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

VIPR1

ID: 1487714484 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 457 (403)
Sequences: 514 (278.7)
Seq/Len: 1.275
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: 1.275).

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
389_C392_N2.8881.00
389_C394_E2.5971.00
388_Y392_N2.4881.00
388_Y394_E2.4000.99
314_C317_R2.2960.99
63_C72_C2.2630.99
68_D72_C2.1550.98
161_T179_M2.0040.97
63_C73_W1.9890.97
390_F394_E1.9830.97
149_G157_L1.9450.97
392_N395_V1.9360.96
76_T82_V1.9250.96
63_C68_D1.8530.95
224_Y236_E1.8180.94
312_F339_L1.7770.93
54_A65_K1.6340.89
65_K75_A1.6330.89
297_I301_I1.6260.89
171_H175_N1.6080.88
342_S373_E1.5900.87
164_L269_F1.5680.86
388_Y395_V1.5500.85
389_C393_G1.5380.85
68_D73_W1.5340.85
388_Y391_L1.5060.83
71_T84_L1.4970.83
294_W298_K1.4940.82
389_C395_V1.4900.82
391_L394_E1.4740.81
277_R283_Y1.4710.81
344_L348_P1.4670.81
149_G153_S1.4660.81
150_Y160_A1.4610.80
315_I323_L1.4450.79
276_A296_I1.4410.79
122_C127_K1.4330.79
255_F258_Y1.4320.79
390_F395_V1.4250.78
236_E240_L1.4220.78
223_Q228_A1.4150.77
172_C185_F1.4100.77
420_H423_G1.4050.77
398_E403_W1.3860.75
418_Y421_P1.3770.75
229_N353_H1.3620.73
384_V392_N1.3610.73
222_F350_F1.3580.73
173_T184_S1.3430.72
146_Y177_I1.3300.71
175_N273_W1.3240.70
216_K282_D1.3240.70
190_A194_I1.3230.70
347_I374_L1.3210.70
236_E263_W1.3160.70
175_N188_R1.3110.69
173_T176_Y1.3110.69
233_L312_F1.3090.69
342_S370_M1.3040.69
268_T272_V1.2930.68
178_H181_L1.2850.67
384_V394_E1.2800.67
244_L338_R1.2790.67
164_L386_I1.2780.67
401_R404_R1.2770.66
67_W70_L1.2760.66
339_L342_S1.2750.66
312_F398_E1.2690.66
174_R178_H1.2610.65
433_Q445_R1.2610.65
153_S157_L1.2570.65
215_C236_E1.2540.64
156_T382_F1.2440.63
188_R195_K1.2360.63
169_K175_N1.2340.63
156_T198_A1.2310.62
63_C67_W1.2290.62
295_W299_G1.2210.61
147_T196_D1.2180.61
264_G388_Y1.2160.61
234_L243_L1.2160.61
312_F342_S1.2120.60
388_Y393_G1.2120.60
297_I338_R1.2090.60
417_K421_P1.2060.60
339_L374_L1.2030.60
146_Y150_Y1.2010.59
224_Y240_L1.1910.58
349_L385_A1.1880.58
159_V183_I1.1850.58
231_F261_I1.1820.58
102_S121_A1.1800.57
193_F342_S1.1800.57
340_A347_I1.1790.57
173_T177_I1.1700.56
418_Y424_G1.1660.56
146_Y164_L1.1660.56
253_K355_I1.1650.56
71_T352_V1.1560.55
420_H432_T1.1550.55
232_W236_E1.1520.55
233_L342_S1.1510.55
169_K312_F1.1480.54
158_L186_I1.1430.54
67_W72_C1.1430.54
175_N195_K1.1410.54
424_G430_C1.1380.53
233_L244_L1.1330.53
286_W343_T1.1300.53
425_S429_T1.1290.52
239_Y262_G1.1270.52
316_I320_L1.1260.52
175_N196_D1.1260.52
190_A271_M1.1260.52
429_T444_A1.1250.52
342_S398_E1.1240.52
431_S434_V1.1240.52
147_T164_L1.1230.52
105_C122_C1.1220.52
147_T176_Y1.1210.52
63_C74_P1.1210.52
216_K343_T1.1130.51
160_A175_N1.1120.51
432_T443_G1.1100.51
295_W302_L1.1100.51
434_V443_G1.1040.50
184_S229_N1.1040.50
184_S353_H1.1000.50
237_G319_L1.0990.49
235_V273_W1.0980.49
184_S277_R1.0970.49
233_L339_L1.0960.49
37_C46_Q1.0950.49
346_L351_G1.0950.49
170_L224_Y1.0930.49
158_L275_I1.0930.49
287_D342_S1.0910.49
420_H424_G1.0910.49
195_K312_F1.0900.49
195_K347_I1.0890.48
241_Y246_V1.0890.48
153_S167_F1.0870.48
174_R181_L1.0840.48
185_F188_R1.0830.48
419_R422_S1.0820.48
229_N263_W1.0800.48
381_G384_V1.0740.47
182_F189_A1.0740.47
308_N322_K1.0740.47
315_I322_K1.0720.47
229_N232_W1.0700.47
224_Y263_W1.0690.46
430_C434_V1.0680.46
188_R312_F1.0680.46
176_Y196_D1.0670.46
270_T274_T1.0640.46
309_F370_M1.0630.46
421_P424_G1.0620.46
109_G112_H1.0610.46
68_D87_P1.0530.45
247_S261_I1.0520.45
189_A195_K1.0490.45
309_F379_F1.0450.44
227_M403_W1.0430.44
72_C87_P1.0420.44
381_G392_N1.0400.44
174_R182_F1.0380.43
103_R188_R1.0360.43
339_L398_E1.0360.43
236_E239_Y1.0320.43
275_I279_H1.0320.43
419_R428_A1.0310.43
309_F317_R1.0300.43
156_T162_A1.0300.43
228_A258_Y1.0290.43
428_A444_A1.0290.43
289_I379_F1.0270.42
275_I278_I1.0240.42
151_G352_V1.0240.42
68_D105_C1.0240.42
312_F353_H1.0230.42
359_F362_D1.0220.42
238_L248_F1.0180.42
246_V282_D1.0160.41
235_V261_I1.0140.41
215_C224_Y1.0140.41
310_I313_I1.0130.41
312_F374_L1.0130.41
196_D312_F1.0130.41
418_Y430_C1.0120.41
434_V445_R1.0100.41
160_A169_K1.0090.41
170_L178_H1.0080.41
344_L347_I1.0080.41
325_P387_L1.0080.41
421_P425_S1.0060.40
149_G167_F1.0040.40
227_M350_F1.0040.40
420_H425_S1.0030.40
236_E262_G1.0020.40
149_G163_I1.0000.40
120_I270_T1.0000.40
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  
4k5yA30.5471000.625Contact Map
4l6rA10.81621000.696Contact Map
4jkvA20.76811000.836Contact Map
4qinA10.665299.90.845Contact Map
2qkhA10.201399.90.848Contact Map
4hj0A20.196999.90.854Contact Map
3c5tA10.210199.90.855Contact Map
4ersA10.196999.90.857Contact Map
4rwfA1099.90.862Contact Map
3n94A10.277999.90.866Contact 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 0.9455 seconds.