May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org

VIPR2

ID: 1489202158 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 438 (390)
Sequences: 633 (364.4)
Seq/Len: 1.623
Nf(neff/√len): 18.5

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: 1.623).

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
376_C379_N2.9541.00
376_C381_E2.6321.00
97_G103_P2.5731.00
301_S304_R2.5181.00
375_Y381_E2.5031.00
57_D61_C2.4401.00
52_C61_C2.3091.00
65_A71_V2.2650.99
375_Y379_N2.2190.99
377_F381_E2.0920.99
145_S163_L2.0220.98
52_C57_D2.0220.98
52_C62_W1.9520.98
379_N382_V1.9330.98
54_G64_P1.8810.97
211_Y223_E1.8390.97
299_F326_L1.8280.97
376_C382_V1.7560.95
57_D62_W1.7490.95
378_L381_E1.7170.95
60_T73_V1.6980.94
329_S360_E1.6310.93
168_S216_N1.5700.91
385_E390_W1.5610.90
133_G141_L1.5120.88
263_R269_T1.4840.87
220_L299_F1.4720.86
302_I310_L1.4690.86
331_L335_P1.4660.86
219_W223_E1.4440.85
159_N259_W1.4420.85
368_G376_C1.4420.85
371_V379_N1.4280.84
228_H301_S1.4210.84
284_I288_I1.4080.83
99_S103_P1.4040.83
376_C380_S1.3920.82
157_T168_S1.3910.82
223_E249_W1.3880.82
133_G147_I1.3870.82
326_L329_S1.3860.81
159_N172_R1.3860.81
209_L337_F1.3800.81
202_C223_E1.3500.79
174_I178_V1.3420.78
158_R162_H1.3300.78
109_C114_P1.3270.77
98_W376_C1.3250.77
272_W287_P1.3240.77
223_E227_L1.3190.77
377_F382_V1.3130.76
155_H159_N1.3110.76
282_W286_I1.3080.76
52_C56_W1.3070.76
148_L255_C1.2970.75
372_A381_E1.2950.75
261_A264_L1.2940.75
220_L329_S1.2900.75
225_L298_L1.2830.74
368_G379_N1.2830.74
42_L54_G1.2800.74
333_L338_G1.2730.73
153_K159_N1.2720.73
375_Y378_L1.2700.73
140_S369_L1.2680.73
407_G410_F1.2670.73
177_L329_S1.2630.72
203_K268_D1.2610.72
388_R391_R1.2570.72
157_T161_I1.2520.71
254_V258_A1.2510.71
404_R407_G1.2420.71
218_F247_I1.2420.71
368_G371_V1.2310.70
371_V381_E1.2290.69
241_F244_Y1.2230.69
405_V411_S1.2150.68
224_G227_L1.2130.68
61_C76_P1.2120.68
222_V259_W1.2060.67
228_H304_R1.2060.67
224_G244_Y1.2020.67
310_L321_S1.1960.66
327_A334_I1.1960.66
97_G109_C1.1950.66
156_C169_F1.1940.66
244_Y301_S1.1920.66
157_T160_Y1.1920.66
368_G381_E1.1860.65
271_C287_P1.1820.65
133_G137_S1.1800.65
166_F173_A1.1770.65
57_D76_P1.1760.64
215_A244_Y1.1740.64
231_L325_R1.1730.64
163_L380_S1.1730.64
211_Y219_W1.1720.64
375_Y382_V1.1720.64
407_G412_R1.1710.64
153_K299_F1.1690.64
307_L311_T1.1680.64
211_Y302_I1.1650.63
302_I306_L1.1630.63
303_I307_L1.1620.63
216_N219_W1.1590.63
329_S357_I1.1570.63
106_V109_C1.1540.62
295_N309_K1.1530.62
36_T39_A1.1490.62
216_N249_W1.1480.62
296_F304_R1.1460.61
299_F329_S1.1440.61
133_G140_S1.1400.61
133_G166_F1.1390.61
56_W59_I1.1380.61
93_C109_C1.1370.61
56_W61_C1.1350.60
147_I154_L1.1350.60
158_R166_F1.1300.60
230_L323_Y1.1300.60
404_R410_F1.1290.60
130_Y161_I1.1240.59
168_S340_H1.1240.59
224_G306_L1.1240.59
281_W285_R1.1230.59
97_G104_D1.1210.59
382_V385_E1.1200.59
162_H165_L1.1180.59
262_A276_D1.1180.59
131_T180_D1.1170.59
97_G105_F1.1170.59
221_L230_L1.1140.58
34_E37_K1.1110.58
169_F172_R1.1110.58
211_Y249_W1.1080.58
148_L373_V1.1070.57
27_F30_E1.1050.57
203_K330_T1.1050.57
295_N306_L1.1030.57
254_V369_L1.1020.57
217_F322_Q1.1020.57
156_C172_R1.0940.56
406_C409_S1.0930.56
90_S108_A1.0920.56
225_L235_L1.0910.56
173_A179_K1.0900.56
96_D257_G1.0880.56
164_N247_I1.0870.55
219_W249_W1.0860.55
230_L371_V1.0770.54
407_G411_S1.0770.54
220_L326_L1.0740.54
319_D358_L1.0730.54
154_L211_Y1.0660.53
369_L373_V1.0630.53
282_W289_L1.0610.53
178_V186_S1.0600.53
262_A283_V1.0590.52
302_I372_A1.0580.52
226_Y248_G1.0530.52
336_L372_A1.0510.52
144_G159_N1.0500.52
98_W103_P1.0490.51
234_M374_L1.0480.51
252_P259_W1.0480.51
216_N291_S1.0480.51
385_E388_R1.0470.51
220_L231_L1.0470.51
227_L249_W1.0450.51
373_V388_R1.0450.51
211_Y227_L1.0450.51
383_Q390_W1.0440.51
38_C42_L1.0440.51
261_A265_Y1.0420.51
202_C211_Y1.0410.51
344_F365_S1.0390.50
341_Y365_S1.0390.50
272_W330_T1.0390.50
409_S412_R1.0380.50
216_N340_H1.0370.50
61_C65_A1.0340.50
161_I165_L1.0320.50
55_V64_P1.0260.49
159_N173_A1.0180.48
334_I361_L1.0170.48
310_L372_A1.0150.48
108_A114_P1.0130.48
160_Y180_D1.0080.47
159_N179_K1.0080.47
372_A376_C1.0060.47
295_N302_I1.0050.47
406_C411_S1.0040.47
72_T90_S1.0030.47
206_L214_M1.0030.47
373_V378_L1.0020.46
271_C283_V1.0020.46
210_Q324_K1.0010.46
236_P311_T1.0010.46
110_G114_P1.0010.46
223_E248_G1.0000.46
222_V247_I1.0000.46
26_R30_E1.0000.46
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  
4k5yA30.57081000.592Contact Map
4l6rA10.83331000.676Contact Map
4jkvA20.81741000.813Contact Map
4qinA10.687299.90.831Contact Map
2x57A30.239799.90.842Contact Map
4hj0A20.200999.90.849Contact Map
3c5tA10.214699.90.849Contact Map
4rwfA1099.90.85Contact Map
2xdgA20.203299.90.852Contact Map
2qkhA10.207899.90.853Contact 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.

Page generated in 1.8194 seconds.