| CCT1 |
| ID: | 1503354684 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 556 (524) | ||
| Sequences: | 2556 (1238) | ||
| Seq/Len: | 4.878 | ||
| Nf(neff/√len): | 54.1 |
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: 4.878).
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 |
| 127_E | 130_R | 4.612 | 1.00 |
| 349_E | 366_N | 4.367 | 1.00 |
| 145_R | 174_D | 3.460 | 1.00 |
| 497_D | 500_Q | 3.409 | 1.00 |
| 228_R | 350_E | 3.321 | 1.00 |
| 149_I | 170_N | 3.321 | 1.00 |
| 416_E | 510_K | 3.257 | 1.00 |
| 208_S | 377_L | 3.150 | 1.00 |
| 132_I | 507_T | 3.035 | 1.00 |
| 412_G | 498_N | 2.985 | 1.00 |
| 279_L | 305_A | 2.915 | 1.00 |
| 125_C | 514_L | 2.890 | 1.00 |
| 100_L | 121_Y | 2.886 | 1.00 |
| 292_I | 307_A | 2.819 | 1.00 |
| 319_I | 364_I | 2.799 | 1.00 |
| 348_A | 364_I | 2.794 | 1.00 |
| 99_E | 102_K | 2.708 | 1.00 |
| 103_N | 443_R | 2.662 | 1.00 |
| 236_C | 325_A | 2.646 | 1.00 |
| 104_A | 121_Y | 2.558 | 1.00 |
| 131_Y | 422_Y | 2.534 | 1.00 |
| 287_L | 364_I | 2.526 | 1.00 |
| 489_D | 492_N | 2.455 | 1.00 |
| 145_R | 177_L | 2.441 | 1.00 |
| 276_Q | 280_A | 2.411 | 1.00 |
| 172_V | 392_L | 2.403 | 1.00 |
| 269_D | 273_E | 2.370 | 1.00 |
| 235_A | 334_L | 2.346 | 1.00 |
| 133_N | 511_V | 2.317 | 1.00 |
| 170_N | 174_D | 2.313 | 1.00 |
| 29_A | 98_A | 2.282 | 1.00 |
| 125_C | 518_T | 2.279 | 1.00 |
| 272_K | 276_Q | 2.238 | 1.00 |
| 229_I | 232_A | 2.172 | 1.00 |
| 92_S | 513_S | 2.131 | 1.00 |
| 153_K | 166_D | 2.100 | 1.00 |
| 56_N | 61_I | 2.048 | 1.00 |
| 408_V | 504_F | 2.042 | 1.00 |
| 132_I | 511_V | 1.966 | 1.00 |
| 203_R | 207_E | 1.891 | 1.00 |
| 123_L | 434_E | 1.885 | 1.00 |
| 121_Y | 441_F | 1.885 | 1.00 |
| 100_L | 441_F | 1.875 | 1.00 |
| 128_A | 419_L | 1.861 | 1.00 |
| 430_M | 438_I | 1.850 | 1.00 |
| 127_E | 438_I | 1.836 | 1.00 |
| 445_L | 514_L | 1.830 | 1.00 |
| 132_I | 415_V | 1.829 | 1.00 |
| 423_L | 438_I | 1.829 | 1.00 |
| 418_A | 471_H | 1.816 | 1.00 |
| 199_K | 386_D | 1.796 | 1.00 |
| 287_L | 311_V | 1.795 | 1.00 |
| 485_W | 497_D | 1.770 | 1.00 |
| 230_V | 350_E | 1.749 | 1.00 |
| 174_D | 212_S | 1.745 | 1.00 |
| 233_K | 282_G | 1.715 | 1.00 |
| 410_P | 414_A | 1.713 | 1.00 |
| 103_N | 106_E | 1.712 | 1.00 |
| 441_F | 518_T | 1.692 | 0.99 |
| 279_L | 303_A | 1.684 | 0.99 |
| 233_K | 347_Q | 1.678 | 0.99 |
| 426_Y | 438_I | 1.675 | 0.99 |
| 265_Q | 269_D | 1.668 | 0.99 |
| 470_F | 486_I | 1.667 | 0.99 |
| 235_A | 345_L | 1.628 | 0.99 |
| 308_V | 362_I | 1.628 | 0.99 |
| 447_V | 451_T | 1.628 | 0.99 |
| 261_D | 265_Q | 1.625 | 0.99 |
| 393_H | 397_C | 1.619 | 0.99 |
| 354_E | 365_K | 1.595 | 0.99 |
| 278_I | 286_I | 1.593 | 0.99 |
| 129_V | 133_N | 1.582 | 0.99 |
| 446_L | 468_R | 1.579 | 0.99 |
| 121_Y | 518_T | 1.572 | 0.99 |
| 415_V | 419_L | 1.568 | 0.99 |
| 489_D | 496_R | 1.567 | 0.99 |
| 458_Q | 490_L | 1.564 | 0.99 |
| 127_E | 131_Y | 1.562 | 0.99 |
| 424_E | 446_L | 1.561 | 0.99 |
| 130_R | 134_E | 1.550 | 0.99 |
| 387_E | 390_R | 1.546 | 0.99 |
| 241_L | 278_I | 1.532 | 0.99 |
| 320_A | 327_I | 1.523 | 0.99 |
| 466_K | 494_K | 1.511 | 0.99 |
| 119_S | 434_E | 1.508 | 0.98 |
| 36_L | 95_I | 1.500 | 0.98 |
| 242_Q | 291_G | 1.497 | 0.98 |
| 127_E | 426_Y | 1.493 | 0.98 |
| 91_T | 394_D | 1.492 | 0.98 |
| 99_E | 447_V | 1.490 | 0.98 |
| 205_Q | 388_M | 1.490 | 0.98 |
| 300_F | 307_A | 1.457 | 0.98 |
| 127_E | 422_Y | 1.453 | 0.98 |
| 256_D | 259_K | 1.443 | 0.98 |
| 131_Y | 418_A | 1.437 | 0.98 |
| 34_S | 43_K | 1.435 | 0.98 |
| 228_R | 352_V | 1.434 | 0.98 |
| 172_V | 395_A | 1.422 | 0.98 |
| 322_A | 367_T | 1.419 | 0.98 |
| 509_V | 513_S | 1.415 | 0.97 |
| 151_A | 408_V | 1.414 | 0.97 |
| 56_N | 390_R | 1.414 | 0.97 |
| 57_D | 394_D | 1.401 | 0.97 |
| 220_V | 306_M | 1.395 | 0.97 |
| 90_T | 394_D | 1.388 | 0.97 |
| 439_A | 443_R | 1.388 | 0.97 |
| 278_I | 283_A | 1.386 | 0.97 |
| 178_A | 212_S | 1.385 | 0.97 |
| 152_A | 399_V | 1.375 | 0.97 |
| 152_A | 173_V | 1.365 | 0.97 |
| 58_G | 91_T | 1.359 | 0.97 |
| 489_D | 501_A | 1.357 | 0.97 |
| 419_L | 445_L | 1.337 | 0.96 |
| 78_L | 93_V | 1.330 | 0.96 |
| 121_Y | 124_A | 1.324 | 0.96 |
| 229_I | 285_V | 1.320 | 0.96 |
| 236_C | 319_I | 1.316 | 0.96 |
| 120_G | 124_A | 1.313 | 0.96 |
| 291_G | 310_R | 1.311 | 0.96 |
| 29_A | 33_K | 1.295 | 0.95 |
| 412_G | 503_V | 1.291 | 0.95 |
| 107_L | 437_A | 1.289 | 0.95 |
| 212_S | 366_N | 1.287 | 0.95 |
| 131_Y | 134_E | 1.286 | 0.95 |
| 220_V | 353_Q | 1.284 | 0.95 |
| 271_T | 295_M | 1.279 | 0.95 |
| 11_R | 529_D | 1.276 | 0.95 |
| 409_V | 415_V | 1.276 | 0.95 |
| 92_S | 448_I | 1.269 | 0.94 |
| 158_S | 391_S | 1.269 | 0.94 |
| 236_C | 320_A | 1.268 | 0.94 |
| 149_I | 153_K | 1.260 | 0.94 |
| 25_A | 101_L | 1.258 | 0.94 |
| 505_E | 510_K | 1.257 | 0.94 |
| 158_S | 162_G | 1.257 | 0.94 |
| 313_K | 317_K | 1.252 | 0.94 |
| 209_M | 376_I | 1.248 | 0.94 |
| 449_P | 467_L | 1.248 | 0.94 |
| 124_A | 438_I | 1.245 | 0.94 |
| 120_G | 437_A | 1.239 | 0.93 |
| 367_T | 370_R | 1.238 | 0.93 |
| 377_L | 385_C | 1.237 | 0.93 |
| 229_I | 284_N | 1.235 | 0.93 |
| 290_G | 310_R | 1.228 | 0.93 |
| 337_E | 340_F | 1.223 | 0.93 |
| 507_T | 511_V | 1.216 | 0.93 |
| 220_V | 362_I | 1.215 | 0.93 |
| 83_D | 394_D | 1.211 | 0.92 |
| 11_R | 14_G | 1.205 | 0.92 |
| 335_E | 343_A | 1.201 | 0.92 |
| 410_P | 485_W | 1.200 | 0.92 |
| 275_I | 299_Y | 1.194 | 0.92 |
| 58_G | 394_D | 1.193 | 0.92 |
| 96_I | 517_A | 1.192 | 0.92 |
| 129_V | 511_V | 1.185 | 0.91 |
| 458_Q | 463_L | 1.185 | 0.91 |
| 262_Q | 265_Q | 1.178 | 0.91 |
| 29_A | 32_V | 1.177 | 0.91 |
| 122_R | 522_I | 1.175 | 0.91 |
| 316_L | 319_I | 1.173 | 0.91 |
| 421_I | 425_N | 1.172 | 0.91 |
| 175_A | 179_I | 1.172 | 0.91 |
| 235_A | 281_T | 1.171 | 0.91 |
| 286_I | 300_F | 1.169 | 0.90 |
| 404_E | 508_I | 1.168 | 0.90 |
| 32_V | 35_S | 1.164 | 0.90 |
| 324_G | 346_G | 1.162 | 0.90 |
| 26_A | 102_K | 1.158 | 0.90 |
| 127_E | 419_L | 1.153 | 0.90 |
| 353_Q | 360_E | 1.151 | 0.90 |
| 221_G | 297_L | 1.151 | 0.90 |
| 349_E | 367_T | 1.151 | 0.90 |
| 73_K | 76_C | 1.147 | 0.89 |
| 298_K | 302_E | 1.146 | 0.89 |
| 121_Y | 437_A | 1.145 | 0.89 |
| 291_G | 309_R | 1.143 | 0.89 |
| 234_I | 348_A | 1.137 | 0.89 |
| 37_G | 40_G | 1.132 | 0.89 |
| 231_N | 517_A | 1.128 | 0.88 |
| 64_L | 225_M | 1.126 | 0.88 |
| 277_K | 280_A | 1.122 | 0.88 |
| 108_V | 116_S | 1.118 | 0.88 |
| 131_Y | 419_L | 1.117 | 0.88 |
| 83_D | 90_T | 1.115 | 0.87 |
| 252_V | 263_I | 1.111 | 0.87 |
| 174_D | 177_L | 1.110 | 0.87 |
| 242_Q | 293_D | 1.103 | 0.87 |
| 130_R | 133_N | 1.099 | 0.86 |
| 420_S | 424_E | 1.098 | 0.86 |
| 178_A | 373_A | 1.097 | 0.86 |
| 24_A | 69_H | 1.094 | 0.86 |
| 425_N | 428_T | 1.093 | 0.86 |
| 259_K | 262_Q | 1.092 | 0.86 |
| 145_R | 170_N | 1.091 | 0.86 |
| 447_V | 450_N | 1.086 | 0.86 |
| 235_A | 271_T | 1.085 | 0.86 |
| 347_Q | 368_K | 1.085 | 0.86 |
| 103_N | 444_S | 1.084 | 0.85 |
| 386_D | 389_E | 1.080 | 0.85 |
| 139_N | 407_S | 1.079 | 0.85 |
| 175_A | 210_L | 1.078 | 0.85 |
| 236_C | 327_I | 1.073 | 0.85 |
| 118_I | 523_T | 1.072 | 0.85 |
| 152_A | 169_A | 1.071 | 0.85 |
| 145_R | 149_I | 1.069 | 0.84 |
| 453_A | 458_Q | 1.068 | 0.84 |
| 236_C | 316_L | 1.064 | 0.84 |
| 36_L | 92_S | 1.064 | 0.84 |
| 69_H | 322_A | 1.060 | 0.84 |
| 135_N | 422_Y | 1.057 | 0.83 |
| 398_V | 402_V | 1.056 | 0.83 |
| 308_V | 327_I | 1.055 | 0.83 |
| 175_A | 503_V | 1.055 | 0.83 |
| 275_I | 296_C | 1.052 | 0.83 |
| 156_M | 161_I | 1.051 | 0.83 |
| 415_V | 507_T | 1.047 | 0.83 |
| 56_N | 394_D | 1.047 | 0.83 |
| 42_D | 387_E | 1.039 | 0.82 |
| 235_A | 278_I | 1.039 | 0.82 |
| 220_V | 229_I | 1.039 | 0.82 |
| 171_M | 208_S | 1.038 | 0.82 |
| 422_Y | 425_N | 1.034 | 0.82 |
| 36_L | 91_T | 1.032 | 0.81 |
| 485_W | 499_K | 1.032 | 0.81 |
| 222_S | 309_R | 1.030 | 0.81 |
| 147_C | 150_N | 1.030 | 0.81 |
| 285_V | 364_I | 1.025 | 0.81 |
| 363_L | 376_I | 1.024 | 0.81 |
| 287_L | 316_L | 1.024 | 0.81 |
| 377_L | 388_M | 1.022 | 0.81 |
| 266_R | 269_D | 1.019 | 0.80 |
| 420_S | 464_V | 1.018 | 0.80 |
| 45_L | 78_L | 1.017 | 0.80 |
| 232_A | 285_V | 1.015 | 0.80 |
| 13_T | 17_I | 1.015 | 0.80 |
| 234_I | 323_S | 1.012 | 0.80 |
| 350_E | 365_K | 1.012 | 0.80 |
| 104_A | 120_G | 1.010 | 0.79 |
| 124_A | 441_F | 1.009 | 0.79 |
| 306_M | 533_L | 1.008 | 0.79 |
| 12_S | 16_T | 1.008 | 0.79 |
| 231_N | 349_E | 1.007 | 0.79 |
| 418_A | 422_Y | 1.004 | 0.79 |
| 306_M | 362_I | 1.002 | 0.79 |
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 | |
| 1q3qA | 4 | 0.9263 | 100 | 0.072 | Contact Map |
| 3j1bA | 16 | 0.9173 | 100 | 0.074 | Contact Map |
| 3iygA | 1 | 0.9496 | 100 | 0.081 | Contact Map |
| 3ruvA | 4 | 0.9209 | 100 | 0.082 | Contact Map |
| 1a6dA | 1 | 0.9047 | 100 | 0.083 | Contact Map |
| 3ko1A | 9 | 0.9083 | 100 | 0.085 | Contact Map |
| 1a6dB | 1 | 0.9029 | 100 | 0.089 | Contact Map |
| 3p9dA | 2 | 0.9658 | 100 | 0.093 | Contact Map |
| 3p9dG | 2 | 0.9083 | 100 | 0.093 | Contact Map |
| 3p9dD | 2 | 0.9191 | 100 | 0.103 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)