| T0826 |
| ID: | 1403223478 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 544 (537) | ||
| Sequences: | 967 (750.6) | ||
| Seq/Len: | 1.801 | ||
| Nf(neff/√len): | 32.4 |
Jackhmmer Results: (2014_04_16)
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: 1.801).
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 |
| 237_V | 430_I | 4.600 | 1.00 |
| 517_T | 537_L | 4.466 | 1.00 |
| 382_S | 422_T | 4.454 | 1.00 |
| 248_G | 257_T | 4.133 | 1.00 |
| 307_L | 518_V | 4.019 | 1.00 |
| 250_N | 269_N | 3.956 | 1.00 |
| 397_K | 424_L | 3.355 | 1.00 |
| 327_C | 331_C | 3.166 | 1.00 |
| 433_V | 447_V | 3.080 | 1.00 |
| 435_R | 438_E | 2.952 | 1.00 |
| 363_D | 436_K | 2.935 | 1.00 |
| 450_V | 511_H | 2.866 | 1.00 |
| 520_G | 535_D | 2.713 | 1.00 |
| 259_L | 431_D | 2.535 | 1.00 |
| 248_G | 255_Q | 2.390 | 1.00 |
| 259_L | 428_Q | 2.389 | 1.00 |
| 392_T | 425_Y | 2.296 | 1.00 |
| 273_V | 509_Y | 2.287 | 1.00 |
| 396_R | 401_T | 2.280 | 1.00 |
| 242_T | 423_V | 2.274 | 1.00 |
| 263_R | 431_D | 2.253 | 1.00 |
| 530_Y | 535_D | 2.218 | 0.99 |
| 363_D | 440_R | 2.131 | 0.99 |
| 242_T | 426_V | 2.113 | 0.99 |
| 245_A | 475_G | 2.075 | 0.99 |
| 356_N | 425_Y | 2.070 | 0.99 |
| 429_F | 433_V | 2.013 | 0.99 |
| 131_G | 135_A | 2.007 | 0.99 |
| 311_V | 522_M | 1.992 | 0.99 |
| 290_T | 304_Q | 1.989 | 0.99 |
| 242_T | 247_W | 1.968 | 0.98 |
| 430_I | 447_V | 1.959 | 0.98 |
| 395_E | 428_Q | 1.916 | 0.98 |
| 462_M | 467_A | 1.910 | 0.98 |
| 252_Y | 420_D | 1.887 | 0.98 |
| 520_G | 530_Y | 1.887 | 0.98 |
| 236_L | 514_Y | 1.883 | 0.98 |
| 59_F | 165_C | 1.849 | 0.97 |
| 242_T | 382_S | 1.831 | 0.97 |
| 255_Q | 424_L | 1.814 | 0.97 |
| 234_V | 374_V | 1.814 | 0.97 |
| 499_C | 540_C | 1.812 | 0.97 |
| 255_Q | 261_A | 1.783 | 0.97 |
| 396_R | 399_T | 1.765 | 0.96 |
| 233_F | 443_L | 1.763 | 0.96 |
| 82_L | 138_Y | 1.757 | 0.96 |
| 62_N | 162_S | 1.743 | 0.96 |
| 103_M | 106_N | 1.726 | 0.96 |
| 246_N | 416_V | 1.713 | 0.96 |
| 276_C | 286_C | 1.711 | 0.96 |
| 248_G | 261_A | 1.707 | 0.95 |
| 465_H | 468_P | 1.702 | 0.95 |
| 474_S | 477_T | 1.694 | 0.95 |
| 79_P | 139_I | 1.694 | 0.95 |
| 244_A | 269_N | 1.685 | 0.95 |
| 516_S | 534_M | 1.681 | 0.95 |
| 52_T | 177_Y | 1.681 | 0.95 |
| 236_L | 374_V | 1.666 | 0.95 |
| 247_W | 379_T | 1.637 | 0.94 |
| 249_L | 257_T | 1.632 | 0.94 |
| 254_R | 420_D | 1.610 | 0.93 |
| 22_Y | 27_L | 1.578 | 0.92 |
| 234_V | 446_V | 1.577 | 0.92 |
| 358_L | 429_F | 1.569 | 0.92 |
| 97_I | 467_A | 1.563 | 0.92 |
| 401_T | 418_T | 1.554 | 0.91 |
| 216_Q | 219_M | 1.543 | 0.91 |
| 79_P | 135_A | 1.528 | 0.91 |
| 49_F | 177_Y | 1.522 | 0.90 |
| 395_E | 425_Y | 1.518 | 0.90 |
| 519_L | 526_N | 1.518 | 0.90 |
| 117_R | 380_I | 1.499 | 0.89 |
| 393_E | 396_R | 1.498 | 0.89 |
| 292_D | 534_M | 1.496 | 0.89 |
| 15_L | 138_Y | 1.496 | 0.89 |
| 348_C | 353_C | 1.487 | 0.89 |
| 257_T | 261_A | 1.475 | 0.88 |
| 317_E | 371_K | 1.470 | 0.88 |
| 273_V | 481_M | 1.468 | 0.88 |
| 214_Y | 305_D | 1.464 | 0.88 |
| 274_R | 477_T | 1.462 | 0.88 |
| 151_E | 155_R | 1.454 | 0.87 |
| 256_T | 420_D | 1.453 | 0.87 |
| 246_N | 420_D | 1.440 | 0.87 |
| 244_A | 478_H | 1.433 | 0.86 |
| 110_T | 114_E | 1.428 | 0.86 |
| 263_R | 435_R | 1.425 | 0.86 |
| 246_N | 475_G | 1.404 | 0.85 |
| 287_M | 450_V | 1.404 | 0.85 |
| 318_V | 334_V | 1.392 | 0.84 |
| 287_M | 514_Y | 1.389 | 0.84 |
| 474_S | 478_H | 1.383 | 0.84 |
| 203_K | 257_T | 1.380 | 0.83 |
| 354_L | 392_T | 1.366 | 0.83 |
| 117_R | 386_T | 1.365 | 0.83 |
| 306_N | 332_G | 1.364 | 0.82 |
| 254_R | 417_N | 1.359 | 0.82 |
| 241_T | 451_S | 1.357 | 0.82 |
| 532_K | 538_A | 1.357 | 0.82 |
| 10_L | 14_A | 1.356 | 0.82 |
| 23_S | 65_F | 1.355 | 0.82 |
| 230_L | 444_E | 1.346 | 0.81 |
| 173_Q | 177_Y | 1.345 | 0.81 |
| 311_V | 374_V | 1.340 | 0.81 |
| 489_F | 517_T | 1.339 | 0.81 |
| 403_D | 418_T | 1.339 | 0.81 |
| 271_P | 505_A | 1.333 | 0.80 |
| 79_P | 138_Y | 1.328 | 0.80 |
| 509_Y | 536_I | 1.325 | 0.80 |
| 249_L | 260_L | 1.316 | 0.79 |
| 195_N | 327_C | 1.313 | 0.79 |
| 263_R | 438_E | 1.309 | 0.79 |
| 362_F | 433_V | 1.306 | 0.79 |
| 311_V | 316_V | 1.304 | 0.78 |
| 218_D | 221_V | 1.299 | 0.78 |
| 233_F | 366_L | 1.288 | 0.77 |
| 503_K | 507_N | 1.285 | 0.77 |
| 526_N | 529_T | 1.281 | 0.77 |
| 468_P | 476_Q | 1.277 | 0.76 |
| 316_V | 522_M | 1.276 | 0.76 |
| 195_N | 331_C | 1.275 | 0.76 |
| 11_G | 14_A | 1.269 | 0.76 |
| 431_D | 435_R | 1.260 | 0.75 |
| 391_Y | 401_T | 1.249 | 0.74 |
| 359_L | 436_K | 1.245 | 0.74 |
| 450_V | 514_Y | 1.242 | 0.73 |
| 111_T | 325_S | 1.240 | 0.73 |
| 359_L | 363_D | 1.233 | 0.73 |
| 214_Y | 333_K | 1.232 | 0.73 |
| 242_T | 451_S | 1.228 | 0.72 |
| 387_Y | 455_E | 1.226 | 0.72 |
| 87_A | 127_I | 1.223 | 0.72 |
| 117_R | 389_E | 1.219 | 0.71 |
| 379_T | 429_F | 1.217 | 0.71 |
| 290_T | 515_F | 1.217 | 0.71 |
| 411_T | 414_T | 1.215 | 0.71 |
| 276_C | 472_A | 1.214 | 0.71 |
| 446_V | 489_F | 1.211 | 0.71 |
| 272_Q | 508_E | 1.210 | 0.71 |
| 280_T | 383_H | 1.193 | 0.69 |
| 420_D | 484_W | 1.186 | 0.68 |
| 321_L | 361_K | 1.183 | 0.68 |
| 309_D | 334_V | 1.183 | 0.68 |
| 311_V | 518_V | 1.182 | 0.68 |
| 267_I | 482_V | 1.180 | 0.68 |
| 312_Q | 335_P | 1.168 | 0.67 |
| 402_C | 410_C | 1.166 | 0.67 |
| 165_C | 168_G | 1.166 | 0.67 |
| 319_T | 373_A | 1.163 | 0.66 |
| 391_Y | 396_R | 1.163 | 0.66 |
| 455_E | 476_Q | 1.159 | 0.66 |
| 358_L | 377_L | 1.154 | 0.65 |
| 274_R | 474_S | 1.151 | 0.65 |
| 374_V | 518_V | 1.150 | 0.65 |
| 136_L | 140_A | 1.149 | 0.65 |
| 392_T | 429_F | 1.147 | 0.65 |
| 214_Y | 217_L | 1.142 | 0.64 |
| 234_V | 518_V | 1.142 | 0.64 |
| 268_V | 505_A | 1.139 | 0.64 |
| 219_M | 313_R | 1.138 | 0.64 |
| 456_S | 476_Q | 1.131 | 0.63 |
| 258_P | 427_D | 1.130 | 0.63 |
| 319_T | 335_P | 1.123 | 0.62 |
| 361_K | 364_E | 1.120 | 0.62 |
| 383_H | 452_D | 1.118 | 0.62 |
| 519_L | 524_I | 1.114 | 0.61 |
| 362_F | 366_L | 1.111 | 0.61 |
| 391_Y | 422_T | 1.111 | 0.61 |
| 314_A | 522_M | 1.109 | 0.61 |
| 235_V | 433_V | 1.109 | 0.61 |
| 483_M | 537_L | 1.106 | 0.61 |
| 237_V | 447_V | 1.103 | 0.60 |
| 363_D | 367_N | 1.094 | 0.59 |
| 284_L | 478_H | 1.089 | 0.59 |
| 266_E | 501_K | 1.087 | 0.59 |
| 309_D | 333_K | 1.087 | 0.59 |
| 118_L | 379_T | 1.073 | 0.57 |
| 366_L | 445_S | 1.070 | 0.57 |
| 129_C | 136_L | 1.060 | 0.56 |
| 11_G | 84_I | 1.059 | 0.56 |
| 305_D | 313_R | 1.057 | 0.55 |
| 273_V | 480_P | 1.054 | 0.55 |
| 485_F | 497_F | 1.052 | 0.55 |
| 327_C | 336_N | 1.050 | 0.55 |
| 356_N | 432_K | 1.049 | 0.55 |
| 130_L | 430_I | 1.048 | 0.54 |
| 280_T | 452_D | 1.044 | 0.54 |
| 140_A | 144_K | 1.042 | 0.54 |
| 301_A | 304_Q | 1.042 | 0.54 |
| 243_R | 468_P | 1.041 | 0.54 |
| 485_F | 489_F | 1.041 | 0.54 |
| 63_F | 163_F | 1.040 | 0.54 |
| 309_D | 512_D | 1.038 | 0.53 |
| 231_R | 521_L | 1.035 | 0.53 |
| 76_V | 79_P | 1.034 | 0.53 |
| 390_R | 449_Y | 1.032 | 0.53 |
| 92_E | 99_F | 1.029 | 0.52 |
| 392_T | 395_E | 1.026 | 0.52 |
| 10_L | 18_F | 1.024 | 0.52 |
| 269_N | 482_V | 1.024 | 0.52 |
| 402_C | 456_S | 1.024 | 0.52 |
| 234_V | 522_M | 1.021 | 0.51 |
| 468_P | 473_P | 1.021 | 0.51 |
| 179_S | 183_N | 1.020 | 0.51 |
| 306_N | 309_D | 1.017 | 0.51 |
| 220_A | 526_N | 1.017 | 0.51 |
| 381_G | 390_R | 1.015 | 0.51 |
| 91_Q | 305_D | 1.014 | 0.51 |
| 497_F | 501_K | 1.014 | 0.51 |
| 414_T | 418_T | 1.013 | 0.51 |
| 392_T | 428_Q | 1.011 | 0.50 |
| 249_L | 269_N | 1.010 | 0.50 |
| 256_T | 260_L | 1.010 | 0.50 |
| 415_L | 418_T | 1.010 | 0.50 |
| 247_W | 333_K | 1.009 | 0.50 |
| 278_T | 320_W | 1.007 | 0.50 |
| 106_N | 468_P | 1.004 | 0.50 |
| 383_H | 453_H | 1.004 | 0.50 |
| 437_L | 447_V | 1.002 | 0.49 |
| 218_D | 529_T | 1.000 | 0.49 |
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 | |
| 4kavA | 1 | 0.6103 | 100 | 0.664 | Contact Map |
| 2vqrA | 1 | 0.5441 | 100 | 0.764 | Contact Map |
| 3b5qA | 2 | 0.5441 | 100 | 0.769 | Contact Map |
| 2w5qA | 1 | 0.579 | 100 | 0.772 | Contact Map |
| 2w8dA | 2 | 0.5809 | 100 | 0.773 | Contact Map |
| 2qzuA | 1 | 0.5625 | 100 | 0.773 | Contact Map |
| 4mhxA | 2 | 0.5276 | 100 | 0.779 | Contact Map |
| 3lxqA | 2 | 0.5735 | 100 | 0.78 | Contact Map |
| 1aukA | 1 | 0.5184 | 100 | 0.781 | Contact Map |
| 1fsuA | 1 | 0.5294 | 100 | 0.781 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)