May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
RLMD - 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD
UniProt: P55135 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG11247
Length: 433 (420)
Sequences: 2810
Seq/Len: 6.69
RLMD
Paralog alert: 0.53 [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
51_E 68_R 4.117 1.00
398_S 429_F 3.859 1.00
409_A 430_S 3.669 1.00
99_L 102_R 3.26 1.00
52_V 64_A 3.171 1.00
105_S 109_A 2.966 1.00
310_S 337_T 2.927 1.00
75_E 99_L 2.906 1.00
19_V 52_V 2.902 1.00
45_L 48_E 2.87 1.00
81_C 87_C 2.775 1.00
81_C 90_C 2.755 1.00
87_C 90_C 2.55 1.00
295_C 313_G 2.542 1.00
66_V 69_R 2.512 1.00
304_L 361_L 2.497 1.00
81_C 162_C 2.496 1.00
20_S 49_N 2.464 1.00
399_E 403_K 2.401 1.00
18_T 49_N 2.376 1.00
100_Q 419_H 2.363 1.00
250_D 253_G 2.297 1.00
158_D 177_R 2.249 1.00
362_L 369_A 2.223 1.00
49_N 71_S 2.219 1.00
277_R 280_E 2.215 1.00
376_I 384_I 2.199 1.00
90_C 162_C 2.18 1.00
87_C 162_C 2.161 1.00
19_V 32_A 2.12 1.00
50_A 69_R 2.082 1.00
126_G 167_P 2.058 1.00
408_I 427_V 2.044 1.00
394_L 427_V 2.042 1.00
278_A 387_V 2.027 1.00
117_S 410_R 2.018 1.00
281_W 410_R 2.004 1.00
150_K 155_D 1.997 1.00
360_V 376_I 1.994 1.00
21_V 44_L 1.987 1.00
97_V 101_Q 1.948 1.00
341_E 346_D 1.934 1.00
53_T 65_K 1.889 1.00
56_E 63_R 1.886 1.00
259_S 323_K 1.882 1.00
44_L 50_A 1.866 1.00
358_D 382_I 1.865 1.00
315_E 321_V 1.861 1.00
108_L 423_L 1.852 1.00
106_A 110_R 1.834 1.00
51_E 70_L 1.834 1.00
383_R 430_S 1.804 1.00
22_N 33_R 1.771 1.00
394_L 425_S 1.761 1.00
289_R 310_S 1.734 1.00
295_C 321_V 1.726 1.00
274_M 414_L 1.723 1.00
407_T 430_S 1.72 1.00
18_T 51_E 1.719 1.00
105_S 118_E 1.702 1.00
69_R 72_D 1.702 1.00
257_T 326_Q 1.694 1.00
24_L 46_P 1.69 1.00
380_E 431_R 1.649 1.00
394_L 398_S 1.629 1.00
276_A 280_E 1.629 1.00
20_S 71_S 1.602 1.00
373_M 400_A 1.601 1.00
75_E 96_S 1.594 1.00
313_G 324_G 1.586 1.00
250_D 255_R 1.583 1.00
290_V 308_A 1.58 1.00
39_L 62_A 1.577 1.00
112_M 398_S 1.573 1.00
21_V 32_A 1.563 0.99
282_L 359_K 1.551 0.99
333_L 336_V 1.549 0.99
301_T 311_V 1.547 0.99
25_D 31_V 1.528 0.99
87_C 93_Q 1.512 0.99
32_A 41_I 1.5 0.99
102_R 105_S 1.499 0.99
326_Q 329_R 1.487 0.99
106_A 109_A 1.487 0.99
390_N 393_T 1.484 0.99
80_R 163_P 1.481 0.99
108_L 413_M 1.469 0.99
373_M 401_L 1.467 0.99
79_P 93_Q 1.462 0.99
166_A 196_Q 1.449 0.99
32_A 52_V 1.444 0.99
167_P 171_A 1.441 0.99
381_P 406_Y 1.44 0.99
291_L 357_F 1.427 0.99
288_D 358_D 1.423 0.99
398_S 408_I 1.418 0.99
377_I 404_A 1.413 0.99
117_S 412_A 1.407 0.99
318_P 322_E 1.399 0.99
96_S 99_L 1.383 0.98
294_F 344_E 1.375 0.98
29_Q 63_R 1.373 0.98
324_G 338_F 1.366 0.98
342_N 345_E 1.363 0.98
105_S 119_V 1.362 0.98
83_H 159_V 1.346 0.98
409_A 428_L 1.345 0.98
45_L 95_A 1.344 0.98
313_G 338_F 1.343 0.98
254_L 302_L 1.339 0.98
360_V 381_P 1.337 0.98
21_V 41_I 1.329 0.98
49_N 70_L 1.326 0.98
398_S 427_V 1.318 0.98
21_V 30_G 1.317 0.98
16_I 51_E 1.304 0.98
384_I 406_Y 1.303 0.97
279_L 307_Q 1.296 0.97
23_D 106_A 1.289 0.97
77_E 96_S 1.286 0.97
112_M 411_L 1.266 0.97
21_V 50_A 1.263 0.97
328_A 338_F 1.26 0.97
131_A 165_L 1.259 0.97
281_W 428_L 1.251 0.97
54_V 64_A 1.246 0.96
23_D 33_R 1.246 0.96
129_R 268_A 1.245 0.96
302_L 328_A 1.243 0.96
53_T 67_V 1.24 0.96
37_K 62_A 1.238 0.96
369_A 373_M 1.238 0.96
272_Q 276_A 1.237 0.96
23_D 31_V 1.236 0.96
302_L 336_V 1.232 0.96
16_I 53_T 1.22 0.96
271_N 299_N 1.22 0.96
322_E 325_Q 1.219 0.96
19_V 39_L 1.219 0.96
90_C 93_Q 1.215 0.96
190_G 195_V 1.203 0.95
18_T 70_L 1.202 0.95
241_T 246_M 1.202 0.95
384_I 401_L 1.2 0.95
33_R 38_T 1.195 0.95
81_C 93_Q 1.193 0.95
80_R 125_W 1.192 0.95
287_E 309_A 1.192 0.95
277_R 281_W 1.191 0.95
282_L 385_V 1.189 0.95
102_R 106_A 1.185 0.95
278_A 361_L 1.183 0.95
144_L 180_L 1.182 0.95
255_R 330_L 1.181 0.95
25_D 29_Q 1.175 0.95
136_N 156_I 1.17 0.94
143_Q 181_G 1.155 0.94
206_R 233_A 1.155 0.94
44_L 66_V 1.155 0.94
429_F 432_V 1.152 0.94
312_V 339_Y 1.149 0.94
293_L 372_V 1.149 0.94
84_F 94_H 1.149 0.94
254_L 306_T 1.148 0.94
31_V 38_T 1.148 0.94
54_V 62_A 1.147 0.94
17_I 34_H 1.147 0.94
327_N 331_N 1.142 0.94
91_Q 421_G 1.142 0.94
285_Q 288_D 1.141 0.93
57_D 62_A 1.139 0.93
277_R 412_A 1.131 0.93
388_S 393_T 1.13 0.93
382_I 430_S 1.123 0.93
278_A 385_V 1.118 0.93
275_V 300_F 1.116 0.92
17_I 32_A 1.109 0.92
48_E 73_S 1.105 0.92
295_C 338_F 1.1 0.92
308_A 335_N 1.099 0.92
109_A 113_K 1.098 0.92
190_G 197_A 1.094 0.91
149_R 154_S 1.092 0.91
81_C 89_G 1.092 0.91
377_I 405_G 1.082 0.91
313_G 336_V 1.081 0.91
266_V 416_M 1.08 0.91
131_A 148_F 1.079 0.91
216_R 220_E 1.077 0.91
407_T 432_V 1.076 0.91
295_C 324_G 1.076 0.91
19_V 41_I 1.064 0.90
55_T 65_K 1.06 0.90
89_G 162_C 1.057 0.90
17_I 52_V 1.056 0.89
284_V 290_V 1.055 0.89
134_S 156_I 1.054 0.89
169_L 194_L 1.051 0.89
231_Y 234_P 1.047 0.89
426_M 430_S 1.046 0.89
305_A 333_L 1.041 0.89
284_V 288_D 1.036 0.88
161_Q 170_E 1.034 0.88
116_V 413_M 1.033 0.88
134_S 149_R 1.031 0.88
45_L 94_H 1.025 0.88
314_V 346_D 1.025 0.88
92_Q 103_S 1.024 0.87
321_V 325_Q 1.022 0.87
266_V 394_L 1.019 0.87
427_V 430_S 1.015 0.87
30_G 44_L 1.013 0.87
230_L 233_A 1.013 0.87
168_Q 171_A 1.009 0.86
165_L 169_L 1 0.86
283_D 383_R 1 0.86
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
1uwvA111000.16Contact Map0.749
2jjqA10.93071000.258Contact Map0.707
3bt7A20.78751000.433Contact Map0.735
3vseA40.7461000.711Contact Map0.426
4dmgA20.73441000.728Contact Map0.46
1wxxA40.72521000.739Contact Map0.601
2b78A10.7461000.747Contact Map0.432
3c0kA20.72751000.76Contact Map0.568
3a27A10.57741000.773Contact Map0.627
2frnA10.58431000.778Contact Map0.635
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 0.0634 seconds.