| CCT3 |
| ID: | 1503354626 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 545 (515) | ||
| Sequences: | 2644 (1306.5) | ||
| Seq/Len: | 5.134 | ||
| Nf(neff/√len): | 57.6 |
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: 5.134).
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 |
| 132_D | 135_S | 4.504 | 1.00 |
| 348_G | 365_D | 3.917 | 1.00 |
| 296_I | 311_A | 3.669 | 1.00 |
| 411_G | 490_M | 3.417 | 1.00 |
| 415_E | 502_K | 3.352 | 1.00 |
| 153_L | 174_N | 3.210 | 1.00 |
| 212_S | 376_L | 3.197 | 1.00 |
| 489_D | 492_E | 3.131 | 1.00 |
| 149_S | 178_D | 3.065 | 1.00 |
| 137_L | 499_L | 3.047 | 1.00 |
| 105_M | 126_Y | 2.980 | 1.00 |
| 130_L | 506_Y | 2.928 | 1.00 |
| 283_I | 309_I | 2.833 | 1.00 |
| 108_V | 442_Q | 2.757 | 1.00 |
| 104_E | 107_S | 2.743 | 1.00 |
| 149_S | 181_K | 2.702 | 1.00 |
| 323_I | 363_I | 2.680 | 1.00 |
| 240_L | 329_A | 2.604 | 1.00 |
| 239_V | 338_L | 2.473 | 1.00 |
| 273_E | 277_Q | 2.442 | 1.00 |
| 207_G | 211_D | 2.429 | 1.00 |
| 136_T | 421_A | 2.427 | 1.00 |
| 280_E | 284_Q | 2.410 | 1.00 |
| 109_A | 126_Y | 2.371 | 1.00 |
| 176_A | 391_L | 2.349 | 1.00 |
| 347_A | 363_I | 2.342 | 1.00 |
| 232_Y | 349_L | 2.338 | 1.00 |
| 34_A | 103_G | 2.327 | 1.00 |
| 97_S | 505_T | 2.324 | 1.00 |
| 130_L | 510_V | 2.317 | 1.00 |
| 276_Q | 280_E | 2.310 | 1.00 |
| 481_N | 484_T | 2.301 | 1.00 |
| 174_N | 178_D | 2.301 | 1.00 |
| 138_K | 503_L | 2.297 | 1.00 |
| 291_I | 363_I | 2.257 | 1.00 |
| 233_I | 236_P | 2.117 | 1.00 |
| 429_M | 437_Y | 2.116 | 1.00 |
| 237_R | 286_K | 2.115 | 1.00 |
| 440_V | 510_V | 2.102 | 1.00 |
| 376_L | 384_L | 2.058 | 1.00 |
| 444_L | 506_Y | 2.056 | 1.00 |
| 61_N | 66_I | 2.030 | 1.00 |
| 141_S | 499_L | 2.019 | 1.00 |
| 137_L | 503_L | 1.975 | 1.00 |
| 128_K | 433_E | 1.945 | 1.00 |
| 233_I | 289_V | 1.943 | 1.00 |
| 446_V | 450_T | 1.935 | 1.00 |
| 137_L | 414_S | 1.928 | 1.00 |
| 157_N | 170_S | 1.927 | 1.00 |
| 407_L | 496_W | 1.896 | 1.00 |
| 291_I | 315_V | 1.896 | 1.00 |
| 425_K | 437_Y | 1.866 | 1.00 |
| 178_D | 216_R | 1.844 | 1.00 |
| 108_V | 111_H | 1.828 | 1.00 |
| 417_A | 470_H | 1.804 | 1.00 |
| 105_M | 440_V | 1.803 | 1.00 |
| 465_S | 486_T | 1.779 | 1.00 |
| 269_Q | 273_E | 1.740 | 1.00 |
| 409_P | 413_A | 1.733 | 1.00 |
| 132_D | 437_Y | 1.728 | 1.00 |
| 126_Y | 440_V | 1.721 | 1.00 |
| 283_I | 307_A | 1.718 | 1.00 |
| 414_S | 418_V | 1.716 | 1.00 |
| 324_A | 331_I | 1.713 | 1.00 |
| 126_Y | 510_V | 1.681 | 0.99 |
| 239_V | 343_V | 1.666 | 0.99 |
| 104_E | 446_V | 1.655 | 0.99 |
| 246_E | 295_G | 1.646 | 0.99 |
| 392_Q | 396_Q | 1.641 | 0.99 |
| 304_L | 311_A | 1.618 | 0.99 |
| 41_L | 100_I | 1.615 | 0.99 |
| 481_N | 488_V | 1.611 | 0.99 |
| 438_R | 442_Q | 1.608 | 0.99 |
| 132_D | 136_T | 1.595 | 0.99 |
| 203_K | 385_S | 1.595 | 0.99 |
| 34_A | 38_R | 1.589 | 0.99 |
| 386_E | 389_R | 1.588 | 0.99 |
| 477_T | 489_D | 1.582 | 0.99 |
| 209_I | 387_V | 1.579 | 0.99 |
| 312_I | 361_T | 1.563 | 0.99 |
| 265_T | 269_Q | 1.530 | 0.99 |
| 176_A | 394_A | 1.523 | 0.99 |
| 133_M | 418_V | 1.520 | 0.99 |
| 422_L | 437_Y | 1.516 | 0.99 |
| 469_K | 478_W | 1.511 | 0.99 |
| 457_A | 482_G | 1.499 | 0.99 |
| 132_D | 425_K | 1.492 | 0.99 |
| 124_S | 433_E | 1.480 | 0.98 |
| 234_K | 349_L | 1.474 | 0.98 |
| 353_K | 364_T | 1.472 | 0.98 |
| 501_V | 505_T | 1.472 | 0.98 |
| 240_L | 324_A | 1.464 | 0.98 |
| 62_D | 393_D | 1.424 | 0.98 |
| 423_T | 445_E | 1.417 | 0.98 |
| 83_I | 98_V | 1.415 | 0.98 |
| 134_I | 138_K | 1.414 | 0.98 |
| 126_Y | 129_A | 1.406 | 0.98 |
| 136_T | 417_A | 1.404 | 0.98 |
| 457_A | 462_L | 1.387 | 0.97 |
| 96_T | 393_D | 1.383 | 0.97 |
| 132_D | 421_A | 1.379 | 0.97 |
| 420_H | 424_E | 1.375 | 0.97 |
| 245_L | 282_I | 1.368 | 0.97 |
| 302_H | 306_R | 1.355 | 0.97 |
| 39_T | 48_K | 1.353 | 0.97 |
| 445_E | 467_R | 1.346 | 0.97 |
| 418_V | 444_L | 1.340 | 0.97 |
| 263_D | 266_R | 1.330 | 0.96 |
| 152_M | 156_I | 1.325 | 0.96 |
| 266_R | 269_Q | 1.324 | 0.96 |
| 63_G | 96_T | 1.320 | 0.96 |
| 142_I | 491_K | 1.309 | 0.96 |
| 61_N | 389_R | 1.306 | 0.96 |
| 424_E | 427_K | 1.304 | 0.96 |
| 366_C | 369_P | 1.302 | 0.96 |
| 481_N | 493_L | 1.298 | 0.96 |
| 326_A | 366_C | 1.297 | 0.96 |
| 108_V | 443_A | 1.291 | 0.95 |
| 16_R | 521_D | 1.291 | 0.95 |
| 236_P | 289_V | 1.287 | 0.95 |
| 290_V | 304_L | 1.282 | 0.95 |
| 153_L | 157_N | 1.281 | 0.95 |
| 125_A | 436_P | 1.279 | 0.95 |
| 97_S | 447_I | 1.267 | 0.95 |
| 136_T | 139_K | 1.266 | 0.95 |
| 287_P | 343_V | 1.266 | 0.95 |
| 125_A | 129_A | 1.258 | 0.95 |
| 497_E | 502_K | 1.257 | 0.95 |
| 182_M | 216_R | 1.255 | 0.94 |
| 391_L | 395_M | 1.254 | 0.94 |
| 95_T | 393_D | 1.253 | 0.94 |
| 155_I | 407_L | 1.252 | 0.94 |
| 294_K | 314_R | 1.251 | 0.94 |
| 127_R | 514_V | 1.249 | 0.94 |
| 175_I | 212_S | 1.238 | 0.94 |
| 374_I | 391_L | 1.238 | 0.94 |
| 216_R | 365_D | 1.237 | 0.94 |
| 411_G | 495_I | 1.234 | 0.94 |
| 275_I | 299_L | 1.231 | 0.94 |
| 279_C | 303_Y | 1.227 | 0.94 |
| 240_L | 323_I | 1.221 | 0.93 |
| 376_L | 387_V | 1.219 | 0.93 |
| 156_I | 398_C | 1.212 | 0.93 |
| 213_C | 375_L | 1.200 | 0.93 |
| 178_D | 181_K | 1.197 | 0.92 |
| 239_V | 285_L | 1.196 | 0.92 |
| 88_D | 393_D | 1.195 | 0.92 |
| 362_F | 375_L | 1.194 | 0.92 |
| 236_P | 350_L | 1.191 | 0.92 |
| 224_V | 310_T | 1.190 | 0.92 |
| 260_R | 263_D | 1.178 | 0.92 |
| 320_N | 323_I | 1.176 | 0.92 |
| 317_K | 321_N | 1.176 | 0.92 |
| 295_G | 314_R | 1.176 | 0.92 |
| 422_L | 441_A | 1.175 | 0.92 |
| 162_T | 390_N | 1.172 | 0.91 |
| 328_G | 344_G | 1.158 | 0.91 |
| 135_S | 138_K | 1.158 | 0.91 |
| 448_P | 466_L | 1.154 | 0.91 |
| 240_L | 331_I | 1.143 | 0.90 |
| 151_M | 154_N | 1.141 | 0.90 |
| 31_K | 107_S | 1.139 | 0.90 |
| 224_V | 361_T | 1.136 | 0.90 |
| 474_N | 478_W | 1.135 | 0.90 |
| 282_I | 287_P | 1.131 | 0.89 |
| 78_K | 81_I | 1.127 | 0.89 |
| 88_D | 95_T | 1.124 | 0.89 |
| 299_L | 303_Y | 1.123 | 0.89 |
| 279_C | 300_A | 1.123 | 0.89 |
| 462_L | 480_V | 1.101 | 0.88 |
| 408_V | 414_S | 1.101 | 0.88 |
| 224_V | 352_I | 1.101 | 0.88 |
| 134_I | 503_L | 1.099 | 0.87 |
| 239_V | 282_I | 1.098 | 0.87 |
| 204_I | 358_E | 1.098 | 0.87 |
| 408_V | 499_L | 1.098 | 0.87 |
| 499_L | 503_L | 1.096 | 0.87 |
| 129_A | 437_Y | 1.086 | 0.87 |
| 140_I | 414_S | 1.085 | 0.87 |
| 18_S | 22_V | 1.085 | 0.87 |
| 498_P | 501_V | 1.079 | 0.86 |
| 239_V | 275_I | 1.076 | 0.86 |
| 149_S | 174_N | 1.074 | 0.86 |
| 461_R | 465_S | 1.072 | 0.86 |
| 29_A | 74_H | 1.071 | 0.86 |
| 149_S | 153_L | 1.070 | 0.85 |
| 403_L | 500_A | 1.069 | 0.85 |
| 352_I | 359_Y | 1.067 | 0.85 |
| 240_L | 320_N | 1.067 | 0.85 |
| 289_V | 363_I | 1.065 | 0.85 |
| 112_F | 436_P | 1.059 | 0.85 |
| 312_I | 331_I | 1.058 | 0.85 |
| 332_V | 338_L | 1.058 | 0.85 |
| 446_V | 449_R | 1.056 | 0.84 |
| 281_D | 284_Q | 1.055 | 0.84 |
| 242_D | 333_S | 1.054 | 0.84 |
| 256_I | 267_I | 1.054 | 0.84 |
| 226_H | 313_R | 1.053 | 0.84 |
| 42_G | 45_S | 1.052 | 0.84 |
| 34_A | 37_I | 1.050 | 0.84 |
| 451_L | 482_G | 1.048 | 0.84 |
| 47_M | 386_E | 1.044 | 0.84 |
| 203_K | 388_E | 1.042 | 0.83 |
| 158_S | 497_E | 1.040 | 0.83 |
| 291_I | 320_N | 1.040 | 0.83 |
| 179_A | 183_V | 1.038 | 0.83 |
| 419_A | 423_T | 1.035 | 0.83 |
| 273_E | 276_Q | 1.034 | 0.83 |
| 113_L | 121_V | 1.034 | 0.83 |
| 104_E | 450_T | 1.032 | 0.83 |
| 102_A | 509_A | 1.027 | 0.82 |
| 225_T | 301_Q | 1.026 | 0.82 |
| 46_M | 119_P | 1.025 | 0.82 |
| 253_Q | 272_E | 1.021 | 0.82 |
| 101_L | 509_A | 1.015 | 0.81 |
| 47_M | 61_N | 1.015 | 0.81 |
| 130_L | 134_I | 1.014 | 0.81 |
| 490_M | 495_I | 1.012 | 0.81 |
| 295_G | 313_R | 1.010 | 0.81 |
| 346_G | 349_L | 1.007 | 0.80 |
| 64_N | 68_R | 1.005 | 0.80 |
| 38_R | 453_Q | 1.005 | 0.80 |
| 105_M | 125_A | 1.004 | 0.80 |
| 50_L | 83_I | 1.004 | 0.80 |
| 61_N | 65_A | 1.002 | 0.80 |
| 410_G | 495_I | 1.001 | 0.80 |
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 | |
| 1a6dB | 1 | 0.9211 | 100 | 0.037 | Contact Map |
| 3ko1A | 9 | 0.9266 | 100 | 0.046 | Contact Map |
| 3j1bA | 16 | 0.9339 | 100 | 0.046 | Contact Map |
| 1q3qA | 4 | 0.9505 | 100 | 0.059 | Contact Map |
| 3ruvA | 4 | 0.9468 | 100 | 0.064 | Contact Map |
| 1a6dA | 1 | 0.9229 | 100 | 0.065 | Contact Map |
| 3p9dH | 2 | 0.9266 | 100 | 0.072 | Contact Map |
| 3p9dG | 2 | 0.9284 | 100 | 0.072 | Contact Map |
| 3iygG | 1 | 0.945 | 100 | 0.074 | Contact Map |
| 3p9dA | 2 | 0.967 | 100 | 0.077 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)