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OPENSEQ.org
TRUD - tRNA pseudouridine synthase D
UniProt: Q57261 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG13109
Length: 349 (335)
Sequences: 792
Seq/Len: 2.36
TRUD
Paralog alert: 0.05 [within 20: 0.01] - 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
209_E 212_K 3.511 1.00
49_L 110_Q 3.251 1.00
49_L 86_E 3.036 1.00
76_A 126_L 2.781 1.00
275_E 298_R 2.739 1.00
207_V 301_M 2.691 1.00
256_T 298_R 2.669 1.00
156_V 333_V 2.653 1.00
58_V 109_C 2.476 1.00
47_R 113_E 2.311 1.00
59_A 89_L 2.26 1.00
25_E 51_N 2.252 1.00
18_G 338_I 2.17 1.00
145_E 149_I 2.064 0.99
53_C 57_F 1.999 0.99
257_A 301_M 1.995 0.99
256_T 275_E 1.977 0.99
26_D 136_R 1.954 0.99
59_A 73_V 1.953 0.99
207_V 257_A 1.923 0.99
19_L 137_E 1.875 0.99
198_A 282_E 1.861 0.99
205_Q 281_A 1.825 0.98
303_L 328_S 1.797 0.98
47_R 88_W 1.779 0.98
309_S 321_R 1.779 0.98
18_G 135_L 1.772 0.98
257_A 275_E 1.767 0.98
74_S 90_C 1.739 0.98
246_R 250_D 1.727 0.98
48_I 89_L 1.725 0.98
68_I 91_A 1.693 0.97
245_Q 249_N 1.648 0.97
149_I 152_C 1.643 0.96
48_I 58_V 1.638 0.96
133_L 334_V 1.624 0.96
52_G 82_H 1.615 0.96
322_F 330_A 1.6 0.96
30_V 130_A 1.59 0.95
303_L 325_P 1.587 0.95
149_I 153_V 1.586 0.95
136_R 159_Y 1.579 0.95
45_L 90_C 1.551 0.95
58_V 62_L 1.521 0.94
148_L 310_W 1.507 0.93
132_T 321_R 1.506 0.93
209_E 277_A 1.498 0.93
8_T 208_A 1.497 0.93
210_R 223_D 1.488 0.93
206_I 258_A 1.486 0.93
234_F 247_R 1.48 0.93
73_V 89_L 1.455 0.92
257_A 298_R 1.449 0.92
40_E 118_K 1.42 0.91
58_V 89_L 1.412 0.90
47_R 86_E 1.409 0.90
76_A 128_G 1.408 0.90
45_L 88_W 1.4 0.90
90_C 117_H 1.378 0.89
73_V 91_A 1.376 0.89
147_R 339_N 1.373 0.88
20_L 334_V 1.366 0.88
134_V 319_E 1.361 0.88
111_V 114_Y 1.358 0.88
63_A 68_I 1.349 0.87
72_E 92_R 1.343 0.87
273_A 277_A 1.342 0.87
225_L 253_L 1.332 0.86
210_R 222_G 1.323 0.86
48_I 111_V 1.316 0.85
51_N 91_A 1.312 0.85
247_R 252_E 1.304 0.85
311_N 319_E 1.298 0.84
260_P 296_A 1.291 0.84
157_P 207_V 1.288 0.84
126_L 329_F 1.281 0.83
78_Q 123_L 1.273 0.83
32_D 323_W 1.269 0.82
165_F 204_N 1.255 0.82
255_I 302_L 1.253 0.81
247_R 253_L 1.248 0.81
76_A 121_L 1.238 0.80
11_H 17_T 1.237 0.80
95_G 116_R 1.236 0.80
225_L 236_A 1.223 0.79
156_V 303_L 1.218 0.79
227_L 232_S 1.218 0.79
134_V 317_T 1.203 0.78
134_V 144_V 1.2 0.77
262_S 293_K 1.194 0.77
30_V 86_E 1.19 0.77
332_S 335_R 1.175 0.75
325_P 328_S 1.171 0.75
203_F 275_E 1.168 0.75
254_M 302_L 1.167 0.75
191_R 203_F 1.165 0.74
202_L 282_E 1.164 0.74
63_A 175_A 1.163 0.74
261_G 296_A 1.154 0.73
74_S 92_R 1.153 0.73
224_A 298_R 1.149 0.73
251_K 302_L 1.147 0.73
154_K 217_N 1.141 0.72
69_H 72_E 1.138 0.72
173_Q 177_R 1.135 0.72
261_G 298_R 1.134 0.71
76_A 124_G 1.125 0.71
197_A 212_K 1.121 0.70
125_A 234_F 1.12 0.70
270_E 273_A 1.119 0.70
205_Q 282_E 1.116 0.70
307_Q 323_W 1.115 0.70
206_I 257_A 1.112 0.69
42_E 169_G 1.104 0.69
132_T 319_E 1.103 0.68
19_L 22_A 1.102 0.68
226_Q 256_T 1.101 0.68
175_A 198_A 1.099 0.68
310_W 318_V 1.099 0.68
209_E 213_K 1.097 0.68
200_S 204_N 1.083 0.66
24_P 82_H 1.08 0.66
210_R 261_G 1.078 0.66
146_Q 149_I 1.067 0.65
246_R 251_K 1.063 0.64
115_A 211_L 1.062 0.64
18_G 38_D 1.061 0.64
206_I 301_M 1.059 0.64
56_R 78_Q 1.059 0.64
124_G 210_R 1.055 0.63
130_A 323_W 1.052 0.63
75_F 89_L 1.05 0.63
249_N 252_E 1.048 0.63
258_A 267_T 1.042 0.62
210_R 298_R 1.042 0.62
33_L 125_A 1.041 0.62
130_A 309_S 1.039 0.62
336_E 339_N 1.03 0.61
230_R 252_E 1.029 0.61
160_F 195_L 1.028 0.60
267_T 275_E 1.027 0.60
246_R 249_N 1.019 0.59
182_N 187_D 1.016 0.59
314_D 317_T 1.015 0.59
8_T 12_G 1.014 0.59
324_L 331_T 1.01 0.58
49_L 112_L 1.01 0.58
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
1szwA211000.065Contact Map0.712
1z2zA20.99141000.11Contact Map0.68
2h80A10.22068.20.977Contact Map0.275
2vd3A20.26368.10.977Contact Map0.151
2dkyA10.24934.40.979Contact Map0.353
1nh8A10.31523.80.98Contact Map0.088
1vsqC10.33243.20.981Contact Map0.022
1d0qA20.21493.10.981Contact Map0.723
2rsxA10.14042.70.981Contact Map0
4jhyA10.19482.70.982Contact Map0
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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