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OPENSEQ.org
CYDA - Cytochrome d ubiquinol oxidase subunit 1
UniProt: P0ABJ9 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG10173
Length: 522 (493)
Sequences: 1279
Seq/Len: 2.59
CYDA
Paralog alert: 0.45 [within 20: 0.00] - ratio of genomes with paralogs
Cluster includes: APPC CYDA
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
170_S 173_E 6.263 1.00
452_A 462_A 5.324 1.00
201_G 430_I 4.921 1.00
276_D 283_K 4.822 1.00
235_I 401_L 4.244 1.00
273_G 282_N 3.649 1.00
128_C 132_L 3.557 1.00
297_T 302_T 3.315 1.00
261_E 308_K 3.311 1.00
276_D 279_E 3.092 1.00
189_A 237_L 2.995 1.00
280_E 308_K 2.954 1.00
294_I 300_V 2.898 1.00
194_T 437_V 2.744 1.00
398_F 402_A 2.725 1.00
44_G 123_K 2.717 1.00
239_D 298_R 2.595 1.00
224_A 407_S 2.587 1.00
34_A 131_W 2.529 1.00
239_D 243_Y 2.486 1.00
197_M 227_G 2.474 1.00
469_G 473_F 2.431 1.00
3_D 6_E 2.273 1.00
442_F 446_Y 2.249 1.00
420_K 424_R 2.236 1.00
243_Y 298_R 2.179 1.00
266_P 290_Y 2.155 1.00
121_L 129_V 2.15 1.00
280_E 380_I 2.148 1.00
410_S 422_L 2.135 1.00
41_V 127_M 2.132 1.00
396_C 400_L 2.034 1.00
290_Y 300_V 2.01 0.99
20_F 187_T 1.973 0.99
270_T 287_Q 1.944 0.99
251_T 310_L 1.92 0.99
282_N 285_A 1.911 0.99
88_V 92_F 1.878 0.99
472_I 476_V 1.854 0.99
399_L 429_G 1.847 0.99
158_D 169_V 1.846 0.99
35_I 39_V 1.838 0.99
38_T 131_W 1.802 0.99
270_T 387_Y 1.765 0.98
26_T 62_N 1.76 0.98
38_T 127_M 1.743 0.98
424_R 428_Y 1.736 0.98
122_G 125_Q 1.718 0.98
231_V 401_L 1.705 0.98
17_M 438_E 1.704 0.98
385_P 446_Y 1.696 0.98
279_E 283_K 1.685 0.98
55_W 219_S 1.68 0.98
421_W 424_R 1.665 0.97
403_I 429_G 1.661 0.97
14_L 479_C 1.655 0.97
268_A 287_Q 1.649 0.97
379_S 458_P 1.644 0.97
172_S 175_V 1.636 0.97
51_M 219_S 1.629 0.97
197_M 403_I 1.62 0.97
58_L 493_M 1.618 0.97
14_L 475_M 1.585 0.96
270_T 273_G 1.584 0.96
4_I 8_S 1.584 0.96
113_L 121_L 1.578 0.96
33_L 130_T 1.577 0.96
17_M 442_F 1.571 0.96
260_W 282_N 1.566 0.96
262_T 303_P 1.552 0.95
8_S 471_L 1.551 0.95
382_R 446_Y 1.545 0.95
221_A 411_V 1.544 0.95
83_Y 86_H 1.532 0.95
92_F 147_A 1.528 0.95
157_S 456_V 1.512 0.95
320_N 347_M 1.508 0.94
168_M 174_L 1.501 0.94
449_Q 459_T 1.491 0.94
37_E 127_M 1.48 0.94
25_L 198_F 1.478 0.94
277_Q 384_A 1.472 0.94
494_F 498_R 1.472 0.94
58_L 198_F 1.465 0.93
196_A 227_G 1.463 0.93
185_V 237_L 1.434 0.92
484_L 488_A 1.429 0.92
46_Q 50_D 1.416 0.92
5_V 463_N 1.415 0.92
273_G 285_A 1.412 0.92
142_L 146_V 1.409 0.91
160_N 163_T 1.407 0.91
4_I 468_A 1.402 0.91
477_L 481_L 1.397 0.91
407_S 422_L 1.379 0.90
392_I 439_A 1.375 0.90
203_S 219_S 1.371 0.90
13_A 446_Y 1.368 0.90
40_Y 49_K 1.366 0.90
406_L 410_S 1.365 0.90
292_L 304_V 1.359 0.89
429_G 432_L 1.357 0.89
60_G 115_F 1.357 0.89
405_A 409_W 1.354 0.89
342_D 346_S 1.351 0.89
106_L 136_G 1.348 0.89
87_Y 166_M 1.346 0.89
317_R 350_D 1.345 0.89
474_S 477_L 1.338 0.88
207_M 213_F 1.337 0.88
392_I 435_I 1.332 0.88
25_L 29_M 1.331 0.88
457_L 462_A 1.329 0.88
200_L 223_A 1.324 0.88
34_A 38_T 1.315 0.87
231_V 235_I 1.312 0.87
135_L 139_L 1.305 0.87
265_A 303_P 1.302 0.86
311_M 376_T 1.294 0.86
18_Y 486_L 1.294 0.86
118_W 126_H 1.293 0.86
33_L 52_T 1.287 0.86
458_P 461_V 1.283 0.85
145_L 180_A 1.283 0.85
53_K 118_W 1.281 0.85
473_F 477_L 1.281 0.85
27_L 191_G 1.279 0.85
146_V 180_A 1.277 0.85
278_E 281_T 1.274 0.85
205_W 209_K 1.257 0.84
36_M 51_M 1.255 0.84
25_L 434_W 1.254 0.84
84_Y 88_V 1.25 0.83
47_I 218_R 1.247 0.83
37_E 118_W 1.245 0.83
197_M 426_A 1.245 0.83
141_A 188_V 1.234 0.82
62_N 198_F 1.232 0.82
229_A 233_S 1.221 0.81
338_Q 342_D 1.218 0.81
90_D 165_R 1.218 0.81
195_G 433_P 1.216 0.81
483_T 487_V 1.216 0.81
114_F 130_T 1.208 0.80
403_I 425_A 1.199 0.80
196_A 223_A 1.198 0.80
363_N 380_I 1.194 0.79
256_I 443_V 1.191 0.79
415_R 418_E 1.19 0.79
98_I 171_F 1.184 0.78
133_V 137_S 1.18 0.78
315_E 319_R 1.17 0.77
305_I 313_Q 1.17 0.77
480_G 484_L 1.165 0.77
395_A 399_L 1.162 0.77
290_Y 302_T 1.155 0.76
242_G 295_I 1.153 0.76
402_A 406_L 1.152 0.76
134_A 138_N 1.148 0.75
190_S 437_V 1.147 0.75
39_V 45_K 1.146 0.75
48_Y 501_P 1.13 0.74
382_R 385_P 1.129 0.74
206_Y 211_R 1.128 0.74
31_F 134_A 1.127 0.73
290_Y 294_I 1.127 0.73
406_L 421_W 1.127 0.73
221_A 225_S 1.125 0.73
160_N 167_E 1.113 0.72
24_P 92_F 1.108 0.72
276_D 281_T 1.108 0.72
396_C 432_L 1.107 0.72
337_D 340_V 1.105 0.71
200_L 224_A 1.105 0.71
246_G 253_L 1.103 0.71
345_N 348_K 1.101 0.71
49_K 53_K 1.099 0.71
184_F 188_V 1.098 0.71
231_V 404_I 1.098 0.71
253_L 256_I 1.096 0.70
273_G 284_F 1.092 0.70
52_T 118_W 1.092 0.70
251_T 307_L 1.088 0.70
334_G 337_D 1.086 0.69
53_K 123_K 1.084 0.69
54_F 500_G 1.084 0.69
138_N 188_V 1.083 0.69
113_L 129_V 1.082 0.69
297_T 301_D 1.075 0.68
31_F 34_A 1.066 0.67
491_F 495_K 1.065 0.67
334_G 340_V 1.063 0.67
403_I 426_A 1.063 0.67
360_Y 378_D 1.06 0.67
208_L 420_K 1.059 0.67
312_V 315_E 1.056 0.66
208_L 427_L 1.054 0.66
403_I 432_L 1.052 0.66
258_A 273_G 1.051 0.66
299_S 302_T 1.05 0.66
153_N 179_V 1.046 0.65
88_V 453_I 1.046 0.65
409_W 412_I 1.046 0.65
46_Q 123_K 1.044 0.65
253_L 292_L 1.043 0.65
330_Q 335_S 1.04 0.65
131_W 135_L 1.036 0.64
39_V 42_L 1.035 0.64
118_W 500_G 1.035 0.64
204_A 423_L 1.032 0.64
335_S 340_V 1.031 0.64
469_G 472_I 1.031 0.64
260_W 280_E 1.03 0.64
49_K 118_W 1.027 0.63
297_T 303_P 1.027 0.63
294_I 298_R 1.024 0.63
253_L 304_V 1.014 0.62
320_N 350_D 1.014 0.62
269_F 295_I 1.012 0.62
5_V 460_A 1.008 0.61
21_L 434_W 1.006 0.61
399_L 402_A 1.001 0.60
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
4m48A10.377457.70.98Contact Map0.161
2a65A10.373629.10.983Contact Map0.23
3mk7A40.375527.70.983Contact Map0.209
1v54A20.413812.10.986Contact Map0.309
3kp9A10.496211.30.986Contact Map0.045
3s8fA10.434990.987Contact Map0.242
3o0rB10.36217.20.987Contact Map0.299
2gsmA20.43150.988Contact Map0.331
3es5A20.1134.90.988Contact Map0.014
3ayfA10.42914.40.989Contact Map0.195
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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