| cox1 |
| ID: | 1499177135 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 500 (499) | ||
| Sequences: | 5451 (1879) | ||
| Seq/Len: | 10.924 | ||
| Nf(neff/√len): | 84.1 |
HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 10.924).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 19_F | 99_F | 3.830 | 1.00 |
| 421_E | 447_T | 3.826 | 1.00 |
| 329_P | 403_T | 3.476 | 1.00 |
| 254_I | 384_T | 3.448 | 1.00 |
| 247_G | 381_P | 3.002 | 1.00 |
| 351_W | 366_L | 2.917 | 1.00 |
| 329_P | 400_S | 2.892 | 1.00 |
| 187_I | 274_G | 2.863 | 1.00 |
| 174_S | 177_Q | 2.849 | 1.00 |
| 416_P | 450_E | 2.817 | 1.00 |
| 263_Y | 267_V | 2.786 | 1.00 |
| 23_A | 106_F | 2.693 | 1.00 |
| 20_G | 70_I | 2.690 | 1.00 |
| 390_A | 468_S | 2.663 | 1.00 |
| 175_Q | 178_T | 2.592 | 1.00 |
| 184_A | 270_M | 2.590 | 1.00 |
| 259_C | 320_M | 2.590 | 1.00 |
| 387_C | 406_W | 2.540 | 1.00 |
| 409_T | 457_A | 2.502 | 1.00 |
| 250_N | 385_T | 2.392 | 1.00 |
| 383_S | 461_W | 2.383 | 1.00 |
| 401_L | 405_I | 2.355 | 1.00 |
| 165_I | 186_L | 2.171 | 1.00 |
| 80_V | 165_I | 2.150 | 1.00 |
| 30_L | 54_I | 2.130 | 1.00 |
| 320_M | 331_M | 2.060 | 1.00 |
| 406_W | 410_P | 2.054 | 1.00 |
| 125_V | 228_I | 2.049 | 1.00 |
| 413_A | 453_S | 2.048 | 1.00 |
| 372_F | 415_D | 2.009 | 1.00 |
| 166_L | 175_Q | 1.990 | 1.00 |
| 399_D | 467_S | 1.951 | 1.00 |
| 2_R | 11_D | 1.942 | 1.00 |
| 258_L | 388_Q | 1.914 | 1.00 |
| 60_F | 125_V | 1.901 | 1.00 |
| 66_M | 379_L | 1.824 | 1.00 |
| 257_M | 388_Q | 1.810 | 1.00 |
| 255_C | 338_Y | 1.803 | 1.00 |
| 162_I | 186_L | 1.799 | 1.00 |
| 180_L | 260_T | 1.786 | 1.00 |
| 36_A | 452_Q | 1.785 | 1.00 |
| 402_W | 463_L | 1.773 | 1.00 |
| 387_C | 403_T | 1.769 | 1.00 |
| 475_S | 478_E | 1.767 | 1.00 |
| 402_W | 460_S | 1.764 | 1.00 |
| 488_G | 491_P | 1.757 | 1.00 |
| 121_T | 140_V | 1.745 | 1.00 |
| 333_W | 383_S | 1.736 | 1.00 |
| 276_N | 305_L | 1.730 | 1.00 |
| 449_F | 453_S | 1.725 | 1.00 |
| 336_S | 407_L | 1.711 | 1.00 |
| 147_L | 203_Y | 1.680 | 1.00 |
| 419_T | 423_Y | 1.677 | 1.00 |
| 416_P | 446_P | 1.672 | 1.00 |
| 333_W | 406_W | 1.671 | 1.00 |
| 287_T | 361_H | 1.669 | 1.00 |
| 42_G | 435_G | 1.656 | 1.00 |
| 83_M | 182_V | 1.644 | 1.00 |
| 46_G | 54_I | 1.628 | 1.00 |
| 235_Y | 239_E | 1.625 | 1.00 |
| 413_A | 450_E | 1.624 | 1.00 |
| 306_Q | 349_L | 1.622 | 1.00 |
| 441_L | 445_T | 1.619 | 1.00 |
| 49_Q | 53_V | 1.610 | 1.00 |
| 400_S | 404_K | 1.593 | 1.00 |
| 487_H | 491_P | 1.581 | 1.00 |
| 187_I | 271_H | 1.580 | 1.00 |
| 336_S | 411_Y | 1.576 | 1.00 |
| 320_M | 335_S | 1.559 | 1.00 |
| 386_S | 461_W | 1.558 | 1.00 |
| 14_T | 78_W | 1.556 | 1.00 |
| 409_T | 456_W | 1.554 | 1.00 |
| 195_V | 242_S | 1.547 | 1.00 |
| 19_F | 102_L | 1.536 | 1.00 |
| 60_F | 143_T | 1.532 | 1.00 |
| 41_P | 441_L | 1.525 | 1.00 |
| 409_T | 460_S | 1.518 | 1.00 |
| 119_A | 143_T | 1.508 | 1.00 |
| 169_K | 172_A | 1.505 | 1.00 |
| 195_V | 278_Y | 1.502 | 1.00 |
| 334_G | 384_T | 1.495 | 1.00 |
| 356_L | 360_L | 1.491 | 1.00 |
| 233_W | 236_S | 1.468 | 1.00 |
| 166_L | 190_V | 1.464 | 1.00 |
| 173_I | 178_T | 1.446 | 1.00 |
| 406_W | 461_W | 1.444 | 1.00 |
| 340_L | 415_D | 1.438 | 1.00 |
| 406_W | 457_A | 1.437 | 1.00 |
| 172_A | 177_Q | 1.428 | 1.00 |
| 250_N | 254_I | 1.424 | 1.00 |
| 487_H | 496_F | 1.412 | 1.00 |
| 415_D | 419_T | 1.403 | 0.99 |
| 474_P | 477_V | 1.393 | 0.99 |
| 406_W | 460_S | 1.393 | 0.99 |
| 248_F | 309_V | 1.388 | 0.99 |
| 209_P | 214_Y | 1.384 | 0.99 |
| 141_D | 210_K | 1.381 | 0.99 |
| 236_S | 239_E | 1.374 | 0.99 |
| 121_T | 130_A | 1.368 | 0.99 |
| 405_I | 460_S | 1.365 | 0.99 |
| 489_C | 492_P | 1.361 | 0.99 |
| 27_G | 61_V | 1.361 | 0.99 |
| 158_A | 189_A | 1.353 | 0.99 |
| 244_R | 248_F | 1.352 | 0.99 |
| 33_L | 54_I | 1.351 | 0.99 |
| 124_T | 232_S | 1.344 | 0.99 |
| 488_G | 492_P | 1.344 | 0.99 |
| 452_Q | 456_W | 1.341 | 0.99 |
| 383_S | 406_W | 1.339 | 0.99 |
| 459_L | 463_L | 1.339 | 0.99 |
| 165_I | 182_V | 1.336 | 0.99 |
| 109_L | 146_S | 1.336 | 0.99 |
| 166_L | 186_L | 1.336 | 0.99 |
| 202_R | 228_I | 1.322 | 0.99 |
| 8_N | 11_D | 1.311 | 0.99 |
| 467_S | 471_S | 1.311 | 0.99 |
| 467_S | 473_K | 1.308 | 0.99 |
| 15_L | 99_F | 1.306 | 0.99 |
| 99_F | 103_P | 1.300 | 0.99 |
| 487_H | 495_T | 1.299 | 0.99 |
| 141_D | 211_N | 1.298 | 0.99 |
| 406_W | 458_P | 1.298 | 0.99 |
| 390_A | 394_Q | 1.296 | 0.99 |
| 158_A | 193_L | 1.296 | 0.99 |
| 39_S | 445_T | 1.292 | 0.99 |
| 254_I | 385_T | 1.283 | 0.99 |
| 24_G | 31_S | 1.279 | 0.99 |
| 402_W | 405_I | 1.279 | 0.99 |
| 173_I | 179_P | 1.278 | 0.99 |
| 205_A | 217_L | 1.273 | 0.99 |
| 332_L | 407_L | 1.271 | 0.99 |
| 476_S | 479_L | 1.269 | 0.99 |
| 148_H | 204_N | 1.268 | 0.99 |
| 94_M | 156_L | 1.268 | 0.99 |
| 460_S | 463_L | 1.265 | 0.99 |
| 15_L | 96_N | 1.260 | 0.99 |
| 65_F | 106_F | 1.258 | 0.99 |
| 396_L | 472_E | 1.254 | 0.99 |
| 351_W | 360_L | 1.253 | 0.99 |
| 32_L | 455_L | 1.253 | 0.99 |
| 19_F | 103_P | 1.252 | 0.99 |
| 350_S | 365_T | 1.251 | 0.99 |
| 125_V | 143_T | 1.249 | 0.99 |
| 405_I | 409_T | 1.248 | 0.99 |
| 368_A | 422_L | 1.246 | 0.98 |
| 256_S | 260_T | 1.240 | 0.98 |
| 472_E | 475_S | 1.238 | 0.98 |
| 494_H | 497_E | 1.231 | 0.98 |
| 254_I | 330_P | 1.230 | 0.98 |
| 466_Y | 470_S | 1.221 | 0.98 |
| 160_N | 164_T | 1.218 | 0.98 |
| 192_L | 196_P | 1.208 | 0.98 |
| 252_S | 316_W | 1.200 | 0.98 |
| 77_N | 95_N | 1.200 | 0.98 |
| 372_F | 419_T | 1.199 | 0.98 |
| 198_R | 234_L | 1.190 | 0.98 |
| 80_V | 182_V | 1.189 | 0.98 |
| 127_P | 228_I | 1.188 | 0.98 |
| 442_T | 446_P | 1.187 | 0.98 |
| 77_N | 160_N | 1.183 | 0.98 |
| 299_F | 354_H | 1.183 | 0.98 |
| 65_F | 150_A | 1.174 | 0.98 |
| 421_E | 424_L | 1.172 | 0.98 |
| 487_H | 492_P | 1.168 | 0.97 |
| 491_P | 496_F | 1.165 | 0.97 |
| 181_F | 185_V | 1.159 | 0.97 |
| 243_T | 374_M | 1.154 | 0.97 |
| 463_L | 466_Y | 1.153 | 0.97 |
| 425_W | 428_W | 1.151 | 0.97 |
| 349_L | 352_P | 1.150 | 0.97 |
| 327_Y | 331_M | 1.141 | 0.97 |
| 463_L | 467_S | 1.137 | 0.97 |
| 125_V | 140_V | 1.135 | 0.97 |
| 93_R | 97_M | 1.134 | 0.97 |
| 258_L | 330_P | 1.133 | 0.97 |
| 410_P | 457_A | 1.130 | 0.97 |
| 48_D | 434_P | 1.129 | 0.97 |
| 125_V | 130_A | 1.127 | 0.97 |
| 392_L | 489_C | 1.123 | 0.97 |
| 487_H | 493_Y | 1.121 | 0.97 |
| 6_S | 11_D | 1.121 | 0.97 |
| 79_L | 83_M | 1.120 | 0.96 |
| 175_Q | 186_L | 1.114 | 0.96 |
| 329_P | 404_K | 1.112 | 0.96 |
| 416_P | 453_S | 1.111 | 0.96 |
| 474_P | 478_E | 1.111 | 0.96 |
| 413_A | 457_A | 1.109 | 0.96 |
| 96_N | 100_W | 1.107 | 0.96 |
| 19_F | 23_A | 1.105 | 0.96 |
| 80_V | 84_I | 1.104 | 0.96 |
| 66_M | 70_I | 1.101 | 0.96 |
| 24_G | 66_M | 1.099 | 0.96 |
| 449_F | 452_Q | 1.098 | 0.96 |
| 25_M | 29_A | 1.095 | 0.96 |
| 70_I | 382_T | 1.094 | 0.96 |
| 357_D | 366_L | 1.087 | 0.96 |
| 111_A | 142_L | 1.086 | 0.96 |
| 34_I | 54_I | 1.086 | 0.96 |
| 208_R | 214_Y | 1.084 | 0.96 |
| 266_M | 270_M | 1.081 | 0.95 |
| 22_W | 26_V | 1.078 | 0.95 |
| 430_S | 433_W | 1.077 | 0.95 |
| 26_V | 61_V | 1.072 | 0.95 |
| 176_Y | 268_W | 1.071 | 0.95 |
| 187_I | 270_M | 1.070 | 0.95 |
| 376_I | 414_R | 1.070 | 0.95 |
| 84_I | 182_V | 1.070 | 0.95 |
| 40_Q | 43_A | 1.068 | 0.95 |
| 486_L | 492_P | 1.067 | 0.95 |
| 121_T | 125_V | 1.064 | 0.95 |
| 283_H | 369_H | 1.063 | 0.95 |
| 29_A | 33_L | 1.063 | 0.95 |
| 237_H | 240_V | 1.063 | 0.95 |
| 368_A | 421_E | 1.060 | 0.95 |
| 254_I | 334_G | 1.055 | 0.95 |
| 383_S | 387_C | 1.052 | 0.95 |
| 17_L | 74_G | 1.050 | 0.94 |
| 420_S | 443_I | 1.047 | 0.94 |
| 386_S | 465_L | 1.043 | 0.94 |
| 332_L | 404_K | 1.041 | 0.94 |
| 14_T | 393_W | 1.041 | 0.94 |
| 381_P | 384_T | 1.040 | 0.94 |
| 130_A | 206_P | 1.039 | 0.94 |
| 241_Y | 246_P | 1.039 | 0.94 |
| 57_A | 113_S | 1.037 | 0.94 |
| 307_Q | 311_K | 1.037 | 0.94 |
| 28_T | 31_S | 1.036 | 0.94 |
| 303_W | 352_P | 1.034 | 0.94 |
| 131_G | 134_A | 1.034 | 0.94 |
| 12_I | 95_N | 1.031 | 0.94 |
| 37_E | 435_G | 1.031 | 0.94 |
| 229_L | 362_D | 1.031 | 0.94 |
| 423_Y | 443_I | 1.030 | 0.94 |
| 208_R | 212_L | 1.030 | 0.94 |
| 67_V | 379_L | 1.025 | 0.93 |
| 9_H | 13_G | 1.024 | 0.93 |
| 76_G | 185_V | 1.024 | 0.93 |
| 417_K | 451_M | 1.021 | 0.93 |
| 258_L | 331_M | 1.016 | 0.93 |
| 344_W | 373_T | 1.016 | 0.93 |
| 477_V | 480_T | 1.016 | 0.93 |
| 286_S | 354_H | 1.015 | 0.93 |
| 288_P | 362_D | 1.008 | 0.93 |
| 162_I | 193_L | 1.008 | 0.93 |
| 412_T | 416_P | 1.006 | 0.93 |
| 148_H | 203_Y | 1.001 | 0.92 |
| 325_E | 331_M | 1.001 | 0.92 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
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-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 1fftA | 2 | 0.978 | 100 | 0.006 | Contact Map |
| 2yevA | 2 | 0.994 | 100 | 0.02 | Contact Map |
| 1v54A | 2 | 1 | 100 | 0.023 | Contact Map |
| 2gsmA | 2 | 0.988 | 100 | 0.024 | Contact Map |
| 3s8fA | 1 | 0.962 | 100 | 0.203 | Contact Map |
| 3ayfA | 1 | 0.894 | 100 | 0.227 | Contact Map |
| 3mk7A | 4 | 0.872 | 100 | 0.239 | Contact Map |
| 3wfdB | 1 | 0.836 | 100 | 0.269 | Contact Map |
| 4o6yA | 2 | 0.29 | 4.2 | 0.98 | Contact Map |
| 4xtlA | 1 | 0.466 | 2.5 | 0.982 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)