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OPENSEQ.org

HET-S -force run

ID: 1428409948 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 289 (283)
Sequences: 236 (207.7)
Seq/Len: 0.834
Nf(neff/√len): 12.3

Jackhmmer Results: (2015_01_07)
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: 0.834).

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
25_F167_V2.0170.94
13_G16_G1.9680.93
80_A174_F1.9680.93
51_R168_D1.9590.93
37_D153_G1.9150.92
47_I83_I1.6750.82
54_R208_D1.6700.82
145_K160_V1.6010.78
278_G282_G1.5860.77
3_E10_G1.5720.77
51_R171_E1.5570.76
27_Y136_R1.5500.75
3_E6_E1.5310.74
138_K144_K1.5190.73
100_R193_D1.5190.73
48_A80_A1.4690.69
101_Y152_D1.4600.69
11_A219_I1.4520.68
80_A84_V1.3880.63
218_K222_I1.3760.62
187_E208_D1.3640.61
4_P8_V1.3530.60
42_Q61_I1.3240.58
10_G32_R1.3170.57
27_Y98_S1.3050.56
21_C50_V1.3040.56
25_F45_L1.2990.55
9_A25_F1.2930.55
129_L166_F1.2830.54
122_G126_H1.2740.53
90_L166_F1.2670.53
44_R175_P1.2620.52
18_F28_V1.2550.52
265_E275_V1.2540.51
15_A204_A1.2360.50
35_G133_V1.2340.50
30_L48_A1.2190.48
63_D160_V1.2120.48
37_D149_A1.1960.46
240_Q244_V1.1960.46
35_G137_Q1.1830.45
69_S163_V1.1830.45
279_N282_G1.1800.45
250_L253_E1.1780.45
5_F10_G1.1750.45
21_C52_L1.1750.45
271_G276_L1.1720.44
93_S119_K1.1710.44
266_T276_L1.1640.44
261_T265_E1.1640.44
8_V168_D1.1620.43
115_D219_I1.1620.43
51_R56_G1.1620.43
239_V243_N1.1610.43
21_C101_Y1.1560.43
266_T272_E1.1530.43
256_I261_T1.1520.43
90_L159_I1.1500.42
250_L254_I1.1480.42
43_L87_I1.1460.42
17_L170_L1.1410.42
50_V187_E1.1410.42
263_S266_T1.1370.41
263_S272_E1.1370.41
259_Q264_V1.1360.41
169_E173_A1.1310.41
54_R151_Y1.1310.41
98_S103_L1.1270.40
268_V280_E1.1270.40
21_C167_V1.1240.40
253_E263_S1.1210.40
271_G280_E1.1200.40
247_A258_D1.1150.39
52_L197_L1.1130.39
21_C152_D1.1110.39
268_V281_Y1.1090.39
266_T269_G1.1080.39
21_C197_L1.1050.39
204_A213_D1.1040.38
132_L135_R1.1030.38
278_G281_Y1.0930.38
260_T266_T1.0930.38
51_R91_F1.0920.37
154_K188_I1.0910.37
93_S201_K1.0910.37
244_V252_G1.0850.37
257_S261_T1.0840.37
96_K121_I1.0840.37
28_V188_I1.0780.36
123_R133_V1.0780.36
251_H255_R1.0770.36
272_E280_E1.0730.36
153_G162_Q1.0720.36
15_A141_S1.0710.36
271_G275_V1.0710.36
272_E276_L1.0680.35
96_K172_K1.0680.35
24_C187_E1.0670.35
28_V180_C1.0630.35
166_F191_V1.0610.35
273_S278_G1.0570.35
18_F27_Y1.0570.35
41_C48_A1.0540.34
270_K274_K1.0520.34
261_T264_V1.0510.34
5_F8_V1.0500.34
23_A185_E1.0490.34
29_Q32_R1.0490.34
56_G61_I1.0490.34
258_D266_T1.0470.34
15_A193_D1.0460.34
266_T274_K1.0430.33
258_D261_T1.0430.33
152_D188_I1.0370.33
260_T267_V1.0360.33
160_V176_I1.0310.33
263_S270_K1.0280.32
166_F173_A1.0280.32
193_D203_A1.0270.32
254_I259_Q1.0270.32
100_R181_H1.0270.32
43_L117_D1.0260.32
5_F61_I1.0250.32
249_A255_R1.0230.32
264_V271_G1.0220.32
245_V264_V1.0220.32
251_H256_I1.0210.32
265_E268_V1.0200.32
244_V251_H1.0180.32
48_A83_I1.0150.31
5_F9_A1.0140.31
56_G157_E1.0140.31
33_H145_K1.0120.31
16_G28_V1.0120.31
53_S145_K1.0110.31
269_G276_L1.0100.31
268_V271_G1.0080.31
256_I260_T1.0070.31
69_S72_P1.0050.31
253_E266_T1.0040.30
101_Y173_A1.0030.30
254_I257_S1.0020.30
35_G95_Q1.0000.30
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: (31Jan15)
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  
2wvqA20.7371000.381Contact Map
2kj3A30.252699.60.777Contact Map
2msvA10.4637150.961Contact Map
4btfA10.615912.90.962Contact Map
4ogqG10.114212.50.962Contact Map
3he4A40.155712.30.962Contact Map
1q90G10.0911.30.963Contact Map
3pltA30.69990.965Contact Map
1w3iA40.33228.40.965Contact Map
5rubA20.19728.40.965Contact 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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