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OPENSEQ.org
TOP3 - DNA topoisomerase 3
UniProt: P14294 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG11014
Length: 653 (609)
Sequences: 3203
Seq/Len: 5.26
TOP3
Paralog alert: 0.53 [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
259_R 263_E 6.073 1.00
292_F 300_E 4.867 1.00
311_N 398_N 4.675 1.00
278_S 469_K 4.501 1.00
214_E 555_K 3.901 1.00
258_H 261_L 3.818 1.00
211_E 559_H 3.809 1.00
580_Q 585_Q 3.586 1.00
404_N 408_R 3.562 1.00
220_D 482_E 3.371 1.00
397_E 401_K 3.329 1.00
326_I 406_I 3.309 1.00
425_I 467_V 3.254 1.00
86_N 90_R 3.217 1.00
285_S 419_V 3.203 1.00
97_E 130_Q 3.162 1.00
281_D 421_R 2.94 1.00
277_T 428_D 2.888 1.00
468_A 471_D 2.864 1.00
203_L 535_L 2.855 1.00
428_D 431_K 2.83 1.00
283_R 419_V 2.75 1.00
139_P 143_E 2.705 1.00
220_D 484_Q 2.688 1.00
423_C 440_F 2.629 1.00
318_K 399_E 2.625 1.00
210_D 490_H 2.524 1.00
533_E 537_K 2.495 1.00
301_A 402_V 2.479 1.00
419_V 443_E 2.465 1.00
587_R 590_D 2.382 1.00
310_Q 314_D 2.354 1.00
275_I 472_E 2.35 1.00
144_R 148_R 2.313 1.00
263_E 267_N 2.308 1.00
420_F 441_L 2.29 1.00
307_L 401_K 2.286 1.00
39_T 88_I 2.264 1.00
421_R 442_A 2.261 1.00
130_Q 151_S 2.253 1.00
77_P 85_L 2.247 1.00
287_S 417_D 2.243 1.00
221_F 483_R 2.237 1.00
278_S 426_E 2.225 1.00
100_H 112_V 2.224 1.00
39_T 87_V 2.212 1.00
310_Q 533_E 2.207 1.00
444_A 448_T 2.192 1.00
206_V 541_L 2.186 1.00
41_C 115_V 2.185 1.00
102_G 112_V 2.185 1.00
438_A 465_P 2.122 1.00
316_C 326_I 2.099 1.00
90_R 94_E 2.094 1.00
204_G 208_R 2.092 1.00
307_L 315_I 2.081 1.00
343_G 388_A 2.077 1.00
284_E 422_K 2.072 1.00
140_Q 144_R 2.062 1.00
272_Q 430_A 2.058 1.00
283_R 442_A 2.017 1.00
207_V 550_S 2.013 1.00
581_I 591_F 2.01 1.00
276_V 427_L 1.983 1.00
267_N 270_S 1.965 1.00
225_K 237_T 1.961 1.00
418_A 441_L 1.952 1.00
85_L 118_Y 1.949 1.00
273_P 472_E 1.941 1.00
307_L 398_N 1.907 1.00
3_L 92_L 1.895 1.00
400_A 404_N 1.886 1.00
424_V 437_K 1.867 1.00
218_A 484_Q 1.848 1.00
426_E 435_V 1.845 1.00
536_F 543_K 1.842 1.00
224_V 262_A 1.835 1.00
306_G 546_R 1.824 1.00
208_R 212_E 1.823 1.00
157_P 584_K 1.82 1.00
300_E 303_K 1.808 1.00
132_C 146_I 1.804 1.00
426_E 433_K 1.79 1.00
268_R 432_G 1.784 1.00
427_L 473_L 1.779 1.00
577_V 594_P 1.774 1.00
219_K 257_L 1.772 1.00
576_S 580_Q 1.73 1.00
27_D 83_K 1.725 1.00
389_R 411_L 1.723 1.00
349_N 356_P 1.722 1.00
227_H 477_K 1.703 1.00
210_D 550_S 1.698 1.00
150_R 154_E 1.696 1.00
542_T 551_T 1.688 1.00
277_T 433_K 1.68 1.00
534_L 538_R 1.679 1.00
223_E 483_R 1.67 0.99
573_H 577_V 1.658 0.99
2_R 97_E 1.638 0.99
336_L 413_Q 1.633 0.99
421_R 440_F 1.631 0.99
259_R 482_E 1.626 0.99
305_F 401_K 1.619 0.99
156_V 160_V 1.616 0.99
275_I 428_D 1.61 0.99
438_A 464_L 1.603 0.99
536_F 548_I 1.6 0.99
260_P 264_H 1.581 0.99
194_S 199_Q 1.579 0.99
283_R 421_R 1.577 0.99
83_K 86_N 1.571 0.99
154_E 159_C 1.558 0.99
261_L 264_H 1.549 0.99
257_L 261_L 1.543 0.99
228_I 427_L 1.535 0.99
194_S 538_R 1.534 0.99
82_T 86_N 1.531 0.99
86_N 89_K 1.527 0.99
228_I 238_A 1.524 0.99
15_I 38_V 1.522 0.99
276_V 473_L 1.52 0.99
307_L 402_V 1.519 0.99
92_L 98_I 1.509 0.99
392_A 400_A 1.507 0.99
227_H 479_E 1.504 0.99
419_V 442_A 1.498 0.99
418_A 447_R 1.492 0.99
396_T 399_E 1.488 0.99
301_A 405_L 1.486 0.99
285_S 417_D 1.475 0.98
2_R 99_V 1.473 0.98
230_T 471_D 1.471 0.98
46_L 118_Y 1.471 0.98
256_L 265_V 1.47 0.98
412_M 450_L 1.466 0.98
238_A 436_A 1.463 0.98
109_Q 113_D 1.45 0.98
486_Q 489_R 1.449 0.98
256_L 262_A 1.433 0.98
16_A 37_V 1.431 0.98
211_E 215_N 1.429 0.98
266_V 270_S 1.428 0.98
467_V 471_D 1.428 0.98
39_T 91_F 1.411 0.98
335_Y 379_D 1.409 0.98
105_D 380_A 1.408 0.98
311_N 314_D 1.405 0.98
264_H 268_R 1.402 0.98
83_K 87_V 1.401 0.98
577_V 586_C 1.396 0.98
99_V 149_L 1.392 0.98
307_L 311_N 1.375 0.97
236_F 427_L 1.374 0.97
274_A 429_I 1.368 0.97
167_R 592_M 1.36 0.97
133_L 150_R 1.354 0.97
143_E 147_D 1.35 0.97
577_V 580_Q 1.342 0.97
279_Y 425_I 1.334 0.97
236_F 467_V 1.329 0.96
490_H 550_S 1.32 0.96
274_A 427_L 1.32 0.96
497_L 532_I 1.318 0.96
98_I 121_L 1.316 0.96
14_A 17_D 1.305 0.96
345_H 349_N 1.3 0.96
580_Q 586_C 1.297 0.96
315_I 402_V 1.289 0.96
42_I 81_V 1.284 0.95
499_A 503_I 1.275 0.95
238_A 427_L 1.271 0.95
297_L 312_V 1.269 0.95
586_C 590_D 1.269 0.95
140_Q 339_E 1.268 0.95
45_L 118_Y 1.266 0.95
600_Y 604_D 1.263 0.95
344_R 411_L 1.262 0.95
314_D 318_K 1.261 0.95
211_E 214_E 1.26 0.95
281_D 423_C 1.26 0.95
397_E 400_A 1.256 0.95
315_I 398_N 1.252 0.95
117_D 120_Q 1.237 0.94
229_V 476_E 1.237 0.94
590_D 593_Q 1.233 0.94
274_A 473_L 1.232 0.94
318_K 322_T 1.226 0.94
4_F 146_I 1.225 0.94
26_G 29_F 1.223 0.94
110_L 162_A 1.219 0.94
224_V 265_V 1.215 0.93
240_W 432_G 1.214 0.93
116_L 129_V 1.212 0.93
157_P 160_V 1.21 0.93
423_C 438_A 1.206 0.93
4_F 36_Q 1.202 0.93
132_C 149_L 1.2 0.93
209_R 212_E 1.199 0.93
358_L 444_A 1.197 0.93
263_E 266_V 1.196 0.93
348_M 411_L 1.195 0.93
325_L 395_L 1.192 0.93
422_K 437_K 1.191 0.93
303_K 452_S 1.19 0.92
416_P 443_E 1.183 0.92
204_G 562_P 1.173 0.92
76_Q 79_P 1.173 0.92
79_P 82_T 1.172 0.92
84_Q 87_V 1.167 0.91
601_Q 605_Q 1.167 0.91
398_N 401_K 1.162 0.91
225_K 481_V 1.156 0.91
194_S 534_L 1.156 0.91
207_V 558_F 1.154 0.91
42_I 84_Q 1.152 0.91
18_V 139_P 1.15 0.91
301_A 312_V 1.14 0.90
224_V 266_V 1.137 0.90
3_L 91_F 1.136 0.90
144_R 147_D 1.135 0.90
216_F 485_T 1.132 0.90
46_L 85_L 1.13 0.90
212_E 491_F 1.13 0.90
224_V 478_G 1.127 0.90
226_A 478_G 1.12 0.89
320_Y 329_P 1.119 0.89
262_A 480_V 1.115 0.89
535_L 541_L 1.111 0.89
136_D 141_A 1.111 0.89
420_F 439_R 1.111 0.89
109_Q 152_N 1.11 0.89
244_E 431_K 1.109 0.88
493_D 543_K 1.109 0.88
274_A 475_C 1.108 0.88
292_F 409_Q 1.107 0.88
228_I 274_A 1.106 0.88
264_H 267_N 1.105 0.88
223_E 481_V 1.103 0.88
266_V 480_V 1.102 0.88
299_I 498_S 1.099 0.88
47_E 166_A 1.098 0.88
58_Y 65_D 1.096 0.88
262_A 478_G 1.096 0.88
224_V 480_V 1.094 0.88
579_T 582_S 1.09 0.87
211_E 555_K 1.087 0.87
227_H 237_T 1.086 0.87
544_K 549_H 1.086 0.87
161_S 582_S 1.08 0.87
317_Q 321_E 1.075 0.86
535_L 539_G 1.072 0.86
226_A 429_I 1.071 0.86
268_R 430_A 1.069 0.86
300_E 304_R 1.067 0.86
407_A 411_L 1.065 0.86
420_F 447_R 1.062 0.85
222_F 259_R 1.056 0.85
597_G 601_Q 1.055 0.85
575_E 578_L 1.055 0.85
499_A 502_G 1.054 0.85
164_A 592_M 1.052 0.85
122_A 128_Q 1.05 0.85
346_A 350_A 1.047 0.84
213_I 490_H 1.047 0.84
281_D 440_F 1.042 0.84
10_S 14_A 1.038 0.84
295_S 525_E 1.036 0.83
307_L 312_V 1.034 0.83
269_I 478_G 1.033 0.83
318_K 396_T 1.03 0.83
475_C 478_G 1.03 0.83
550_S 555_K 1.029 0.83
309_A 529_A 1.028 0.83
286_E 447_R 1.027 0.83
541_L 548_I 1.026 0.83
241_Q 435_V 1.025 0.83
491_F 499_A 1.021 0.82
424_V 435_V 1.02 0.82
597_G 600_Y 1.017 0.82
371_R 417_D 1.013 0.82
210_D 214_E 1.011 0.81
298_Q 529_A 1.009 0.81
37_V 91_F 1.003 0.81
344_R 410_Y 1.003 0.81
543_K 546_R 1.001 0.80
280_N 424_V 1 0.80
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
1i7dA10.97241000.085Contact Map0.705
1mw9X10.86061000.227Contact Map0.754
2gaiA20.86831000.246Contact Map0.678
4dduA10.79331000.275Contact Map0.72
1gkuB10.77791000.283Contact Map0.644
1vddA40.203799.60.917Contact Map0.66
2fcjA30.17398.30.951Contact Map0.592
3vdpA40.17980.956Contact Map0.598
1r7jA10.14484.90.976Contact Map0.86
2x4hA40.203781.10.977Contact Map0.679
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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