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

BUBR1 -force run

ID: 1469272605 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 299 (263)
Sequences: 224 (159.4)
Seq/Len: 0.852
Nf(neff/√len): 9.8

Jackhmmer Results: (2016_04)
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: 0.852).

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
99_L113_R2.7581.00
93_R96_L2.4620.99
44_A49_S2.0420.95
44_A51_C2.0130.94
173_K182_W1.8960.91
209_F269_K1.8210.89
128_Q131_F1.7720.87
209_F267_Y1.7520.86
41_L59_K1.7260.85
124_N127_L1.7030.84
235_L238_R1.6860.83
41_L144_F1.5990.79
99_L267_Y1.5990.79
144_F171_R1.5580.76
162_Q166_A1.5230.74
59_K63_E1.5200.74
211_P214_E1.4790.71
123_Q126_G1.4730.70
45_L52_N1.4700.70
120_A178_Q1.4550.69
39_S43_G1.4440.68
123_Q128_Q1.4300.67
179_A182_W1.4170.66
162_Q167_P1.4100.65
126_G132_P1.3850.63
159_P289_F1.3680.62
64_Y211_P1.3620.61
146_E214_E1.3610.61
45_L56_Q1.3510.61
55_L93_R1.3480.60
41_L63_E1.3390.60
113_R267_Y1.3350.59
96_L285_R1.3220.58
104_K268_C1.3160.58
138_N141_I1.3150.57
45_L289_F1.3020.56
51_C175_N1.3010.56
174_E182_W1.2890.55
123_Q127_L1.2820.55
115_G119_K1.2780.54
57_Q61_A1.2770.54
71_G75_X1.2720.54
166_A209_F1.2710.54
51_C174_E1.2660.53
174_E214_E1.2660.53
44_A55_L1.2600.53
54_T65_E1.2590.53
109_A113_R1.2510.52
155_E221_V1.2510.52
62_F214_E1.2320.50
168_P214_E1.2270.50
212_Y284_I1.2250.50
141_I161_V1.2220.49
239_K242_K1.2210.49
272_I280_S1.2140.49
62_F66_I1.2130.48
166_A171_R1.2080.48
272_I281_F1.2070.48
143_V180_G1.2030.48
58_Q65_E1.2020.47
175_N282_E1.1970.47
101_S143_V1.1920.47
92_Q181_P1.1880.46
125_R128_Q1.1820.46
62_F280_S1.1820.46
59_K209_F1.1800.46
174_E282_E1.1790.45
244_E248_L1.1780.45
96_L143_V1.1670.44
56_Q79_X1.1630.44
118_L124_N1.1620.44
96_L174_E1.1530.43
58_Q143_V1.1520.43
109_A115_G1.1470.43
68_F71_G1.1440.42
96_L281_F1.1410.42
226_K236_S1.1370.42
108_R284_I1.1350.42
115_G269_K1.1310.41
223_T239_K1.1300.41
139_S254_H1.1300.41
209_F266_M1.1210.40
87_E91_P1.1170.40
61_A212_Y1.1110.40
40_T69_Y1.1100.39
226_K232_N1.1060.39
54_T98_E1.1020.39
46_A156_L1.1010.39
109_A214_E1.1000.39
139_S143_V1.1000.39
182_W285_R1.0940.38
59_K269_K1.0920.38
246_D251_V1.0890.38
75_X130_P1.0840.37
62_F269_K1.0800.37
127_L130_P1.0790.37
201_A289_F1.0770.37
43_G47_Q1.0760.37
100_K207_P1.0750.37
75_X296_Q1.0750.37
164_W171_R1.0730.36
182_W283_E1.0730.36
65_E97_A1.0720.36
144_F226_K1.0700.36
181_P274_A1.0640.36
95_T99_L1.0600.35
136_Q139_S1.0580.35
48_E281_F1.0530.35
207_P224_P1.0510.35
54_T289_F1.0460.34
229_P270_E1.0390.34
269_K278_E1.0390.34
233_H238_R1.0350.33
47_Q112_I1.0310.33
45_L54_T1.0300.33
93_R285_R1.0280.33
176_E236_S1.0280.33
42_Q207_P1.0250.33
283_E286_A1.0250.33
234_I276_V1.0180.32
180_G185_G1.0160.32
188_L191_R1.0160.32
181_P272_I1.0120.32
178_Q204_A1.0100.31
75_X157_S1.0100.31
145_D214_E1.0100.31
54_T58_Q1.0080.31
125_R129_N1.0040.31
73_X78_X1.0040.31
143_V166_A1.0030.31
56_Q77_X1.0020.31
166_A287_E1.0020.31
144_F222_M1.0000.31
273_Y280_S1.0000.31
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  
2wviA10.270998.50.876Contact Map
4a1gA40.21498.20.886Contact Map
4ggdC20.026898.10.889Contact Map
3eslA20.3344980.892Contact Map
4aezC30.284397.70.899Contact Map
4bl0B20.140597.20.908Contact Map
2i3sB30.110495.50.923Contact Map
4b94A40.2241870.94Contact Map
2i3tB40.1204860.941Contact Map
4h7yA40.220768.70.95Contact 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.

Page generated in 0.4749 seconds.