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bubr1 1-430

ID: 1460039068 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 430 (414)
Sequences: 906 (639)
Seq/Len: 2.188
Nf(neff/√len): 31.4

Jackhmmer Results: (2015_08)
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: 2.188).

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
163_E199_R3.2051.00
156_I188_R2.5801.00
105_A124_L2.2761.00
63_E104_R2.1811.00
86_E127_K2.1090.99
85_T101_L2.0800.99
82_I124_L1.9390.99
366_L369_R1.9070.99
175_F196_F1.8170.98
172_D193_H1.8160.98
177_E181_Q1.8120.98
115_Y120_R1.8100.98
196_F199_R1.7690.98
163_E175_F1.7650.98
65_E80_R1.7600.98
167_N170_K1.7120.97
76_D80_R1.6390.96
63_E81_Y1.6020.95
310_A313_W1.6010.95
175_F193_H1.5930.95
121_F125_W1.5730.94
122_L142_L1.5700.94
82_I105_A1.5560.94
87_Q127_K1.5370.93
71_G78_W1.5230.93
193_H196_F1.4910.92
192_Q195_Q1.4910.92
73_D120_R1.4760.92
129_G151_L1.4630.91
224_R227_L1.4610.91
147_I178_G1.4570.91
163_E196_F1.4560.91
85_T89_Y1.4390.90
304_K313_W1.4280.90
103_E128_L1.4250.90
342_P345_E1.3860.88
25_S45_L1.3850.88
306_N313_W1.3810.87
125_W142_L1.3690.87
74_P120_R1.3680.87
119_P151_L1.3580.86
109_L121_F1.3570.86
143_H158_W1.3540.86
102_L135_P1.3290.85
135_P145_Q1.3150.84
28_N35_G1.3080.83
367_S371_P1.3080.83
73_D115_Y1.3020.83
293_Q297_A1.2980.83
172_D175_F1.2960.83
274_V277_E1.2860.82
125_W178_G1.2830.82
78_W134_E1.2770.81
142_L147_I1.2770.81
29_V38_M1.2760.81
84_W89_Y1.2750.81
69_Y78_W1.2640.80
340_F345_E1.2620.80
293_Q298_P1.2500.79
158_W167_N1.2490.79
125_W163_E1.2470.79
22_W29_V1.2410.79
339_S344_V1.2400.79
81_Y139_Y1.2370.78
32_L36_R1.2310.78
74_P115_Y1.2230.77
132_C138_M1.2190.77
122_L148_G1.2150.77
142_L148_G1.2150.77
78_W105_A1.2120.76
340_F346_E1.2110.76
300_M305_E1.2100.76
156_I178_G1.2050.76
122_L151_L1.2030.76
89_Y96_S1.2030.76
13_E17_L1.2020.75
80_R128_L1.2000.75
97_N103_E1.1860.74
163_E171_A1.1840.74
125_W148_G1.1840.74
115_Y118_D1.1810.74
370_K374_E1.1780.73
374_E381_R1.1770.73
367_S370_K1.1760.73
109_L120_R1.1720.73
121_F157_S1.1720.73
101_L121_F1.1700.73
359_E362_I1.1650.72
31_P34_Q1.1640.72
122_L125_W1.1640.72
117_S151_L1.1630.72
305_E310_A1.1520.71
158_W184_E1.1440.70
291_T295_W1.1410.70
162_Y167_N1.1410.70
318_S321_H1.1390.70
125_W138_M1.1380.70
19_G22_W1.1370.70
29_V45_L1.1360.69
103_E107_E1.1350.69
158_W181_Q1.1340.69
163_E193_H1.1340.69
339_S345_E1.1310.69
363_N367_S1.1290.69
121_F132_C1.1250.68
193_H197_Q1.1240.68
299_P308_L1.1230.68
27_E35_G1.1230.68
304_K310_A1.1210.68
254_Q258_L1.1110.67
295_W299_P1.1100.67
358_I363_N1.1090.67
63_E78_W1.1050.66
58_Q61_A1.1020.66
106_V124_L1.0980.66
148_G178_G1.0970.66
365_I370_K1.0970.66
116_Y125_W1.0960.65
57_Q60_R1.0950.65
21_E33_R1.0910.65
78_W104_R1.0890.65
151_L188_R1.0870.65
121_F141_Y1.0860.64
105_A130_R1.0840.64
340_F343_Y1.0840.64
130_R157_S1.0830.64
156_I192_Q1.0820.64
100_T110_Q1.0820.64
137_D145_Q1.0820.64
65_E77_V1.0810.64
109_L118_D1.0800.64
158_W174_I1.0780.64
155_Y162_Y1.0780.64
148_G196_F1.0770.63
296_I304_K1.0740.63
284_T290_P1.0740.63
374_E377_D1.0720.63
154_F158_W1.0700.63
378_P382_V1.0670.62
78_W86_E1.0660.62
118_D171_A1.0650.62
148_G154_F1.0650.62
148_G171_A1.0600.62
65_E69_Y1.0590.62
305_E313_W1.0580.61
106_V121_F1.0580.61
132_C145_Q1.0580.61
79_D83_S1.0570.61
176_Q193_H1.0570.61
172_D196_F1.0560.61
99_S128_L1.0560.61
248_A251_A1.0550.61
22_W42_Q1.0540.61
143_H146_G1.0540.61
143_H154_F1.0520.61
95_E102_L1.0510.61
151_L191_S1.0480.60
282_A286_E1.0460.60
276_D280_D1.0460.60
71_G77_V1.0450.60
302_R305_E1.0450.60
24_L44_A1.0440.60
62_F77_V1.0430.60
216_V221_V1.0430.60
27_E31_P1.0420.60
193_H199_R1.0410.60
391_E394_E1.0400.59
172_D176_Q1.0380.59
77_V85_T1.0360.59
343_Y346_E1.0360.59
403_I411_S1.0350.59
129_G177_E1.0340.59
139_Y175_F1.0320.59
178_G189_L1.0320.59
153_Q156_I1.0310.58
36_R41_L1.0310.58
226_T230_L1.0310.58
133_N136_L1.0300.58
156_I160_E1.0300.58
28_N36_R1.0290.58
91_Q94_K1.0280.58
361_S364_H1.0260.58
358_I361_S1.0250.58
175_F199_R1.0250.58
151_L178_G1.0230.58
337_L340_F1.0230.58
259_Q264_Q1.0210.57
353_M358_I1.0210.57
357_K360_P1.0200.57
335_A351_P1.0180.57
107_E138_M1.0180.57
162_Y172_D1.0170.57
152_A185_P1.0160.57
186_L240_A1.0160.57
392_K401_E1.0150.57
378_P381_R1.0150.57
94_K101_L1.0140.57
354_T359_E1.0130.56
332_A335_A1.0110.56
66_I158_W1.0100.56
301_P304_K1.0090.56
53_N57_Q1.0090.56
381_R384_S1.0090.56
141_Y147_I1.0080.56
62_F81_Y1.0080.56
370_K373_K1.0080.56
142_L178_G1.0080.56
363_N366_L1.0060.56
277_E305_E1.0060.56
116_Y121_F1.0050.56
86_E192_Q1.0040.55
24_L45_L1.0030.55
310_A317_R1.0030.55
339_S347_T1.0020.55
136_L161_E1.0010.55
29_V42_Q1.0010.55
363_N369_R1.0000.55
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  
4aezC30.48841000.457Contact Map
2wviA10.37211000.521Contact Map
3eslA20.44191000.527Contact Map
4a1gA40.34881000.544Contact Map
4b94A40.311699.90.785Contact Map
4h7yA40.311699.80.814Contact Map
4ggdC20.018698.50.906Contact Map
4bl0B20.197.60.924Contact Map
2i3sB30.076796.60.935Contact Map
2ondA20.523394.50.944Contact 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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