| tatotal8 |
| ID: | 1485458092 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 541 (526) | ||
| Sequences: | 1289 (917.9) | ||
| Seq/Len: | 2.451 | ||
| Nf(neff/√len): | 40.0 |
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: 2.451).
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 |
| 243_V | 442_I | 4.784 | 1.00 |
| 312_V | 522_L | 4.746 | 1.00 |
| 254_S | 263_F | 4.571 | 1.00 |
| 394_N | 434_A | 4.523 | 1.00 |
| 256_N | 274_N | 4.317 | 1.00 |
| 409_K | 436_L | 3.662 | 1.00 |
| 374_D | 448_W | 3.322 | 1.00 |
| 332_S | 336_M | 3.300 | 1.00 |
| 445_S | 460_M | 3.079 | 1.00 |
| 521_T | 540_I | 3.039 | 1.00 |
| 265_Q | 440_D | 2.717 | 1.00 |
| 254_S | 261_D | 2.711 | 1.00 |
| 133_G | 137_S | 2.682 | 1.00 |
| 463_V | 515_H | 2.672 | 1.00 |
| 524_K | 538_A | 2.534 | 1.00 |
| 278_V | 513_L | 2.518 | 1.00 |
| 408_A | 413_V | 2.488 | 1.00 |
| 447_Q | 450_Q | 2.395 | 1.00 |
| 265_Q | 443_A | 2.355 | 1.00 |
| 81_I | 141_A | 2.298 | 1.00 |
| 404_D | 437_A | 2.295 | 1.00 |
| 248_A | 435_L | 2.288 | 1.00 |
| 261_D | 267_A | 2.267 | 1.00 |
| 276_S | 510_D | 2.251 | 1.00 |
| 248_A | 438_T | 2.238 | 1.00 |
| 407_F | 440_D | 2.237 | 1.00 |
| 295_Y | 309_Q | 2.118 | 1.00 |
| 316_L | 526_F | 2.071 | 1.00 |
| 367_V | 437_A | 2.046 | 0.99 |
| 81_I | 137_S | 2.038 | 0.99 |
| 251_D | 488_E | 2.014 | 0.99 |
| 533_V | 538_A | 1.982 | 0.99 |
| 240_V | 386_L | 1.954 | 0.99 |
| 407_F | 437_A | 1.949 | 0.99 |
| 242_F | 518_I | 1.931 | 0.99 |
| 248_A | 394_N | 1.931 | 0.99 |
| 84_L | 140_V | 1.929 | 0.99 |
| 248_A | 253_V | 1.912 | 0.99 |
| 105_M | 108_N | 1.897 | 0.99 |
| 252_H | 428_I | 1.879 | 0.99 |
| 250_A | 274_N | 1.857 | 0.99 |
| 89_V | 129_I | 1.849 | 0.99 |
| 281_C | 291_C | 1.838 | 0.99 |
| 524_K | 533_V | 1.812 | 0.98 |
| 475_V | 480_M | 1.811 | 0.98 |
| 358_T | 362_N | 1.805 | 0.98 |
| 374_D | 378_A | 1.803 | 0.98 |
| 520_P | 537_T | 1.793 | 0.98 |
| 221_Y | 224_K | 1.786 | 0.98 |
| 236_K | 457_D | 1.784 | 0.98 |
| 242_F | 386_L | 1.783 | 0.98 |
| 269_I | 443_A | 1.780 | 0.98 |
| 408_A | 411_T | 1.777 | 0.98 |
| 279_T | 490_R | 1.777 | 0.98 |
| 252_H | 432_D | 1.763 | 0.98 |
| 63_L | 164_S | 1.760 | 0.98 |
| 240_V | 459_S | 1.759 | 0.98 |
| 369_M | 441_F | 1.759 | 0.98 |
| 258_Y | 432_D | 1.734 | 0.98 |
| 26_L | 66_T | 1.734 | 0.98 |
| 25_F | 30_A | 1.731 | 0.98 |
| 244_V | 289_V | 1.723 | 0.98 |
| 441_F | 445_S | 1.714 | 0.98 |
| 254_S | 267_A | 1.709 | 0.98 |
| 292_M | 518_I | 1.688 | 0.97 |
| 24_V | 59_F | 1.669 | 0.97 |
| 365_R | 404_D | 1.663 | 0.97 |
| 405_E | 408_A | 1.649 | 0.97 |
| 253_V | 391_Q | 1.646 | 0.97 |
| 255_F | 263_F | 1.635 | 0.97 |
| 442_I | 460_M | 1.631 | 0.97 |
| 130_I | 134_V | 1.630 | 0.96 |
| 322_S | 383_K | 1.620 | 0.96 |
| 260_R | 432_D | 1.607 | 0.96 |
| 487_K | 490_R | 1.603 | 0.96 |
| 399_Y | 468_E | 1.591 | 0.96 |
| 60_G | 167_L | 1.584 | 0.96 |
| 311_N | 337_D | 1.564 | 0.95 |
| 110_L | 205_L | 1.528 | 0.94 |
| 261_D | 436_L | 1.523 | 0.94 |
| 278_V | 494_A | 1.523 | 0.94 |
| 502_T | 521_T | 1.522 | 0.94 |
| 372_G | 375_D | 1.513 | 0.94 |
| 423_E | 426_S | 1.511 | 0.94 |
| 487_K | 491_S | 1.497 | 0.94 |
| 18_L | 140_V | 1.490 | 0.93 |
| 461_L | 496_F | 1.489 | 0.93 |
| 461_L | 494_A | 1.489 | 0.93 |
| 469_S | 489_Q | 1.479 | 0.93 |
| 292_M | 463_V | 1.475 | 0.93 |
| 408_A | 415_E | 1.475 | 0.93 |
| 373_L | 387_I | 1.469 | 0.93 |
| 262_T | 432_D | 1.469 | 0.93 |
| 523_L | 530_A | 1.449 | 0.92 |
| 321_V | 526_F | 1.448 | 0.92 |
| 239_L | 377_V | 1.435 | 0.92 |
| 326_R | 369_M | 1.429 | 0.91 |
| 413_V | 430_A | 1.420 | 0.91 |
| 326_R | 372_G | 1.414 | 0.91 |
| 112_T | 116_E | 1.411 | 0.91 |
| 269_I | 450_Q | 1.409 | 0.91 |
| 449_L | 460_M | 1.402 | 0.90 |
| 223_A | 318_R | 1.401 | 0.90 |
| 240_V | 522_L | 1.379 | 0.89 |
| 407_F | 436_L | 1.377 | 0.89 |
| 316_L | 386_L | 1.376 | 0.89 |
| 252_H | 488_E | 1.335 | 0.87 |
| 391_Q | 441_F | 1.332 | 0.87 |
| 25_F | 29_T | 1.328 | 0.87 |
| 138_L | 142_F | 1.319 | 0.86 |
| 242_F | 388_M | 1.306 | 0.86 |
| 373_L | 445_S | 1.302 | 0.85 |
| 64_L | 168_I | 1.300 | 0.85 |
| 63_L | 160_L | 1.300 | 0.85 |
| 463_V | 518_I | 1.300 | 0.85 |
| 250_A | 491_S | 1.295 | 0.85 |
| 243_V | 460_M | 1.292 | 0.85 |
| 255_F | 266_L | 1.288 | 0.85 |
| 386_L | 522_L | 1.280 | 0.84 |
| 82_L | 86_M | 1.275 | 0.84 |
| 119_D | 392_M | 1.270 | 0.83 |
| 389_L | 445_S | 1.267 | 0.83 |
| 273_T | 496_F | 1.262 | 0.83 |
| 224_K | 318_R | 1.255 | 0.82 |
| 297_G | 537_T | 1.251 | 0.82 |
| 444_Q | 447_Q | 1.242 | 0.81 |
| 373_L | 377_V | 1.236 | 0.81 |
| 404_D | 407_F | 1.235 | 0.81 |
| 69_L | 79_V | 1.234 | 0.81 |
| 410_F | 436_L | 1.233 | 0.81 |
| 413_V | 416_G | 1.232 | 0.81 |
| 223_A | 319_L | 1.223 | 0.80 |
| 289_V | 491_S | 1.215 | 0.79 |
| 200_Y | 203_G | 1.212 | 0.79 |
| 64_L | 161_I | 1.212 | 0.79 |
| 223_A | 532_K | 1.211 | 0.79 |
| 14_S | 17_V | 1.210 | 0.79 |
| 248_A | 263_F | 1.208 | 0.79 |
| 81_I | 140_V | 1.207 | 0.79 |
| 94_T | 101_Y | 1.207 | 0.79 |
| 23_A | 27_T | 1.203 | 0.79 |
| 323_I | 339_L | 1.201 | 0.78 |
| 253_V | 263_F | 1.198 | 0.78 |
| 241_V | 445_S | 1.186 | 0.77 |
| 459_S | 502_T | 1.185 | 0.77 |
| 147_Y | 153_G | 1.185 | 0.77 |
| 296_L | 305_T | 1.175 | 0.76 |
| 332_S | 341_K | 1.166 | 0.75 |
| 310_E | 318_R | 1.165 | 0.75 |
| 19_V | 22_V | 1.154 | 0.74 |
| 319_L | 526_F | 1.152 | 0.74 |
| 255_F | 272_V | 1.150 | 0.74 |
| 336_M | 341_K | 1.145 | 0.74 |
| 370_L | 374_D | 1.145 | 0.74 |
| 367_V | 444_Q | 1.145 | 0.74 |
| 402_R | 462_Y | 1.138 | 0.73 |
| 60_G | 171_P | 1.138 | 0.73 |
| 437_A | 440_D | 1.137 | 0.73 |
| 313_L | 339_L | 1.136 | 0.73 |
| 99_T | 480_M | 1.130 | 0.72 |
| 438_T | 442_I | 1.126 | 0.72 |
| 316_L | 321_V | 1.124 | 0.72 |
| 83_L | 87_G | 1.124 | 0.72 |
| 13_V | 17_V | 1.123 | 0.72 |
| 245_G | 285_T | 1.120 | 0.71 |
| 278_V | 492_V | 1.119 | 0.71 |
| 316_L | 522_L | 1.108 | 0.70 |
| 260_R | 429_N | 1.107 | 0.70 |
| 106_L | 205_L | 1.107 | 0.70 |
| 481_P | 489_Q | 1.105 | 0.70 |
| 403_Y | 413_V | 1.094 | 0.69 |
| 498_T | 502_T | 1.090 | 0.68 |
| 375_D | 378_A | 1.089 | 0.68 |
| 370_L | 448_W | 1.088 | 0.68 |
| 473_N | 488_E | 1.087 | 0.68 |
| 84_L | 137_S | 1.086 | 0.68 |
| 275_F | 494_A | 1.086 | 0.68 |
| 223_A | 226_A | 1.085 | 0.68 |
| 80_L | 84_L | 1.084 | 0.68 |
| 312_V | 526_F | 1.083 | 0.68 |
| 85_I | 133_G | 1.083 | 0.68 |
| 314_D | 339_L | 1.079 | 0.67 |
| 443_A | 447_Q | 1.078 | 0.67 |
| 372_G | 377_V | 1.077 | 0.67 |
| 100_V | 192_Y | 1.074 | 0.67 |
| 469_S | 486_P | 1.072 | 0.66 |
| 197_M | 332_S | 1.068 | 0.66 |
| 296_L | 309_Q | 1.068 | 0.66 |
| 314_D | 338_K | 1.066 | 0.66 |
| 119_D | 398_A | 1.065 | 0.66 |
| 273_T | 509_T | 1.062 | 0.65 |
| 272_V | 495_F | 1.062 | 0.65 |
| 90_T | 101_Y | 1.059 | 0.65 |
| 285_T | 395_H | 1.051 | 0.64 |
| 403_Y | 433_N | 1.050 | 0.64 |
| 415_E | 430_A | 1.049 | 0.64 |
| 254_S | 262_T | 1.048 | 0.64 |
| 242_F | 463_V | 1.047 | 0.64 |
| 496_F | 521_T | 1.043 | 0.63 |
| 274_N | 495_F | 1.042 | 0.63 |
| 238_R | 526_F | 1.040 | 0.63 |
| 251_D | 487_K | 1.038 | 0.63 |
| 13_V | 21_S | 1.037 | 0.63 |
| 243_V | 445_S | 1.036 | 0.63 |
| 190_R | 200_Y | 1.033 | 0.62 |
| 281_C | 414_C | 1.033 | 0.62 |
| 153_G | 157_R | 1.032 | 0.62 |
| 121_L | 156_R | 1.031 | 0.62 |
| 134_V | 382_G | 1.030 | 0.62 |
| 414_C | 422_C | 1.029 | 0.62 |
| 22_V | 80_L | 1.027 | 0.62 |
| 197_M | 336_M | 1.025 | 0.61 |
| 241_V | 389_L | 1.024 | 0.61 |
| 205_L | 263_F | 1.019 | 0.61 |
| 499_D | 502_T | 1.018 | 0.60 |
| 432_D | 468_E | 1.018 | 0.60 |
| 261_D | 264_P | 1.016 | 0.60 |
| 315_T | 318_R | 1.013 | 0.60 |
| 311_N | 335_V | 1.012 | 0.60 |
| 298_A | 482_N | 1.012 | 0.60 |
| 294_S | 328_N | 1.012 | 0.60 |
| 311_N | 314_D | 1.012 | 0.60 |
| 371_V | 534_K | 1.011 | 0.60 |
| 440_D | 443_A | 1.011 | 0.60 |
| 403_Y | 434_A | 1.010 | 0.60 |
| 250_A | 256_N | 1.001 | 0.59 |
| 264_P | 439_D | 1.001 | 0.59 |
| 297_G | 300_E | 1.000 | 0.58 |
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 | 0.586 | 100 | 0.653 | Contact Map |
| 4tn0A | 3 | 0.549 | 100 | 0.661 | Contact Map |
| 3b5qA | 2 | 0.5416 | 100 | 0.752 | Contact Map |
| 2vqrA | 1 | 0.5434 | 100 | 0.756 | Contact Map |
| 4upkA | 3 | 0 | 100 | 0.76 | Contact Map |
| 4uphA | 4 | 0 | 100 | 0.761 | Contact Map |
| 2qzuA | 1 | 0.5619 | 100 | 0.763 | Contact Map |
| 4mhxA | 2 | 0.5268 | 100 | 0.767 | Contact Map |
| 4uplA | 2 | 0 | 100 | 0.769 | Contact Map |
| 2w5qA | 1 | 0.5823 | 100 | 0.769 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)