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OPENSEQ.org
TRMA - tRNA (uracil(54)-C(5))-methyltransferase
UniProt: P23003 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG11022
Length: 366 (353)
Sequences: 2892
Seq/Len: 8.19
TRMA
Paralog alert: 0.54 [within 20: 0.01] - ratio of genomes with paralogs
Cluster includes: RLMC RLMD TRMA
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
333_L 363_L 4.294 1.00
343_E 364_T 4.206 1.00
13_A 16_A 3.806 1.00
19_V 23_Q 3.372 1.00
234_R 261_Q 3.188 1.00
219_C 237_A 3.078 1.00
14_Q 353_Y 2.733 1.00
334_E 338_Q 2.706 1.00
228_L 297_F 2.699 1.00
296_I 313_V 2.611 1.00
298_V 305_L 2.549 1.00
73_R 92_I 2.528 1.00
202_W 205_D 2.425 1.00
65_D 70_S 2.41 1.00
329_L 361_V 2.371 1.00
342_V 361_V 2.362 1.00
184_V 247_A 2.352 1.00
171_R 180_I 2.326 1.00
11_Y 15_L 2.323 1.00
206_V 344_R 2.317 1.00
43_H 82_E 2.235 1.00
215_L 293_C 2.228 1.00
239_E 245_V 2.223 1.00
219_C 245_V 2.202 1.00
265_M 270_F 2.161 1.00
20_V 24_S 2.144 1.00
203_A 322_I 2.124 1.00
318_R 364_T 2.096 1.00
22_L 357_M 2.061 1.00
182_R 250_Y 2.054 1.00
341_K 364_T 2.031 1.00
294_E 317_P 2.015 1.00
329_L 359_C 2.005 1.00
199_M 348_F 1.991 1.00
20_V 23_Q 1.938 1.00
169_D 180_I 1.915 1.00
16_A 19_V 1.9 1.00
313_V 319_I 1.896 1.00
237_A 248_A 1.895 1.00
167_Y 182_R 1.875 1.00
201_E 205_D 1.86 1.00
82_E 86_Q 1.813 1.00
22_L 347_L 1.784 1.00
225_S 235_V 1.773 1.00
325_N 328_T 1.76 1.00
329_L 333_L 1.758 1.00
305_L 310_E 1.734 1.00
214_L 232_F 1.734 1.00
310_E 335_T 1.734 1.00
266_A 269_E 1.714 1.00
204_L 231_N 1.713 1.00
207_T 295_T 1.703 1.00
257_I 260_V 1.67 1.00
10_Q 13_A 1.658 1.00
26_M 333_L 1.646 1.00
242_K 246_A 1.642 1.00
171_R 178_E 1.626 1.00
248_A 262_I 1.623 1.00
133_R 137_E 1.608 1.00
310_E 336_L 1.587 1.00
206_V 362_L 1.585 1.00
250_Y 253_A 1.581 1.00
307_S 311_K 1.571 1.00
161_I 166_D 1.562 1.00
343_E 362_L 1.551 1.00
213_D 234_R 1.54 1.00
48_A 80_A 1.527 1.00
180_I 254_A 1.51 1.00
237_A 262_I 1.497 1.00
333_L 342_V 1.465 0.99
46_M 193_A 1.463 0.99
16_A 20_V 1.454 0.99
252_I 262_I 1.453 0.99
26_M 345_L 1.449 0.99
207_T 320_L 1.433 0.99
58_D 96_R 1.429 0.99
317_P 364_T 1.422 0.99
87_L 118_A 1.42 0.99
51_R 71_R 1.416 0.99
333_L 361_V 1.413 0.99
246_A 249_Q 1.396 0.99
59_L 95_V 1.389 0.99
196_N 223_N 1.382 0.99
319_I 340_H 1.37 0.99
319_I 336_L 1.369 0.99
179_M 229_A 1.366 0.99
237_A 260_V 1.352 0.99
226_L 252_I 1.345 0.99
203_A 320_L 1.345 0.99
197_I 201_E 1.331 0.99
202_W 206_V 1.331 0.99
97_N 138_A 1.33 0.99
51_R 64_F 1.326 0.99
171_R 176_G 1.312 0.98
202_W 346_A 1.306 0.98
219_C 248_A 1.301 0.98
229_A 257_I 1.298 0.98
64_F 69_K 1.288 0.98
137_E 141_D 1.286 0.98
203_A 297_F 1.284 0.98
169_D 182_R 1.28 0.98
226_L 260_V 1.271 0.98
361_V 364_T 1.268 0.98
296_I 316_Y 1.25 0.98
117_Q 165_Q 1.249 0.98
323_S 328_T 1.243 0.98
219_C 262_I 1.241 0.98
48_A 63_I 1.24 0.98
191_P 329_L 1.237 0.98
226_L 257_I 1.237 0.98
236_L 263_I 1.231 0.97
148_L 152_L 1.227 0.97
138_A 142_A 1.223 0.97
316_Y 340_H 1.219 0.97
83_L 86_Q 1.217 0.97
80_A 84_I 1.211 0.97
200_L 224_F 1.202 0.97
191_P 350_Q 1.188 0.97
293_C 296_I 1.18 0.96
149_N 152_L 1.18 0.96
199_M 350_Q 1.18 0.96
232_F 259_N 1.177 0.96
344_R 362_L 1.176 0.96
23_Q 27_A 1.171 0.96
193_A 196_N 1.171 0.96
245_V 264_R 1.161 0.96
87_L 90_A 1.161 0.96
225_S 260_V 1.156 0.96
245_V 249_Q 1.155 0.96
218_Y 268_E 1.151 0.96
332_N 335_T 1.146 0.96
335_T 338_Q 1.141 0.95
179_M 226_L 1.129 0.95
208_K 318_R 1.126 0.95
53_W 71_R 1.122 0.95
322_I 360_G 1.12 0.95
26_M 330_C 1.118 0.95
179_M 230_R 1.11 0.95
84_I 110_Y 1.106 0.94
93_A 142_A 1.099 0.94
251_N 255_N 1.097 0.94
360_G 364_T 1.096 0.94
124_Y 148_L 1.093 0.94
216_E 237_A 1.092 0.94
121_S 185_E 1.09 0.94
76_S 85_N 1.082 0.94
342_V 363_L 1.08 0.93
307_S 335_T 1.076 0.93
238_T 270_F 1.075 0.93
287_D 290_S 1.072 0.93
214_L 228_L 1.07 0.93
26_M 329_L 1.066 0.93
207_T 318_R 1.063 0.93
242_K 264_R 1.063 0.93
321_Y 329_L 1.059 0.93
345_L 361_V 1.059 0.93
214_L 295_T 1.058 0.93
90_A 142_A 1.049 0.92
187_S 244_S 1.044 0.92
250_Y 254_A 1.043 0.92
298_V 313_V 1.042 0.92
363_L 366_K 1.04 0.92
117_Q 169_D 1.039 0.92
169_D 254_A 1.035 0.91
209_G 295_T 1.034 0.91
217_L 309_T 1.032 0.91
202_W 360_G 1.032 0.91
295_T 320_L 1.012 0.90
52_I 104_K 1.005 0.90
204_L 227_A 1 0.89
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
3bt7A211000.182Contact Map0.756
1uwvA10.92081000.308Contact Map0.754
2jjqA10.86071000.322Contact Map0.75
3vseA40.86891000.623Contact Map0.412
4dmgA20.86071000.646Contact Map0.491
1wxxA40.84151000.664Contact Map0.603
2b78A10.86611000.67Contact Map0.416
3c0kA20.85791000.682Contact Map0.569
2frnA10.6941000.713Contact Map0.62
3a27A10.67491000.715Contact Map0.621
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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