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av1_cp 30-238 1-205 20-205 -force run

ID: 1513798384 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 186 (186)
Sequences: 169 (59)
Seq/Len: 0.909
Nf(neff/√len): 4.3

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: 0.909).

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
82_D89_E1.7860.89
120_T129_K1.7810.89
85_Q114_L1.6760.84
73_F115_R1.6340.82
115_R120_T1.5700.79
114_L120_T1.4850.73
114_L139_R1.4310.69
142_N145_V1.4240.69
81_V89_E1.4150.68
144_V147_N1.3840.65
88_G93_M1.3790.65
148_Q163_M1.3770.65
154_Y160_N1.3470.62
175_V178_T1.3460.62
73_F94_F1.3380.61
12_F27_V1.3360.61
81_V106_V1.3240.60
7_C10_Q1.3180.60
3_C10_Q1.3130.59
73_F83_K1.3070.59
178_T185_F1.2920.57
121_V130_E1.2870.57
182_R186_Y1.2830.57
167_A171_A1.2810.56
167_A170_H1.2810.56
10_Q20_H1.2800.56
65_N68_N1.2780.56
173_N176_Y1.2690.55
178_T184_Y1.2640.55
98_P101_A1.2590.54
147_N150_E1.2570.54
16_H25_M1.2510.54
109_D112_Q1.2340.52
146_Y149_Q1.2330.52
54_K67_T1.2310.52
1_R59_E1.2180.51
165_Y170_H1.2140.50
115_R129_K1.2140.50
36_L107_H1.2140.50
169_T177_A1.2050.50
3_C6_P1.1930.49
122_T126_Y1.1860.48
73_F107_H1.1860.48
122_T125_Q1.1820.48
38_H42_K1.1800.47
162_L177_A1.1800.47
172_S175_V1.1670.46
3_C7_C1.1670.46
122_T127_A1.1590.45
59_E62_K1.1590.45
144_V149_Q1.1590.45
16_H23_K1.1540.45
122_T128_S1.1540.45
37_T42_K1.1520.45
7_C20_H1.1510.45
121_V131_Q1.1420.44
175_V185_F1.1420.44
13_E27_V1.1350.43
116_K120_T1.1350.43
178_T182_R1.1300.43
78_R84_P1.1290.43
10_Q29_D1.1220.42
153_K156_N1.1220.42
101_A109_D1.1200.42
171_A177_A1.1150.42
51_V107_H1.1110.41
86_D89_E1.1030.41
146_Y150_E1.0990.40
40_V44_F1.0980.40
83_K94_F1.0890.39
4_E11_S1.0840.39
1_R30_V1.0800.39
6_P10_Q1.0780.38
76_R79_R1.0740.38
39_R47_K1.0710.38
81_V114_L1.0560.36
177_A180_K1.0560.36
16_H19_Q1.0490.36
89_E106_V1.0480.36
4_E24_V1.0430.35
3_C20_H1.0400.35
151_A158_S1.0340.35
112_Q129_K1.0340.35
115_R139_R1.0330.35
38_H43_R1.0330.35
5_G20_H1.0320.34
104_K112_Q1.0310.34
167_A177_A1.0220.34
93_M96_N1.0220.34
145_V149_Q1.0200.34
77_D87_F1.0190.33
86_D90_V1.0110.33
106_V148_Q1.0100.33
156_N160_N1.0090.33
10_Q17_D1.0090.33
81_V107_H1.0080.33
168_C177_A1.0070.32
37_T43_R1.0070.32
6_P20_H1.0060.32
54_K58_D1.0050.32
1_R4_E1.0040.32
144_V150_E1.0030.32
4_E10_Q1.0030.32
143_Y152_G1.0010.32
120_T139_R1.0000.32
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  
2h8eA10.33335.30.98Contact Map
3i9v220.30654.50.981Contact Map
3k7lA10.31183.90.981Contact Map
3u4vA20.37633.20.982Contact Map
1e3pA10.29032.90.982Contact Map
3rjrA40.3712.80.982Contact Map
1wqeA10.0432.80.982Contact Map
2plxB10.13982.60.983Contact Map
3u58A40.33332.20.983Contact Map
1vtze300.78492.10.983Contact 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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