OPENSEQ.org
3wbf

ID: 1517967808 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 299 (299)
Sequences: 426 (239.9)
Seq/Len: 1.425
Nf(neff/√len): 13.9

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: 1.425).

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
187_L196_V4.8621.00
165_R219_V3.3851.00
116_V268_A3.2741.00
194_A197_E3.1381.00
195_E199_A3.0601.00
78_E100_L2.9931.00
187_L193_F2.8641.00
161_I167_A2.7331.00
198_R202_T2.5871.00
105_D109_R2.5501.00
87_T100_L2.5421.00
271_Q281_I2.5001.00
158_V183_V2.3731.00
52_V58_L2.3490.99
193_F196_V2.2980.99
134_E142_T2.2720.99
7_A61_V2.2540.99
128_I283_V2.2410.99
116_V281_I2.2280.99
289_G297_K2.2130.99
18_A65_L2.1830.99
106_P110_E2.1380.99
172_I184_Y2.1340.99
78_E87_T2.0220.98
197_E201_K2.0110.98
162_P199_A1.9730.98
125_T247_F1.9370.97
162_P195_E1.9110.97
96_D99_D1.8880.97
55_I64_A1.8530.96
247_F283_V1.8330.96
132_L247_F1.8080.95
6_V28_M1.8010.95
107_V111_H1.7900.95
165_R188_E1.7800.95
264_A278_M1.7650.94
148_P172_I1.7620.94
32_G52_V1.7020.93
180_K212_R1.6830.92
80_M83_R1.6330.91
86_H268_A1.6250.91
55_I81_L1.6160.90
33_V42_T1.5300.87
87_T115_A1.5160.86
182_A214_T1.5070.85
140_G233_R1.4820.84
7_A64_A1.4660.83
132_L282_P1.4510.82
162_P188_E1.4470.82
293_A297_K1.4390.82
113_A272_K1.3850.78
132_L283_V1.3770.78
131_A279_I1.3590.76
150_M168_L1.3590.76
128_I247_F1.3590.76
116_V119_A1.3440.75
166_D225_V1.3400.75
158_V167_A1.3360.75
87_T275_C1.3300.74
32_G58_L1.3270.74
66_L246_R1.3240.74
8_V19_L1.3180.73
33_V44_P1.3170.73
24_A139_K1.3010.72
161_I199_A1.2910.71
114_A273_P1.2900.71
16_R33_V1.2830.70
236_V242_N1.2810.70
22_V25_A1.2800.70
112_G162_P1.2800.70
33_V49_V1.2690.69
90_S261_M1.2330.66
240_T291_R1.2320.66
131_A135_F1.2310.66
104_L279_I1.2230.65
65_L261_M1.2180.64
57_Q99_D1.2170.64
195_E201_K1.2170.64
93_I208_R1.2120.64
9_V81_L1.1970.62
225_V241_H1.1960.62
102_R105_D1.1920.62
119_A258_A1.1900.62
125_T240_T1.1870.61
22_V262_V1.1560.58
114_A272_K1.1560.58
244_L250_R1.1400.57
168_L225_V1.1380.57
102_R296_R1.1280.56
133_L245_F1.1150.54
268_A281_I1.1150.54
9_V64_A1.1130.54
78_E104_L1.1120.54
167_A252_N1.1080.54
83_R110_E1.0990.53
50_R165_R1.0950.52
64_A81_L1.0910.52
165_R296_R1.0910.52
125_T132_L1.0860.51
191_A280_E1.0840.51
16_R187_L1.0750.50
22_V28_M1.0700.50
137_A245_F1.0690.50
172_I214_T1.0650.49
290_D293_A1.0640.49
119_A278_M1.0610.49
100_L275_C1.0600.49
21_A196_V1.0530.48
119_A268_A1.0530.48
9_V115_A1.0500.48
76_Y80_M1.0480.48
291_R295_I1.0390.47
54_D57_Q1.0370.46
22_V60_G1.0370.46
155_S159_K1.0280.45
44_P47_T1.0260.45
271_Q282_P1.0250.45
198_R281_I1.0240.45
166_D219_V1.0220.45
157_A161_I1.0190.45
9_V66_L1.0190.45
90_S259_Q1.0100.44
5_R115_A1.0090.44
157_A160_A1.0080.43
172_I175_G1.0070.43
55_I276_Y1.0050.43
114_A268_A1.0000.43
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  
3bioA20.97991000.52Contact Map
3wgqA20.991000.557Contact Map
3wycA201000.559Contact Map
1f06A20.98331000.574Contact Map
3wb9A30.99331000.588Contact Map
1p9lA20.779399.80.847Contact Map
4ywjA20.836199.80.85Contact Map
3ijpA20.80699.80.855Contact Map
1dihA10.842899.70.867Contact Map
2czcA40.886399.60.877Contact 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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