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CYDD - ATP-binding/permease protein CydD
UniProt: P29018 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG11405
Length: 588 (574)
Sequences: 20839
Seq/Len: 36.30
CYDD
Paralog alert: 0.94 [within 20: 0.61] - ratio of genomes with paralogs
Cluster includes: CYDC CYDD MDLA MDLB MSBA YDDA YOJI
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
354_E 368_P 5.412 1.00
465_S 475_V 5.334 1.00
377_Q 552_V 4.913 1.00
351_E 372_T 4.767 1.00
374_P 377_Q 4.717 1.00
353_E 405_S 4.448 1.00
567_Y 577_F 4.419 1.00
440_R 452_E 4.331 1.00
437_A 441_D 4.223 1.00
552_V 564_Q 4.161 1.00
460_D 465_S 3.989 1.00
353_E 407_R 3.909 1.00
465_S 469_P 3.778 1.00
405_S 412_E 3.641 1.00
367_G 560_R 3.601 1.00
440_R 476_D 3.568 1.00
349_T 372_T 3.493 1.00
356_F 368_P 3.487 1.00
459_L 475_V 3.3 1.00
451_S 454_E 3.282 1.00
352_A 355_L 3.239 1.00
574_G 578_A 3.234 1.00
440_R 444_L 3.213 1.00
393_L 540_V 3.206 1.00
452_E 456_Q 3.089 1.00
447_R 454_E 2.999 1.00
443_V 459_L 2.982 1.00
440_R 455_L 2.929 1.00
578_A 582_A 2.928 1.00
457_A 461_N 2.891 1.00
426_S 504_C 2.817 1.00
393_L 508_L 2.799 1.00
443_V 455_L 2.78 1.00
566_R 569_E 2.78 1.00
351_E 407_R 2.761 1.00
373_L 379_A 2.684 1.00
456_Q 460_D 2.666 1.00
371_F 554_W 2.661 1.00
563_E 575_G 2.592 1.00
456_Q 465_S 2.516 1.00
417_S 420_S 2.495 1.00
473_Q 477_T 2.488 1.00
424_H 505_S 2.479 1.00
563_E 574_G 2.472 1.00
349_T 374_P 2.466 1.00
364_T 367_G 2.452 1.00
444_L 455_L 2.359 1.00
356_F 403_Q 2.357 1.00
349_T 375_A 2.322 1.00
464_V 467_F 2.311 1.00
554_W 564_Q 2.307 1.00
352_A 371_F 2.3 1.00
156_V 160_P 2.296 1.00
563_E 573_A 2.279 1.00
503_P 535_Q 2.239 1.00
378_R 550_W 2.217 1.00
456_Q 469_P 2.177 1.00
529_N 549_D 2.091 1.00
457_A 460_D 2.054 1.00
354_E 370_N 2.044 1.00
557_Q 576_P 2.023 1.00
373_L 538_L 2.018 1.00
356_F 364_T 2.006 1.00
379_A 552_V 2.002 1.00
458_A 462_A 1.977 1.00
366_A 369_L 1.952 1.00
444_L 452_E 1.934 1.00
459_L 468_L 1.915 1.00
381_L 392_L 1.899 1.00
453_Q 456_Q 1.896 1.00
350_I 538_L 1.891 1.00
454_E 503_P 1.832 1.00
412_E 415_D 1.832 1.00
325_K 329_E 1.767 1.00
521_E 543_Q 1.76 1.00
562_I 576_P 1.757 1.00
268_F 272_Y 1.75 1.00
563_E 578_A 1.742 1.00
20_S 97_A 1.728 1.00
220_R 223_A 1.719 1.00
379_A 554_W 1.719 1.00
392_L 556_M 1.718 1.00
565_G 569_E 1.717 1.00
554_W 561_I 1.713 1.00
541_T 546_D 1.706 1.00
454_E 457_A 1.705 1.00
463_W 523_R 1.703 1.00
357_I 391_S 1.69 1.00
452_E 476_D 1.683 1.00
548_A 568_A 1.678 1.00
466_E 469_P 1.677 1.00
378_R 539_M 1.671 1.00
368_P 560_R 1.667 1.00
16_Q 101_Q 1.66 1.00
456_Q 475_V 1.648 1.00
461_N 530_A 1.645 1.00
480_G 485_R 1.633 1.00
67_T 71_L 1.632 1.00
557_Q 562_I 1.629 1.00
381_L 554_W 1.622 1.00
18_V 21_Q 1.614 1.00
105_R 109_A 1.613 1.00
516_L 524_V 1.603 1.00
129_Q 323_S 1.589 1.00
571_S 581_L 1.587 1.00
377_Q 551_D 1.585 1.00
439_L 494_V 1.583 1.00
459_L 465_S 1.573 1.00
401_S 413_L 1.571 1.00
105_R 332_L 1.549 1.00
50_Q 277_D 1.537 1.00
358_T 402_Y 1.532 1.00
450_A 501_L 1.521 1.00
530_A 533_L 1.52 1.00
473_Q 478_P 1.515 1.00
452_E 455_L 1.513 1.00
397_S 427_W 1.481 1.00
12_W 329_E 1.467 1.00
408_I 506_L 1.466 1.00
349_T 409_N 1.466 1.00
471_L 477_T 1.462 1.00
371_F 392_L 1.458 1.00
443_V 501_L 1.458 1.00
468_L 475_V 1.458 1.00
569_E 573_A 1.457 1.00
197_A 234_D 1.454 1.00
522_Q 526_E 1.454 1.00
406_L 413_L 1.445 1.00
380_V 550_W 1.443 1.00
357_I 400_L 1.435 1.00
269_G 273_L 1.432 1.00
384_R 576_P 1.431 1.00
436_A 478_P 1.41 1.00
464_V 468_L 1.408 1.00
444_L 450_A 1.408 1.00
115_Q 400_L 1.406 0.99
159_F 163_W 1.404 0.99
461_N 500_L 1.395 0.99
479_V 486_L 1.393 0.99
186_G 189_D 1.39 0.99
374_P 552_V 1.384 0.99
553_I 567_Y 1.381 0.99
458_A 500_L 1.376 0.99
385_S 520_S 1.373 0.99
395_A 406_L 1.37 0.99
46_A 50_Q 1.369 0.99
369_L 392_L 1.368 0.99
369_L 561_I 1.361 0.99
163_W 167_L 1.358 0.99
426_S 499_A 1.353 0.99
384_R 557_Q 1.351 0.99
526_E 530_A 1.345 0.99
108_Q 332_L 1.334 0.99
211_G 433_Q 1.327 0.99
357_I 395_A 1.323 0.99
336_Q 417_S 1.317 0.99
447_R 450_A 1.313 0.99
541_T 547_L 1.303 0.99
224_E 445_L 1.302 0.99
576_P 579_T 1.297 0.99
488_V 493_R 1.291 0.99
102_V 327_F 1.285 0.99
454_E 501_L 1.283 0.99
556_M 561_I 1.281 0.99
470_L 490_Q 1.279 0.99
411_I 415_D 1.278 0.99
467_F 490_Q 1.275 0.99
352_A 396_L 1.272 0.99
469_P 474_G 1.265 0.99
351_E 410_G 1.26 0.99
192_R 322_D 1.259 0.99
348_V 409_N 1.257 0.99
216_R 221_G 1.252 0.99
380_V 547_L 1.248 0.99
396_L 538_L 1.23 0.98
346_D 349_T 1.229 0.98
459_L 464_V 1.221 0.98
159_F 166_A 1.221 0.98
226_E 230_S 1.22 0.98
222_E 226_E 1.219 0.98
532_S 537_T 1.217 0.98
347_P 409_N 1.211 0.98
450_A 454_E 1.211 0.98
356_F 367_G 1.208 0.98
200_R 234_D 1.207 0.98
473_Q 476_D 1.203 0.98
178_L 182_L 1.203 0.98
353_E 370_N 1.201 0.98
378_R 537_T 1.201 0.98
105_R 328_M 1.201 0.98
358_T 364_T 1.194 0.98
568_A 572_V 1.192 0.98
443_V 494_V 1.191 0.98
463_W 520_S 1.189 0.98
162_N 271_S 1.183 0.98
350_I 408_I 1.176 0.98
132_D 320_A 1.17 0.97
241_E 244_R 1.167 0.97
352_A 392_L 1.165 0.97
480_G 483_A 1.159 0.97
567_Y 571_S 1.159 0.97
224_E 227_S 1.157 0.97
228_I 232_S 1.155 0.97
33_V 79_V 1.15 0.97
456_Q 459_L 1.148 0.97
469_P 475_V 1.147 0.97
453_Q 457_A 1.146 0.97
440_R 475_V 1.143 0.97
118_P 121_S 1.14 0.97
418_P 422_R 1.139 0.97
354_E 403_Q 1.136 0.97
204_H 231_A 1.134 0.97
463_W 526_E 1.133 0.97
208_R 224_E 1.133 0.97
486_L 494_V 1.132 0.97
411_I 416_L 1.123 0.97
197_A 200_R 1.123 0.97
457_A 503_P 1.113 0.96
379_A 538_L 1.11 0.96
63_L 67_T 1.11 0.96
355_L 395_A 1.108 0.96
467_F 471_L 1.108 0.96
479_V 485_R 1.096 0.96
385_S 493_R 1.095 0.96
458_A 501_L 1.094 0.96
117_K 121_S 1.091 0.96
466_E 470_L 1.089 0.96
266_V 270_F 1.089 0.96
19_I 97_A 1.087 0.96
428_V 496_V 1.084 0.96
455_L 475_V 1.084 0.96
464_V 470_L 1.083 0.96
105_R 108_Q 1.075 0.95
349_T 410_G 1.069 0.95
496_V 509_L 1.067 0.95
25_N 29_L 1.065 0.95
100_R 104_D 1.062 0.95
290_G 293_A 1.057 0.95
351_E 370_N 1.057 0.95
50_Q 279_G 1.057 0.95
375_A 505_S 1.057 0.95
351_E 405_S 1.057 0.95
21_Q 25_N 1.055 0.95
30_L 79_V 1.053 0.95
428_V 499_A 1.051 0.94
268_F 271_S 1.051 0.94
115_Q 394_N 1.05 0.94
405_S 414_R 1.046 0.94
451_S 501_L 1.045 0.94
64_L 68_L 1.044 0.94
401_S 406_L 1.039 0.94
197_A 238_R 1.038 0.94
543_Q 546_D 1.037 0.94
373_L 536_T 1.034 0.94
440_R 456_Q 1.031 0.94
121_S 199_A 1.025 0.93
441_D 444_L 1.02 0.93
30_L 82_L 1.02 0.93
220_R 224_E 1.01 0.93
110_G 333_A 1.01 0.93
125_L 326_T 1.009 0.93
321_A 325_K 1.006 0.93
352_A 406_L 1.005 0.93
375_A 409_N 1.005 0.93
350_I 506_L 1.003 0.93
432_P 495_A 1.001 0.92
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
3qf4B10.98131000.157Contact Map0.717
3b5xA20.97791000.168Contact Map0.104
4a82A40.9661000.168Contact Map0.078
3b60A40.97791000.17Contact Map0.75
4f4cA10.98471000.171Contact Map0.714
3qf4A10.98131000.174Contact Map0.736
2yl4A10.97961000.181Contact Map0.705
3g5uA20.98471000.187Contact Map0.684
3nh6A10.49491000.433Contact Map0.768
3vx4A20.46091000.496Contact Map0.842
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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