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twa1

ID: 1516820589 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 228 (217)
Sequences: 683 (508.8)
Seq/Len: 3.147
Nf(neff/√len): 34.5

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: 3.147).

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_V3.9191.00
78_Q81_E3.8651.00
117_E120_A2.3451.00
80_Q108_H2.3141.00
103_H175_E2.2001.00
67_R177_N2.1391.00
112_L121_A1.9331.00
6_K9_E1.9140.99
177_N181_L1.8550.99
33_I37_L1.8390.99
77_G169_R1.7600.99
111_E114_R1.7170.99
74_I176_V1.7130.99
67_R181_L1.7070.99
213_Y216_M1.6600.98
107_Q168_Q1.6550.98
145_R162_D1.6540.98
30_N49_F1.6190.98
17_E21_N1.5690.97
34_M46_A1.5470.97
149_L164_L1.5380.97
190_P193_A1.5370.97
6_K10_I1.5300.97
101_Y105_Q1.5180.96
154_S157_E1.5160.96
111_E169_R1.5090.96
94_L100_L1.4330.95
2_S5_E1.4320.95
83_I124_F1.4210.94
110_I114_R1.4090.94
6_K11_T1.4080.94
2_S6_K1.3840.93
7_P10_I1.3790.93
5_E11_T1.3760.93
3_Y6_K1.3250.91
212_K218_D1.3130.90
4_A10_I1.3080.90
8_D13_D1.3060.90
151_A155_P1.2930.90
74_I79_I1.2770.89
5_E17_E1.2650.88
43_K65_D1.2650.88
108_H112_L1.2590.88
198_L201_W1.2480.87
149_L152_F1.2470.87
67_R173_W1.2390.87
77_G111_E1.2340.86
50_R55_I1.2330.86
107_Q172_V1.2320.86
34_M38_V1.2260.86
42_F133_G1.2200.86
6_K13_D1.2180.85
94_L143_M1.2020.84
4_A7_P1.1990.84
9_E13_D1.1980.84
87_N143_M1.1880.83
5_E8_D1.1850.83
17_E22_L1.1820.83
30_N143_M1.1730.82
102_F113_I1.1680.82
4_A9_E1.1630.82
9_E12_K1.1550.81
30_N33_I1.1430.80
116_R121_A1.1420.80
207_D213_Y1.1420.80
3_Y8_D1.1320.79
11_T17_E1.1230.78
107_Q199_L1.1110.77
2_S11_T1.1090.77
3_Y14_E1.1060.77
90_H183_Y1.0840.75
29_M36_Y1.0730.74
82_A104_L1.0720.74
140_L144_E1.0720.74
77_G177_N1.0710.74
125_A148_A1.0650.73
11_T212_K1.0610.73
4_A11_T1.0600.73
206_L214_P1.0580.72
99_Y139_C1.0550.72
12_K18_K1.0470.71
82_A173_W1.0430.71
8_D216_M1.0410.71
109_L144_E1.0390.70
72_E76_K1.0320.70
73_M78_Q1.0300.69
77_G91_P1.0290.69
149_L163_L1.0290.69
107_Q147_L1.0270.69
198_L202_A1.0240.69
169_R177_N1.0150.68
114_R164_L1.0090.67
109_L113_I1.0080.67
42_F177_N1.0040.67
199_L213_Y1.0020.66
4_A8_D1.0010.66
15_W19_L1.0000.66
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  
4zheA401000.514Contact Map
2xtcA20.324686.30.914Contact Map
2d68A20.342171.20.925Contact Map
1uujA40.342141.90.938Contact Map
2j4bA50.583322.30.946Contact Map
2xpiA20.7193210.946Contact Map
4bzjA20.820218.90.948Contact Map
4ui9F20160.949Contact Map
3uq3A10.61415.50.949Contact Map
4apoA20.600914.80.95Contact 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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