OPENSEQ.org
twa1-757seq

ID: 1516896718 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 228 (218)
Sequences: 1238 (857.5)
Seq/Len: 5.679
Nf(neff/√len): 58.1

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: 5.679).

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_I176_V4.0841.00
117_E120_A3.3401.00
78_Q81_E3.2991.00
77_G169_R2.6201.00
80_Q108_H2.4021.00
74_I176_V2.3531.00
177_N181_L2.3061.00
103_H175_E2.2001.00
34_M46_A2.1781.00
111_E169_R2.1081.00
30_N49_F2.1071.00
112_L121_A2.0531.00
101_Y105_Q2.0021.00
33_I37_L1.9991.00
67_R177_N1.9731.00
110_I114_R1.8611.00
82_A104_L1.8431.00
67_R181_L1.8051.00
154_S157_E1.7251.00
77_G111_E1.6391.00
17_E21_N1.5870.99
145_R162_D1.5400.99
9_E13_D1.5380.99
213_Y216_M1.5330.99
9_E12_K1.4890.99
8_D13_D1.4050.98
67_R173_W1.4000.98
149_L164_L1.3710.98
107_Q111_E1.3600.97
107_Q168_Q1.3390.97
111_E114_R1.3310.97
198_L201_W1.3280.97
149_L152_F1.3140.97
11_T17_E1.2620.96
11_T14_E1.2540.95
85_L89_L1.2390.95
218_D221_K1.2340.95
74_I79_I1.2230.95
76_K81_E1.2230.95
212_K215_K1.2220.94
33_I36_Y1.2190.94
109_L144_E1.2110.94
83_I124_F1.2070.94
90_H180_V1.1920.93
109_L113_I1.1890.93
151_A155_P1.1870.93
17_E20_N1.1800.93
108_H112_L1.1730.93
72_E76_K1.1670.93
217_T221_K1.1590.92
20_N24_V1.1550.92
10_I14_E1.1450.92
78_Q115_Q1.1440.92
17_E22_L1.1320.91
190_P193_A1.1310.91
15_W19_L1.1310.91
13_D17_E1.1310.91
125_A147_L1.1300.91
10_I13_D1.1270.91
125_A129_L1.1200.90
69_K85_L1.1170.90
33_I205_E1.1160.90
83_I87_N1.1140.90
216_M221_K1.1130.90
84_A123_E1.1090.90
8_D11_T1.0960.89
211_V214_P1.0930.89
125_A128_Q1.0830.88
197_K201_W1.0810.88
34_M38_V1.0770.88
35_N203_Q1.0680.87
106_Q142_E1.0660.87
13_D18_K1.0660.87
18_K21_N1.0630.87
217_T220_S1.0610.87
65_D68_I1.0570.87
66_E89_L1.0520.86
9_E17_E1.0510.86
102_F109_L1.0450.86
216_M219_L1.0440.86
13_D20_N1.0420.86
8_D14_E1.0400.85
212_K216_M1.0360.85
91_P94_L1.0340.85
30_N33_I1.0330.85
108_H128_Q1.0330.85
207_D213_Y1.0230.84
46_A82_A1.0220.84
218_D225_E1.0200.84
89_L122_L1.0180.84
94_L100_L1.0180.84
14_E20_N1.0170.84
12_K18_K1.0170.84
125_A148_A1.0170.84
149_L169_R1.0170.84
210_K214_P1.0130.83
217_T222_G1.0120.83
67_R180_V1.0110.83
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  
4zheA401000.403Contact Map
2xtcA20.324685.50.901Contact Map
1uujA40.3465600.919Contact Map
2d68A20.342159.10.92Contact Map
2j4bA50.583344.50.927Contact Map
3eupA20.837724.10.936Contact Map
2vxgA20.561419.80.939Contact Map
2nxpA80.649118.90.939Contact Map
4j8fA10.679817.70.94Contact Map
3u0rA10.723715.90.941Contact 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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