520.80
143_Q158_M1.5070.77
80_Q109_L1.4770.75
170_V173_T1.4770.75
11_H20_M1.4730.75
137_N140_V1.4220.71
76_V84_E1.4160.71
8_E22_I1.4120.70
162_A166_A1.4100.70
162_A165_H1.4030.70
5_Q15_H1.3880.68
68_F89_F1.3860.68
109_L115_T1.3840.68
2_C5_Q1.3840.68
60_N63_N1.3540.66
93_P96_A1.3540.66
139_V142_N1.3470.65
149_Y155_N1.3440.65
2_C15_H1.3220.63
168_N171_Y1.2920.60
49_K62_T1.2770.59
141_Y144_Q1.2750.59
173_T177_R1.2460.56
31_L102_H1.2350.55
73_R79_P1.2330.55
160_Y165_H1.2300.55
142_N145_E1.2290.54
116_V125_E1.2270.54
9_S20_M1.2140.53
166_A172_A1.2140.53
76_V101_V1.2020.52
104_D107_Q1.2010.52
167_S170_V1.2010.52
109_L134_R1.1980.52
33_H37_K1.1950.51
162_A172_A1.1870.51
5_Q24_D1.1850.50
1_P5_Q1.1710.49
32_T37_K1.1690.49
11_H18_K1.1660.49
113_Y128_L1.1610.48
8_E12_D1.1610.48
172_A175_K1.1600.48
54_E57_K1.1580.48
164_T172_A1.1460.47
9_S16_I1.1450.47
157_L172_A1.1380.46
16_I20_M1.1330.46
110_R124_K1.1330.46
1_P15_H1.1260.45
7_F22_I1.1200.44
71_R74_R1.1200.44
110_R134_R1.1190.44
139_V144_Q1.1070.43
141_Y145_E1.1040.43
68_F102_H1.0970.42
117_T120_Q1.0920.42
170_V177_R1.0910.42
84_E101_V1.0880.42
81_D84_E1.0880.42
116_V126_Q1.0850.41
49_K53_D1.0830.41
31_L80_Q1.0800.41
12_D19_V1.0790.41
11_H121_Y1.0790.41
111_K115_T1.0760.40
12_D15_H1.0640.39
155_N170_V1.0630.39
117_T121_Y1.0610.39
117_T122_A1.0610.39
148_K151_N1.0600.39
5_Q12_D1.0570.39
96_A104_D1.0570.39
172_A177_R1.0530.38
35_V39_F1.0530.38
154_E157_L1.0500.38
81_D85_V1.0490.38
117_T123_S1.0490.38
88_M129_V1.0430.38
34_R42_K1.0360.37
107_Q124_K1.0310.36
162_A167_S1.0260.36
33_H38_G1.0260.36
3_K15_H1.0240.36
50_I62_T1.0240.36
76_V109_L1.0220.36
4_V12_D1.0200.36
83_G89_F1.0150.35
31_L109_L1.0140.35
6_S10_R1.0100.35
32_T38_G1.0070.34
155_N159_L1.0070.34
151_N155_N1.0060.34
72_D82_F1.0030.34
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  
3cxkA20.29388.20.976Contact Map
1e3pA10.28256.70.977Contact Map
2kd2A10.18085.40.978Contact Map
4wsbB10.63844.10.98Contact Map
1svbA10.33333.80.98Contact Map
4n4bA10.19773.60.98Contact Map
2lw6A10.26552.60.982Contact Map
1vtze300.83622.60.982Contact Map
2plxB10.14692.40.982Contact Map
2h8eA10.35031.80.983Contact 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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