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split B HVI

ID: 1513986545 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 233 (207)
Sequences: 340 (270.6)
Seq/Len: 1.643
Nf(neff/√len): 18.8

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: 1.643).

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
86_I115_V2.9611.00
2_S5_V2.1870.99
102_G111_G2.0240.99
83_S124_E1.9710.98
121_L124_E1.8340.97
66_V133_R1.6810.94
63_R82_R1.5860.91
102_G113_A1.5710.91
107_P115_V1.5690.91
23_R30_R1.5500.90
55_T58_E1.5460.90
111_G131_F1.5270.89
172_D176_W1.5170.89
32_L53_P1.4810.87
176_W206_W1.4360.85
99_W124_E1.4340.85
78_A83_S1.4190.84
82_R99_W1.3750.81
101_V134_L1.3450.79
11_N19_K1.3280.78
99_W107_P1.3120.77
92_M99_W1.3030.76
20_W225_S1.2960.75
91_R138_D1.2950.75
119_G122_V1.2690.73
51_V91_R1.2650.73
44_L111_G1.2520.72
78_A109_F1.2430.71
41_R51_V1.2300.70
217_A228_P1.2290.70
50_E116_E1.2280.70
66_V207_L1.2100.68
177_L215_V1.2100.68
152_H202_K1.2070.68
183_S196_G1.2000.67
139_W142_P1.2000.67
176_W228_P1.1880.66
71_L211_A1.1850.66
98_T137_V1.1680.64
85_A117_A1.1680.64
62_A103_V1.1660.64
73_C77_R1.1630.64
166_S180_I1.1580.63
100_C133_R1.1580.63
97_A115_V1.1540.63
16_W94_G1.1540.63
90_C97_A1.1530.63
155_L227_E1.1440.62
166_S226_L1.1400.61
70_S77_R1.1380.61
73_C81_Q1.1380.61
66_V215_V1.1360.61
59_A96_W1.1320.60
179_D196_G1.1280.60
145_A212_R1.1280.60
122_V125_G1.1200.59
39_R49_G1.1150.59
51_V97_A1.1130.58
89_L115_V1.1080.58
230_A233_R1.1030.57
8_Q83_S1.0990.57
135_I162_E1.0970.57
58_E80_L1.0930.56
44_L76_L1.0900.56
46_R129_D1.0900.56
51_V137_V1.0880.56
20_W165_A1.0870.56
25_A85_A1.0870.56
174_R207_L1.0830.55
15_S18_T1.0810.55
61_A225_S1.0800.55
180_I213_E1.0780.55
82_R91_R1.0720.54
49_G94_G1.0720.54
214_R226_L1.0660.54
93_R98_T1.0660.54
14_L30_R1.0610.53
101_V121_L1.0610.53
118_E121_L1.0570.53
44_L91_R1.0570.53
82_R124_E1.0560.53
100_C134_L1.0540.52
82_R123_E1.0520.52
217_A229_L1.0500.52
116_E134_L1.0490.52
163_T178_A1.0470.52
105_R124_E1.0470.52
33_A40_I1.0440.51
73_C124_E1.0430.51
57_E224_E1.0410.51
177_L216_L1.0410.51
78_A82_R1.0410.51
83_S99_W1.0380.51
20_W157_G1.0360.50
179_D227_E1.0330.50
35_K39_R1.0310.50
145_A168_A1.0290.50
78_A99_W1.0270.49
65_A155_L1.0250.49
82_R208_T1.0230.49
62_A124_E1.0200.49
26_V132_S1.0160.48
145_A155_L1.0140.48
74_A153_R1.0130.48
94_G97_A1.0120.48
41_R45_L1.0110.48
68_A119_G1.0090.48
28_A31_L1.0090.48
76_L82_R1.0080.47
29_A70_S1.0080.47
66_V86_I1.0060.47
81_Q117_A1.0060.47
31_L182_H1.0050.47
63_R74_A1.0050.47
26_V30_R1.0050.47
210_E214_R1.0030.47
66_V157_G1.0020.47
163_T212_R1.0010.47
83_S91_R1.0000.47
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  
4fgqA20.609430.20.934Contact Map
2hlyA10.669511.60.946Contact Map
4u65E20.596610.50.947Contact Map
2f4mA10.83262.70.96Contact Map
3isrA40.77682.20.962Contact Map
1p94A20.31761.40.966Contact Map
3vj8A10.28761.40.966Contact Map
1zugA10.304710.968Contact Map
1r69A10.27040.90.969Contact Map
2l5bA10.1330.90.97Contact 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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