May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
TRUB - tRNA pseudouridine synthase B
UniProt: P60340 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG11177
Length: 314 (298)
Sequences: 1777
Seq/Len: 5.96
TRUB
Paralog alert: 0.01 [within 20: 0.00] - ratio of genomes with paralogs
GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:
i j Scaled Score Prob
18_D 201_R 4.025 1.00
118_D 152_P 3.909 1.00
120_E 152_P 3.822 1.00
87_D 94_Q 3.699 1.00
17_L 28_A 3.57 1.00
134_K 138_E 3.283 1.00
105_A 109_A 3.136 1.00
16_L 54_M 3.025 1.00
77_R 171_E 2.801 1.00
89_S 185_D 2.689 1.00
111_A 187_L 2.588 1.00
75_R 171_E 2.486 1.00
50_L 92_D 2.464 1.00
118_D 154_T 2.428 1.00
21_Q 52_T 2.332 1.00
114_T 190_K 2.327 1.00
125_M 148_R 2.272 1.00
81_R 167_E 2.271 1.00
75_R 173_H 2.258 1.00
263_Y 268_N 2.256 1.00
129_L 151_R 2.222 1.00
80_A 184_I 2.192 1.00
172_I 183_I 2.182 1.00
85_R 189_E 2.168 1.00
159_L 171_E 2.161 1.00
32_V 41_A 2.069 1.00
161_I 171_E 2.062 1.00
157_E 173_H 2.026 1.00
44_T 58_C 2.022 1.00
188_G 195_A 2.016 1.00
264_F 283_V 2.005 1.00
52_T 201_R 1.967 1.00
58_C 66_S 1.962 1.00
136_L 148_R 1.962 1.00
32_V 57_I 1.956 1.00
38_A 59_L 1.953 1.00
112_L 158_L 1.952 1.00
81_R 198_I 1.932 1.00
107_Q 110_A 1.906 1.00
82_L 168_L 1.903 1.00
80_A 195_A 1.875 1.00
188_G 194_G 1.874 1.00
296_E 306_R 1.851 1.00
89_S 182_T 1.844 1.00
77_R 169_E 1.825 1.00
104_S 107_Q 1.824 1.00
112_L 160_F 1.82 1.00
119_I 153_I 1.819 1.00
188_G 193_C 1.811 1.00
257_P 260_S 1.795 1.00
80_A 168_L 1.781 1.00
18_D 52_T 1.766 1.00
122_I 150_A 1.749 1.00
135_K 138_E 1.724 1.00
91_A 196_H 1.723 1.00
78_V 197_V 1.719 1.00
139_Y 144_I 1.711 1.00
184_I 197_V 1.711 1.00
182_T 185_D 1.7 1.00
125_M 136_L 1.695 1.00
80_A 170_L 1.683 1.00
109_A 160_F 1.667 1.00
134_K 139_Y 1.638 1.00
85_R 96_V 1.633 1.00
115_F 190_K 1.63 1.00
215_T 218_H 1.626 1.00
14_V 58_C 1.607 0.99
79_I 169_E 1.594 0.99
256_L 264_F 1.589 0.99
131_Y 148_R 1.588 0.99
73_D 173_H 1.573 0.99
67_Q 307_R 1.552 0.99
113_D 116_R 1.535 0.99
75_R 204_A 1.534 0.99
305_P 308_L 1.525 0.99
120_E 150_A 1.483 0.99
282_R 291_F 1.48 0.99
264_F 293_G 1.476 0.99
78_V 170_L 1.456 0.99
54_M 213_M 1.41 0.98
105_A 163_H 1.403 0.98
112_L 170_L 1.389 0.98
148_R 182_T 1.369 0.98
26_N 33_K 1.364 0.98
26_N 30_Q 1.363 0.98
38_A 41_A 1.357 0.98
163_H 168_L 1.346 0.98
36_Y 59_L 1.34 0.97
17_L 219_L 1.337 0.97
109_A 116_R 1.324 0.97
85_R 97_E 1.31 0.97
31_K 34_R 1.303 0.97
10_D 39_N 1.28 0.96
131_Y 136_L 1.273 0.96
16_L 213_M 1.251 0.96
85_R 194_G 1.249 0.96
245_D 284_T 1.247 0.96
26_N 29_L 1.226 0.95
283_V 295_G 1.224 0.95
210_V 213_M 1.219 0.95
81_R 84_Q 1.215 0.95
164_E 169_E 1.213 0.95
61_E 64_K 1.206 0.94
217_E 220_R 1.199 0.94
116_R 158_L 1.193 0.94
87_D 126_Y 1.189 0.94
71_D 176_K 1.177 0.93
242_M 246_S 1.163 0.93
95_I 98_E 1.157 0.93
82_L 191_L 1.156 0.93
66_S 70_L 1.146 0.92
54_M 205_V 1.145 0.92
82_L 195_A 1.141 0.92
251_Y 294_M 1.136 0.92
130_K 135_K 1.125 0.91
108_L 163_H 1.123 0.91
134_K 142_Q 1.118 0.91
157_E 171_E 1.116 0.91
115_F 186_D 1.11 0.91
171_E 203_L 1.102 0.90
84_Q 98_E 1.099 0.90
172_I 180_I 1.095 0.90
79_I 167_E 1.08 0.89
293_G 303_V 1.075 0.89
78_V 184_I 1.07 0.88
218_H 221_E 1.068 0.88
111_A 190_K 1.067 0.88
15_L 32_V 1.056 0.87
154_T 175_S 1.054 0.87
264_F 292_I 1.051 0.87
160_F 163_H 1.047 0.87
125_M 145_E 1.046 0.87
79_I 199_Y 1.044 0.87
72_S 206_S 1.037 0.86
51_A 129_L 1.035 0.86
293_G 308_L 1.031 0.86
21_Q 50_L 1.03 0.86
87_D 96_V 1.028 0.85
86_T 95_I 1.025 0.85
125_M 182_T 1.022 0.85
108_L 168_L 1.015 0.84
125_M 146_V 1.015 0.84
32_V 59_L 1.014 0.84
263_Y 266_N 1.001 0.83
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.
HHsearch Results: 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-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.
PDB Chains Cov P(%) HHΔ   Acc
1k8wA111000.124Contact Map0.841
1r3eA10.92041000.135Contact Map0.823
1sgvA20.92041000.141Contact Map0.817
3u28A10.88541000.305Contact Map0.794
2apoA10.8791000.315Contact Map0.876
2ausC20.87581000.319Contact Map0.859
2v9kA10.56051000.742Contact Map0.672
1kskA10.554199.60.84Contact Map0.624
4lgtA20.576498.70.897Contact Map0.672
1vioA20.58698.50.903Contact Map0.661
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 0.227 seconds.